UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

 

FORM10-Q

 

(Mark One)

QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 20172018

OR

TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

Commission File Number:001-36370

 

LOGO

APPLIED GENETIC TECHNOLOGIES CORPORATION

(Exact Name of Registrant as Specified in Its Charter)

 

 

Delaware

Delaware59-3553710

(State or Other Jurisdiction of

Incorporation or Organization)

(I.R.S. Employer

Identification No.)

14193 NW 119th Terrace

Suite 10

Alachua, Florida 32615

(Address of Principal Executive Offices, Including Zip Code)

(386)462-2204

(Registrant’s Telephone Number, Including Area Code)

 

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  ☒    No  ☐

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of RegulationS-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  ☒    No  ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, anon-accelerated filer, or a smaller reporting company or an emerging growth company. See definitions of “large accelerated filer,” “accelerated filer” andfiler,” “smaller reporting company,” and “emerging growth company” in Rule12b-2 of the Exchange Act.

 

Large accelerated filer

Accelerated filer

Non-accelerated filer

☐  (Do not check if a smaller reporting company)

Smaller reporting company

Emerging growth company

Growth Company

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act  ☒

Indicate by check mark whether the registrant is a shell company (as defined in Rule12b-2 of the Exchange Act).    Yes  ☐    No  ☒

The number of shares of the registrant’s common stock outstanding as of October 31, 20172018 was 18,093,235.18,133,993.

 

 

 


APPLIED GENETIC TECHNOLOGIES CORPORATION

FORM10-Q

FOR THE QUARTER ENDED SEPTEMBERSeptember 30, 20172018

TABLE OF CONTENTS

 

Pages

Pages

PART I. FINANCIAL INFORMATION

ITEM 1.

FINANCIAL STATEMENTS

3

Condensed Balance Sheets (Unaudited) as of September 30, 20172018 and June 30, 2017

3

Condensed Statements of Operations (Unaudited) for the three months ended September 30, 20172018 and 20162017

4

Condensed Statements of Stockholders’ Equity (Unaudited) for the three months ended September 30, 2018 and 2017

5
Condensed Statements of Cash Flows (Unaudited) for the three months ended September 30, 20172018 and 20162017

5

6

Notes to Condensed Financial Statements (Unaudited)

6

7

ITEM 2.

MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

18

19

ITEM 3.

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

25

ITEM 4.

CONTROLS AND PROCEDURES

25

PART II. OTHER INFORMATION

ITEM 1.

LEGAL PROCEEDINGS

26

ITEM 1A.

RISK FACTORS

26

ITEM 2.

UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

26

ITEM 6.

EXHIBITS

26

SignaturesSIGNATURES

27

27


PARTPART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

APPLIED GENETIC TECHNOLOGIES CORPORATION

CONDENSED BALANCE SHEETS

(Unaudited)

 

 

 

September 30,

 

 

June 30,

 

In thousands, except per share data

 

2017

 

 

2017

 

ASSETS

 

 

 

 

 

 

 

 

Current assets:

 

 

 

 

 

 

 

 

Cash and cash equivalents

 

$

48,734

 

 

$

30,706

 

Investments

 

 

76,469

 

 

 

95,994

 

Grants receivable

 

 

182

 

 

 

174

 

Prepaid and other current assets

 

 

3,228

 

 

 

3,361

 

Total current assets

 

 

128,613

 

 

 

130,235

 

Investments, net of current portion

 

 

4,385

 

 

 

11,749

 

Property and equipment, net

 

 

2,621

 

 

 

2,661

 

Investment in Bionic Sight

 

 

2,000

 

 

 

2,000

 

Other assets

 

 

1,355

 

 

 

1,278

 

Total assets

 

$

138,974

 

 

$

147,923

 

LIABILITIES AND STOCKHOLDERS' EQUITY

 

 

 

 

 

 

 

 

Current liabilities:

 

 

 

 

 

 

 

 

Accounts payable

 

$

2,468

 

 

$

998

 

Accrued expenses and other liabilities

 

 

5,423

 

 

 

6,162

 

Deferred revenue

 

 

14,651

 

 

 

20,996

 

Total current liabilities

 

 

22,542

 

 

 

28,156

 

Deferred revenue, net of current portion

 

 

1,029

 

 

 

4,438

 

Total liabilities

 

 

23,571

 

 

 

32,594

 

Stockholders' equity:

 

 

 

 

 

 

 

 

Common stock—par value $.001 per share; shares authorized: 150,000

      at September 30, 2017 and June 30, 2017; shares issued and outstanding:

     18,093 and 18,088 at September 30, 2017 and June 30, 2017, respectively.

 

 

18

 

 

 

18

 

Additional paid-in capital

 

 

206,408

 

 

 

204,937

 

Accumulated deficit

 

 

(91,023

)

 

 

(89,626

)

Total stockholders' equity

 

 

115,403

 

 

 

115,329

 

Total liabilities and stockholders' equity

 

$

138,974

 

 

$

147,923

 

In thousands, except per share data

  September 30,
2018
  June 30,
2018
 

ASSETS

   

Current assets:

   

Cash and cash equivalents

  $26,472  $31,065 

Investments

   78,968   73,840 

Grants receivable

   219   210 

Prepaid and other current assets

   2,527   4,009 
  

 

 

  

 

 

 

Total current assets

   108,186   109,124 
  

 

 

  

 

 

 

Property and equipment, net

   5,016   5,254 

Intangible assets, net

   949   968 

Investment in Bionic Sight

   1,972   1,980 

Other assets

   1,205   1,206 
  

 

 

  

 

 

 

Total assets

  $117,328  $118,532 
  

 

 

  

 

 

 

LIABILITIES AND STOCKHOLDERS’ EQUITY

   

Current liabilities:

   

Accounts payable

  $3,029  $945 

Accrued and other liabilities

   5,677   7,155 

Deferred revenue

   16,319   6,295 
  

 

 

  

 

 

 

Total current liabilities

   25,025   14,395 
  

 

 

  

 

 

 

Deferred revenue, net of current portion

   9,106   610 

Other liabilities

   4,258   4,345 
  

 

 

  

 

 

 

Total liabilities

   38,389   19,350 
  

 

 

  

 

 

 

Stockholders’ equity:

   

Preferred stock, par value $.001 per share, 5,000 shares authorized; no shares issued and outstanding

   —     —   

Common stock, par value $.001 per share, 150,000 shares authorized; 18,143 and 18,137 shares issued; 18,130 and 18,126 shares outstanding at September 30, and June 30, 2018, respectively

   18   18 

Additionalpaid-in capital

   211,320   210,139 

Shares held in treasury of: 13 and 11 at September 30, 2018 and June 30, 2018 respectively

   (57  (49

Accumulated deficit

   (132,342  (110,926
  

 

 

  

 

 

 

Total stockholders’ equity

   78,939   99,182 
  

 

 

  

 

 

 

Total liabilities and stockholders’ equity

  $117,328  $118,532 
  

 

 

  

 

 

 

The accompanying notes are an integral part of the financial statements.


APPLIED GENETIC TECHNOLOGIES CORPORATION

CONDENSED STATEMENTS OF OPERATIONS

(Unaudited)

 

   For the Three Months Ended September 30, 

In thousands, except per share amounts

  2018  2017 

Revenue:

   

Collaboration revenue

  $14,025  $10,308 

Grant and other revenue

   9   7 
  

 

 

  

 

 

 

Total revenue

   14,034   10,315 
  

 

 

  

 

 

 

Operating expenses:

   

Research and development

   10,065   8,276 

General and administrative and other

   3,213   3,706 
  

 

 

  

 

 

 

Total operating expenses

   13,278   11,982 
  

 

 

  

 

 

 

Income (loss) from operations

   756   (1,667

Other income:

   

Investment income, net

   471   270 
  

 

 

  

 

 

 

Total other income, net

   471   270 
  

 

 

  

 

 

 

Income (loss) before provision for income taxes and equity in net losses of affiliate

   1,227   (1,397

Provision for income taxes

   19   —   
  

 

 

  

 

 

 

Income (loss) before equity in net losses of affiliate

   1,208   (1,397

Equity in net losses of affiliate

   (8  —   
  

 

 

  

 

 

 

Net income (loss)

  $1,200  $(1,397
  

 

 

  

 

 

 

Weighted Average Shares Outstanding

   

Weighted average shares outstanding - basic

   18,128   18,088 

Weighted average shares outstanding - diluted

   18,158   18,088 

Net income (loss) per common share

   

Net income (loss) per share, basic

  $0.07  $(0.08

Net income (loss) per share, diluted

  $0.07  $(0.08

The accompanying notes are an integral part of the financial statements.

 

 

For the Three Months Ended September 30,

 

In thousands, except per share amounts

 

2017

 

 

2016

 

Revenue:

 

 

 

 

 

 

 

 

Collaboration revenue

 

$

10,308

 

 

$

11,772

 

Grant and other revenue

 

 

7

 

 

 

34

 

Total revenue

 

 

10,315

 

 

 

11,806

 

Operating expenses:

 

 

 

 

 

 

 

 

Research and development

 

 

8,276

 

 

 

5,571

 

General and administrative and other

 

 

3,706

 

 

 

2,846

 

Total operating expenses

 

 

11,982

 

 

 

8,417

 

Income (loss) from operations

 

 

(1,667

)

 

 

3,389

 

Other income:

 

 

 

 

 

 

 

 

Investment income, net

 

 

270

 

 

 

236

 

Total other income, net

 

 

270

 

 

 

236

 

Income (loss) before provision for income taxes

 

 

(1,397

)

 

 

3,625

 

Provision for income taxes

 

 

-

 

 

 

600

 

Net income (loss)

 

$

(1,397

)

 

$

3,025

 

Net earnings per share, basic

 

$

(0.08

)

 

$

0.17

 

Net earnings per share, diluted

 

$

(0.08

)

 

$

0.16

 

Weighted average shares outstanding - basic

 

 

18,088

 

 

 

18,050

 

Weighted average shares outstanding - diluted

 

 

18,088

 

 

 

18,445

 

APPLIED GENETIC TECHNOLOGIES CORPORATION

CONDENSED STATEMENT OF STOCKHOLDERS’ EQUITY

(Unaudited)

 

   Common Stock   Treasury Stock  Additional
Paid-in
Capital
   Accumulated
Deficit
  Total 

In thousands

  Outstanding
Shares
   Amount   Outstanding
Shares
   Amount 

Balance, June 30, 2017

   18,088   $18    —     $—    $204,937   $(89,626 $115,329 

Share based compensation expense

   —      —      —      —     1,469    —     1,469 

Shares issued under employee plans

   5    —      —      —     2    —     2 

Net loss

   —      —      —      —     —      (1,397  (1,397
  

 

 

   

 

 

   

 

 

   

 

 

  

 

 

   

 

 

  

 

 

 

Balance, September 30, 2017

   18,093   $18    —     $ —    $ 206,408   $(91,023 $115,403 
  

 

 

   

 

 

   

 

 

   

 

 

  

 

 

   

 

 

  

 

 

 

Balance, June 30, 2018

   18,126   $18    11   $(49 $210,139   $(110,926 $99,182 

Cumulative impact of adopting Topic 606 on July 1, 2018

   —      —      —      —     —     $(22,616  (22,616

Share based compensation expense

   —      —      —      —     1,181    —     1,181 

Shares issued under employee plans

   4    —      2    (8  —      —     (8

Net income

   —      —      —      —     —      1,200   1,200 
  

 

 

   

 

 

   

 

 

   

 

 

  

 

 

   

 

 

  

 

 

 

Balance, September 30, 2018

   18,130   $18    13   $(57 $211,320   $(132,342 $78,939 
  

 

 

   

 

 

   

 

 

   

 

 

  

 

 

   

 

 

  

 

 

 

The accompanying notes are an integral part of the financial statements.

 


APPLIED GENETIC TECHNOLOGIES CORPORATION

CONDENSED STATEMENTS OF CASH FLOWS

(Unaudited)

 

 

 

For the Three Months Ended September 30,

 

In thousands

 

2017

 

 

2016

 

Cash flows from operating activities

 

 

 

 

 

 

 

 

Net (loss) income

 

$

(1,397

)

 

$

3,025

 

Adjustments to reconcile net income (loss) to net cash used in operating activities:

 

 

 

 

 

 

 

 

Share-based compensation expense

 

 

1,469

 

 

 

1,420

 

Depreciation and amortization

 

 

234

 

 

 

201

 

Investment premium accretion

 

 

82

 

 

 

200

 

Changes in operating assets and liabilities:

 

 

 

 

 

 

 

 

Grants receivable

 

 

(8

)

 

 

920

 

Prepaid and other current assets

 

 

(8

)

 

 

482

 

Accounts payable

 

 

1,470

 

 

 

(249

)

Deferred revenue

 

 

(9,754

)

 

 

(11,725

)

Accrued expenses and other liabilities

 

 

(739

)

 

 

(69

)

Net cash used in operating activities:

 

 

(8,651

)

 

 

(5,795

)

Cash flows from investing activities

 

 

 

 

 

 

 

 

Purchase of property and equipment

 

 

(130

)

 

 

(21

)

Purchase of and capitalized costs related to intangible assets

 

 

-

 

 

 

(49

)

Maturity of investments

 

 

26,807

 

 

 

35,358

 

Purchase of investments

 

 

-

 

 

 

(2,400

)

Net cash provided by investing activities:

 

 

26,677

 

 

 

32,888

 

Cash flows from financing activities

 

 

 

 

 

 

 

 

Proceeds from exercise of common stock options

 

 

2

 

 

 

19

 

Net cash provided by financing activities:

 

 

2

 

 

 

19

 

Net increase in cash and cash equivalents

 

 

18,028

 

 

 

27,112

 

Cash and cash equivalents, beginning of period

 

 

30,706

 

 

 

28,868

 

Cash and cash equivalents, end of period

 

$

48,734

 

 

$

55,980

 

 

 

 

 

 

 

 

 

 

Supplemental disclosure of cash flow information

 

 

 

 

 

 

 

 

Cash paid during the year for income taxes

 

$

670

 

 

$

-

 

   For the Three Months Ended September 30, 

In thousands

              2018                          2017             

Cash flows from operating activities

   

Net income (loss)

  $1,200  $(1,397

Adjustments to reconcile net income (loss) to net cash used in operating activities:

   

Share-based compensation expense

   1,181   1,469 

Depreciation and amortization

   321   234 

Recovery of bad debts

   (369  —   

Investment premium accretion

   (142  82 

Equity in net losses of affiliate

   8   —   

Changes in operating assets and liabilities:

   

Grants receivable

   (9  (8

Prepaid and other assets

   723   (8

Deferred revenues

   (2,967  (9,754

Accounts payable

   2,084   1,470 

Accrued and other liabilities

   (1,447  (739
  

 

 

  

 

 

 

Net cash provided by (used in) operating activities

   583   (8,651
  

 

 

  

 

 

 

Cash flows from investing activities

   

Purchase of property and equipment

   (41  (130

Purchase of and capitalized costs related to intangible assets

   (23  —   

Maturities of investments

   24,736   26,807 

Purchases of investments

   (29,722  —   
  

 

 

  

 

 

 

Net cash (used in) provided by investing activities

   (5,050  26,677 
  

 

 

  

 

 

 

Cash flows from financing activities

   

Proceeds from exercise of common stock options

   —     2 

Deferred offering costs

   (113  —   

Payments made toward capital lease obligations

   (13  —   
  

 

 

  

 

 

 

Net cash (used in) provided by financing activities

   (126  2 
  

 

 

  

 

 

 

Net change in cash and cash equivalents

   (4,593  18,028 

Cash and cash equivalents, beginning of period

   31,065   30,706 
  

 

 

  

 

 

 

Cash and cash equivalents, end of period

  $26,472  $48,734 
  

 

 

  

 

 

 

Supplemental disclosure of cash flow information

   

Cash paid during the period for income taxes

  $—    $670 

Shares issued for no consideration

  $8  $—   

The accompanying notes are an integral part of the financial statements.


APPLIED GENETIC TECHNOLOGIES CORPORATION

NOTES TO CONDENSED FINANCIAL STATEMENTS (UNAUDITED)

1.

Organization and Operations:

Applied Genetic Technologies Corporation (the “Company” or “AGTC”) was incorporated as a Florida corporation on January 19, 1999 and reincorporated as a Delaware corporation on October 24, 2003. The Company is a clinical-stage biotechnology company that uses a proprietary gene therapy platform to develop transformational genetic therapies for patients suffering from rare and debilitating diseases.

In July 2015, the Company entered into a collaboration agreement (the “Collaboration Agreement”) with Biogen MA, Inc., a wholly owned subsidiary of Biogen Inc. (“Biogen”), pursuant to which the Company and Biogen will collaborate to develop, seek regulatory approval for and commercialize gene therapy products to treatX-linked retinoschisis (“XLRS”),X-linked retinitis pigmentosa (“XLRP”), and discovery programs targeting three indications based on the Company’s adeno-associated virus vector technologies. The Collaboration Agreement became effective in August 2015. The Collaboration Agreement and other transactions with Biogen are discussed further in Note 6 to these financial statements.

The Company has devoted substantially all of its efforts to research and development, including clinical trials. The Company has not completed the development of any products. The Company has generated revenue from collaboration agreements, sponsored research payments and grants, but has not generated product revenue to date and is subject to a number of risks similar to those of other early stage companies in the biotechnology industry, including dependence on key individuals, the difficulties inherent in the development of commercially viable products, the need to obtain additional capital necessary to fund the development of its products, development by the Company or its competitors of technological innovations, risks of failure of clinical studies, protection of proprietary technology, compliance with government regulations and ability to transition to large-scale production of products. As of September 30, 2017,2018, the Company had an accumulated deficit of $91.0$132.3 million. While the Company expects to continue to generate some revenue from partnering, including under the collaboration with Biogen, the Company expects to incur losses for the foreseeable future. The Company has funded its operations to date primarily through public offerings of its common stock, private placements of its preferred stock, and collaborations. At September 30, 2017,2018, the Company had cash and cash equivalents and liquid investments of $129.6$105.4 million.

 

2.

Summary of Significant Accounting Policies:

Basis of presentation

The accompanying unaudited condensed financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“GAAP”) and, in the opinion of management, include all adjustments necessary for a fair presentation of the Company’s financial position, results of operations, and cash flows for each period presented.

The adjustments referred to above are of a normal and recurring nature. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to U.S. Securities and Exchange Commission (“SEC”) rules and regulations for interim reporting.

Certain amounts reported previously have been reclassified to conform to the current period presentation, with no effect on stockholders’ equity or net income (loss) as previously presented. See Note 7 for a discussion on a revision of prior financial results presented related to the recording of our income tax provision for fiscal year 2017.

The Condensed Balance Sheet as of June 30, 20172018 was derived from audited financial statements, but does not include all disclosures required by GAAP. These Unaudited Condensed Financial Statements should be read in conjunction with the audited financial statements included in the Company’s 20172018 Annual Report on Form10-K, as amended, (“June 201730, 2018 Form10-K”). Results of operations for the three months ended September 30, 20172018 are not necessarily indicative of the results to be expected for the full year or any other interim period.

Segment reporting

Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision-maker in making decisions regarding resource allocation and assessing performance. To date, we have viewed our operations and managed our business as one segment.

Use of estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amount of revenues and expenses during the reporting period.periods. Actual results could differ from those estimates.


Cash and cash equivalents

Cash consists of funds held in bank accounts. Cash equivalents consist of short-term, highly liquid investments with original maturities of 90 days or less at the time of purchase and generally include money market accounts.

Investments

The Company’s investments consist of certificates of deposit and debt securities classified as held-to-maturity.held-to maturity. Management determines the appropriate classification of debt securities at the time of purchase and reevaluates such designation as of each balance sheet date. Debt securities are classified asheld-to-maturity when the Company has the positive intent and ability to hold the securities tomaturity. Held-to-maturity securities are stated at amortized cost, adjusted for amortization of premiums and accretion of discounts to maturity. Such amortization is included in investment income. Interest on securities classified asheld-to-maturity is included in investment income.

The Company uses the specific identification method to determine the cost basis of securities sold.

Investments are considered to be impaired when a decline in fair value is judged to be other-than-temporary. The Company evaluates an investment for impairment by considering the length of time and extent to which market value has been less than cost or amortized cost, the financial condition and near-term prospects of the issuer as well as specific events or circumstances that may influence the operations of the issuer and the Company’s intent to sell the security or the likelihood that it will be required to sell the security before recovery of the entire amortized cost. Once a decline in fair value is determined to be other-than-temporary, an impairment charge is recorded to otherinvestment income (expense) and a new cost basis in the investment is established.

Fair value of financial instruments

The Company is required to disclose information on all assets and liabilities reported at fair value that enables an assessment of the inputs used in determining the reported fair values. The Financial Accounting Standards Board (“FASB”) Accounting Standard Codification (“ASC”) Topic 820,Fair Value Measurements and Disclosures, establishes a hierarchy of inputs used when available. Observable inputs are inputs that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability, and are developed based on the best information available in the circumstances. The fair value hierarchy applies only to the valuation inputs used in determining the reported fair value of financial instruments and is not a measure of the investment credit quality. The three levels of the fair value hierarchy are described below:

Level 1—Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the measurement date.

Level 2—Valuations based on quoted prices for similar assets or liabilities in markets that are not active or for which all significant inputs are observable, either directly or indirectly.

Level 3—Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and unobservable.

To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized in Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement.

Revenue recognition

TheEffective July 1, 2018, the Company has primarily generated revenue through collaboration agreements, sponsored research arrangementsadopted the provisions of ASC Topic 606,Revenue from Contracts with nonprofit organizations forCustomers,(“Topic 606”), using the development and commercializationmodified retrospective transition method. Under this method, the Company recorded the cumulative effect of product candidates and revenues from federal research and development grant programs. The Company recognizes revenue when amounts are realized or realizable and earned. Revenue is considered realizable and earned wheninitially applying the following criteria are met: (i) persuasive evidence of an arrangement exists; (ii) delivery has occurred or services have been rendered; (iii) the price is fixed or determinable; and (iv) collectionnew standard to all contracts in process as of the amounts duedate of adoption. This standard applies to all contracts with customers, except for contracts that are reasonably assured.within the scope of other standards.

Amounts received prior to satisfying

The adoption of the new revenue recognition criteria are recorded asguidance resulted in an increase of $22.6 million in deferred revenue in the Company’s balance sheets. Amounts expected to be recognizedand accumulated deficit as revenue within the 12 months following the balance sheet date are classified as current liabilities. The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of


research and development expenses, as the Company has the risks and rewards as the principal in the research and development activities.

The Company evaluates the terms of sponsored research agreement grants and federal grants to assess the Company’s obligations and if the Company’s obligations are satisfied by the passage of time, revenue is recognized on a straight-line basis. In situations where the performance of the Company’s obligations has been satisfied when the grant is received, revenue is recognized upon receipt of the grant. Certain grants contain refund provisions. The Company reviews those refund provisions to determine the likelihood of repayment. If the likelihood of repayment of the grant is determined to be remote, the grant is recognized as revenue. If the probability of repayment is determined to be more than remote, the Company records the grant as a deferred revenue liability, until such time that the grant requirements have been satisfied.

Collaboration revenue

On July 1, 2015, the Company entered into a Collaboration Agreement with Biogen.  This collaboration is discussed further in Note 6 of notes to the financial statements.  The terms of the Collaboration Agreement and other potential collaboration or commercialization agreements the Company may enter into generally contain multiple elements, or deliverables, which may include, among others, (i) licenses, or options to obtain licenses, to its technology, and (ii) research and development activities to be performed on behalf of the collaborative partner.  Payments made under such arrangements typically include one or more of the following: non-refundable, up-front license fees; option exercise fees; funding of research and/or development efforts; milestone payments; and royalties on future product sales.

Multiple element arrangements are analyzed to determine whether the deliverables within the agreement can be separated or whether they must be accounted for as a single unit of accounting.  Deliverables under an agreement are required to be accounted for as separate units of accounting provided that (i) a delivered item has value to the customer on a stand-alone basis; and (ii) if the agreement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The allocation of consideration amongst the deliverables under the agreement is derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence of fair value is not available. If the delivered element does not have stand-alone value or if the fair value of any of the undelivered elements cannot be determined, the arrangement is then accounted for as a single unit of accounting, and the Company recognizes the consideration received under the arrangement as revenue on a straight-line basis over the estimated period of performance.

The Company determines the estimated selling price for deliverables within each agreement using vendor-specific objective evidence, or VSOE, of selling price, if available, third-party evidence, or TPE, of selling price if VSOE is not available, or best estimate of selling price, or BESP, if neither VSOE nor TPE are available.  Determining the best estimate of selling price for a deliverable requires significant judgment.  The Company uses BESP to estimate the selling price related to licenses to its proprietary technology, since it often does not have VSOE or TPE of selling price for these deliverables.  In those circumstances where it utilizes BESP to determine the estimated selling price of a license to our proprietary technology, the Company considers market conditions as well as entity-specific factors, including those factors contemplated in negotiating the agreements as well as internally developed models that include assumptions related to the market opportunity, estimated development costs, probability of success and the time needed to commercialize a product candidate pursuant to the license.  In validating its best estimate of selling price, the Company evaluates whether changes in the key assumptions used to determine the best estimate of selling price will have a significant effect on the allocation of arrangement consideration among multiple deliverables.

If the delivered element does not have stand-alone value or if the fair value of any of the undelivered elements cannot be determined, the arrangement is then accounted for as a single unit of accounting, and the Company recognizes the consideration received under the arrangement as revenue on a straight-line basis over our estimated period of performance.  The Company’s anticipated periods of performance, typically the terms of our research and development obligations, are subject to estimates by management and may change over the course of the collaboration agreement.  Such changes could have a material impact on the amount of revenue we record in future periods.

Milestone revenue

The Company applies the milestone method of accounting to recognize revenue from milestone payments when earned, as evidenced by written acknowledgement from the collaborator or other persuasive evidence that the milestone has been achieved and the payment is non-refundable, provided that the milestone event is substantive.  A milestone event is defined as an event (i) that can only be achieved based in whole or in part on either the Company’s performance or on the occurrence of a specific outcome resulting from the Company’s performance; (ii) for which there is substantive uncertainty at the inception of the arrangement that the event will be achieved; and (iii) that would result in additional payments being due to the Company. Events for which the occurrence is either contingent solely upon the passage of time or the result of a counterparty’s performance are not considered to be milestone events. A milestone event is substantive if all of the following conditions are met: (i) the consideration is commensurate with either the Company’s performance to achieve the milestone, or the enhancement of the


value to the delivered item(s) as a result of a specific outcome resulting from the Company’s performance to achieve the milestone; (ii) the consideration relates solely to past performance; and (iii) the consideration is reasonable relative to all the deliverables and payment terms (including other potential milestone consideration) within the arrangement.

The Company assesses whether a milestone is substantive at the inception of the arrangement. If a milestone is deemed non-substantive, the Company accounts for that milestone payment in accordance with the multiple element arrangements guidance and recognizes revenue consistent with the related units of accounting for the arrangement over the related performance period.

No milestone revenues were recognized during2018. For the three months ended September 30, 20172018, revenue increased by $1.5 million, net income increased by $1.5 million and basic and diluted net income per share increased by $0.08 per share based on revenue recognition under Topic 606 as compared to the Company’s prior revenue recognition methodology under ASC 605, Revenue Recognition. These changes were primarily caused by the differences in determining and allocating transaction price and recognizing revenue on a proportional performance basis under Topic 606.

The Company may enter into collaboration agreements which are within the scope of Topic 606, under which the Company licenses rights to its technology and certain of the Company’s product candidates and performs research and development services for third parties. The terms of these arrangements typically may include payment of one or 2016.more of the following:non-refundable,up-front fees; reimbursement of research and development costs; development, regulatory and commercial milestone payments; and royalties on net sales of licensed products.

Under Topic 606, an entity recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. To determine the appropriate amount of revenue to be recognized for arrangements determined to be within the scope of Topic 606, the Company performs the following five steps: (i) identification of the contract; (ii) determination of whether the promised goods or services are performance obligations; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. The Company only applies the five-step model to contracts when it is probable that the entity will collect consideration it is entitled to in exchange for the goods or services it transfers to the customer.

Performance obligations are promises to transfer distinct goods or services to the customer. Promised goods or services are considered distinct when (i) the customer can benefit from the good or service on its own or together with other readily available resources and (ii) the promised good or service is separately identifiable from other promises in the contract. In assessing whether promised good or services are distinct, the Company considers factors such as the stage of development of the underlying intellectual property, the capabilities of the customer to develop the intellectual property on their own or whether the required expertise is readily available.

The Company estimates the transaction price based on the amount expected to be received for transferring the promised goods or services in the contract. The consideration may include both fixed consideration or variable consideration. At the inception of an arrangement that includes variable consideration and at each reporting period, the Company evaluates the amount of potential payment and the likelihood that the payments will be received. The Company utilizes either the most likely amount method or expected amount method to estimate the amount to be received based on which method better predicts the amount expected to be received. If it is probable that a significant revenue reversal would not occur, the variable consideration is included in the transaction price. The Company will assess its revenue generating arrangements in order to determine whether a significant financing component exists and conclude that a significant financing component does not exist in any of its arrangements if: (a) the promised consideration approximates the cash selling price of the promised goods and services or any significant difference is due to factors other than financing; and (b) timing of payment approximates the transfer of goods and services and performance is over a relatively short period of time within the context of the entire term of the contract.

The Company’s contracts will often include development and regulatory milestone payments. At contract inception and at each reporting period, the Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the Company’s control or the customer’s control, such as regulatory approvals, are not included in the transaction price. At the end of each subsequent reporting period, the Companyre-evaluates the probability of achievement of such development milestones and any related constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulativecatch-up basis, which would affect collaboration revenues and earnings in the period of adjustment.

For arrangements that may include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). To date, the Company has not recognized any royalty revenue resulting from any of the Company’s collaboration arrangements.

The Company allocates the transaction price based on the estimated standalone selling price of the underlying performance obligations or in the case of certain variable consideration to one or more performance obligations. The Company must develop assumptions that require judgment to determine the stand-alone selling price for each performance obligation identified in the contract. The Company utilizes key assumptions to determine the stand-alone selling price, which may include other comparable transactions, pricing considered in negotiating the transaction and the estimated costs to complete the respective performance obligation. Certain variable consideration is allocated specifically to one or more performance obligations in a contract when the terms of the variable consideration relate to the satisfaction of the performance obligation and the resulting amounts allocated to each performance obligation are consistent with the amounts the Company would expect to receive for each performance obligation.

For performance obligations consisting of licenses and other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue fromnon-refundable,up-front fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. If the license to the Company’s intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, the Company will recognize revenue fromnon-refundable,up-front fees allocated to the license when the license is transferred to the customer and the customer is able to use and benefit from the license.

The Company receives payments from its customers based on billing terms established in each contract. Such billings generally have30-day payment terms. Upfront payments and fees are recorded as deferred revenue upon receipt or when due until the Company performs its obligations under these arrangements. Amounts are recorded as accounts receivable when the right to consideration is unconditional.

Income taxes

The Company uses the asset and liability method for accounting for income taxes. Under this method, deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective income tax bases. Deferred tax assets and liabilities are measured using enacted rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled.

ForThe Tax Cut and Jobs Act (the “Tax Act”) was enacted on December 22, 2017. The Tax Act contains several key provisions including, among other things, reducing the three months ended September 30, 2017, no incomeU.S. federal corporate tax expense was recognized. Forrate from 35% to 21%. In addition, federal net operating losses (“NOLs”) will be carried forward indefinitely, but will be subject to an 80% utilization against taxable income. The Company follows the three months ended September 30, 2016,guidance in SEC Staff Accounting Bulletin 118 (SAB 118) which provides additional clarification regarding the Company recorded an income tax provisionapplication of $0.6 million, related to the Company’s federal alternative minimum taxable income (“AMTI”) and state income taxASC Topic 740 in multiple statessituations where the Company is doing business.does not have the necessary information available, prepared, or analyzed in reasonable detail to complete the accounting for certain income tax effects of the Act for the reporting period in which the Act was enacted. SAB 118 provides for a measurement period beginning in the reporting period that includes the Act’s enactment date and ending when the Company has obtained, prepared, and analyzed the information needed in order to complete the accounting requirements but in no circumstances should the measurement period extend beyond one year from the enactment date. The Company calculates its AMTI usinghas enacted the alternative minimumreduction in tax (“AMT”) system.rate effective January 1, 2018, which resulted in a decrease to the deferred tax asset and a decrease to the valuation allowance. The Company’s federalCompany is in the process of evaluating the Tax Act changes in section 162(m), Internal Revenue Code of 1986, regarding deductions for excessive employee compensation. The Company continues to gather and analyze information, including the definition of an employee contract for stock grants not vested as of the enactment date of the Act. It is the intention of the Company to complete the necessary analysis within the measurement period however the Company anticipates that any adjustment would be a decrease to deferred tax asset and valuation allowance with no impact to income tax liability is the greater of the tax computed using the regular tax system or the tax under the AMT system. Corporations are exempt from AMT for all prior years in which their annual gross receipts for the 3-year period ending before the current tax year did not exceed $7.5 million. As of September 30, 2017, the Company no longer qualifies for the small company exclusion. The AMT system limits the use of net operating losses used by taxpayers to offset taxable income.expense.

As required by U.S. GAAP, the Company recognizes the financial statement benefit of a tax position only after determining that the relevant tax authority would more likely than not sustain the position following an audit. For tax positions meeting themore-likely-than-not threshold, the amount recognized in the financial statements is the largest benefit that has a greater than 50 percent likelihood of being realized upon ultimate settlement with the relevant tax authority. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense. The Company is subject to examination of its income tax returns in the federal and state income tax jurisdictions in which it operates. On December 28, 2015, the United States Internal Revenue Service, or IRS, notified the Company of an income tax audit for the tax period ending June 30, 2014. As of June 30, 2017, the IRS audit was closed and the Company incurred no penalties or payment liabilities for its income tax positions.

For the three months ended September 30, 2016,2018, the Company’s $0.6 million of tax expense included an increase in the uncertain tax position liability of $0.2 million$18,919 related to uncertainty in how states may tax income from the Biogen Collaboration Agreement. The full amount ofinterest on the uncertain tax position. The uncertain tax position reflected on the balance sheet within accrued expenses and other liabilitiesliability as of September 30, 2017 is $950,000. This collaboration agreement is described in more detail in Note 6 of the notes to the financial statements.     2018 and June 30, 2018 was $1,977,919 and $1,959,000, respectively.

Research and development

Research and development costs include costs incurred in identifying, developing and testing product candidates and generally comprise compensation and related benefits andnon-cash share-based compensation to research related employees; laboratory costs; animal and laboratory maintenance and supplies; rent; utilities; clinical andpre-clinical expenses; and payments for sponsored research, scientific and regulatory consulting fees and testing.

As part of the process of preparing its financial statements, the Company is required to estimate its accrued expenses. This process involves reviewing quotations and contracts, identifying services that have been performed on its behalf and estimating the level of service performed and the associated cost incurred for the service whenservices for which the Company has not yet been invoiced or otherwise notified of the actual cost. The majority of the Company’s service providers invoice the Company monthly in arrears for services performed or when contractual milestones are met. The Company makes estimates of its accrued expenses as of each balance sheet date in its financial statements based on facts and circumstances known to it at that time. The significant estimates in the Company’s accrued research and development expenses are related to expenses incurred with respect to academic research centers, contract research organizations, (“CROs”), and other vendors in connection with research and development activities for which it has not yet been invoiced.

There may be instances in which the Company’s service providers require advance payments at the inception of a contract or in which payments made to these vendors will exceed the level of services provided, resulting in a prepayment of the research and development expense. Such prepayments are charged to research and development expense as and when the service is provided or when a specific milestone outlined in the contract is reached.


Prepayments related to research and development activities were $1.6$1.0 million and $1.5$1.0 million at September 30, 20172018 and June 30, 2017,2018, respectively, and are included within the Prepaidprepaid and other current assets line item on the unaudited condensed balance sheets.

Share-based compensation

The Company accounts for share-based awards issued to employees in accordance with ASC Topic 718, Compensation—Stock Compensation (“ASC 718”) and generally recognizes share-based compensation expense on a straight-line basis over the periods during which the employees are required to provide service in exchange for the award. In addition, the Company issues stock options and restricted shares of common stock tonon-employees in exchange for consulting services and accounts for these in accordance with the provisions of ASC Subtopic505-50,Equity-Based Payments toNon-employees (“ASC505-50”). Under ASC505-50, share-based awards tonon-employees are subject to periodic fair valuere-measurement over their vesting terms.

For purposes of calculating stock-based compensation, the Company estimates the fair value of stock options using a Black-Scholes option-pricing model. The determination of the fair value of share-based payment awards utilizing the Black-Scholes model is affected by the Company’s stock price and a number of assumptions, including expected volatility, expected life, risk-free interest rate and expected dividends. TheHistorically, the expected volatility iswas primarily based on the historical volatility of peer company data. For the three months ended September 30, 2018, the expected volatility is based on the historical volatility of the company stock price. If the Company had used peer company data whilefor the three months ended September 30, 2018, share-based compensation expense for the quarter would have differed by an insignificant amount. The expected life of the stock options is based on historical and other economic data trended into the future. The risk-free interest rate assumption is based on observed interest rates appropriate for the expected terms of the Company’s stock options. The dividend yield assumption is based on the Company’s history and expectation of no dividend payouts. If factors change and the Company employs different assumptions, stock-based compensation expense may differ significantly from what has been recorded in the past. If there is a difference between the assumptions used in determining stock-based compensation expense and the actual factors which become known over time, specifically with respect to anticipated forfeitures, the Company may change the input factors used in determining stock-based compensation costs for future grants. These changes, if any, may materially impact the Company’s results of operations in the period such changes are made.

Net income (loss) income per share

Basic net earningsincome (loss) per share is calculated by dividing net earningsincome (loss) by the weighted average shares outstanding during the period, without consideration for common stock equivalents. Diluted net earningsincome (loss) per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net earningsincome (loss) per share calculation,calculations, stock options and warrants are considered to be common stock equivalents.  The dilutive impact ofequivalents if they are dilutive. For the three-month period ended September 30, 2018, stock options and warrants forwere dilutive and increased common stock equivalents outstanding by 29,744 shares. For the three months ended September 30, 2017 totaled 0.2 million shares. The dilutive impact of stock options and warrants have been excluded from the calculation of diluted net loss per share for the for the three months ended September 30, 2017, as their effect would be anti-dilutive. Therefore, for the three months endedthree-month period ending September 30, 2017, basic and diluted net loss per share are the same.same due to stock options and warrants being considered anti-dilutive. If stock options and warrants had been dilutive, their impact would have increased common stock equivalents outstanding at September 30, 2017 by 0.2 million shares.

Comprehensive income (loss)

Comprehensive income or loss

Comprehensive income or loss(loss) consists of net income or loss(loss) and changes in equity during a period from transactions and other equity and circumstances generated fromnon-owner sources. The Company’s net income or loss(loss) equals comprehensive income or loss(loss) for bothall periods presented.

New accounting pronouncementsAccounting Pronouncements

In May 2017, the FASB issued Accounting Standards Update (“ASU”)No. 2017-09,Scope of Modification Accounting, which amends ASC Topic 718,Compensation – Stock Compensation. The amendments in this Update provide guidance about which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting in Topic 718. The amendments are effective for fiscal years beginning after December 15, 2017, and interim periods within those fiscal years and early adoption is permitted. The Company is currently in the process of evaluating the impact of adoption of this standard on its financial statements.

In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting, which amends ASC Topic 718, Compensation – Stock Compensation.  The amendments simplify several aspects of the accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, forfeitures, and classification on the statement of cash flows.  The amendments are effective for fiscal years beginning after December 15, 2016, and interim periods within those fiscal years and early adoption is permitted. The Company has adopted this standard for its 2018in the first quarter of fiscal year2019 and it did not have a material effect on its balance sheets, results of operations or cash flows.financial statements.


In February 2016, the FASB issued ASUNo. 2016-02,Leases (Topic 842)in order to increase transparency and comparability among organizations by recognizing lease assets and lease liabilities on the balance sheet for those leases previously classified as operating leases under GAAP. The standard requires, in most instances, a lessee to recognize on its balance sheet a liability to make lease payments (the lease liability) and also aright-of-use asset representing its right to use the underlying asset for the lease term. The amendments are effective for fiscal years beginning after December 15, 2018, including interim periods within those periods, using a modified retrospective approach and early adoption is permitted. The Company is currently in the process of evaluating the impact of adoption of this standard on its financial statements.

In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606)Topic 606, which replaces the existing accounting standards for revenue recognition with a single comprehensive five-step model. The core principle is to recognize revenue upon the transfer of goods or services to customers at an amount that reflects the consideration expected to be received. It also requires enhanced disclosures about revenue, provides guidance for transactions that were not previously addressed comprehensively, and improves guidance for multiple-element arrangements. The guidance applies to any entity that either enters into contracts with customers to transfer goods or services or enters into contracts for the transfer of nonfinancial assets unless those contracts are within the scope of other standards. Since its issuance, the FASB has amended several aspects of the new guidance, including provisions that address revenue recognition associated with the licensing of intellectual property. In July 2015, the FASB delayed the effective date of this guidance by one year. The guidance is now effective for public companies for annual periods beginning after December 15, 2017 as well as interim periods within those annual periods using either the full retrospective approach or modified retrospective approach. The Company is working through an adoption plan which will include a review of collaboration agreements, applying the five-step model ofadopted the new standard and comparing the results to the Company’s current accounting. As part of this, the Company is evaluating the method of adoption and assessing changes that might be necessary to its processes, internal controls and address changes in financial reporting. Effectiveeffective July 1, 2018 using the Company will be revising its revenue recognition accounting policy and expanding revenue disclosuresmodified retrospective approach. Refer to reflect the requirements of the amended revenue recognition guidance. Because of the nature of the work that remains, at this time the Company is unable to reasonably estimateNote 6 for the impact of adoption on its financial statements.adoption.

3.

Share-based Compensation Plans:

The Company uses stock options and awards of restricted stock to provide long-term incentives for its employees,non-employee directors and certain consultants. The Company has two equity compensation plans under which awards are currently authorized for issuance, the 2013 Employee Stock Purchase Plan and the 2013 Equity and Incentive Plan. No awards have been issued to date under the 2013 Employee Stock Purchase Plan and all of the 128,571 shares previously authorized under this plan remain available for issuance. A summary of the stock option activity for the three months ended September 30, 20172018 and 20162017 is as follows:

 

 

September 30,

 

  For the Three Months Ended September 30, 

 

2017

 

 

 

 

2016

 

  2018   2017 

(In thousands, except per share amounts)

 

Shares

 

 

Weighted

Average

Exercise

Price

 

 

 

 

Shares

 

 

Weighted

Average

Exercise

Price

 

  Shares   Weighted
Average
Exercise
Price
   Shares   Weighted
Average
Exercise
Price
 

Outstanding at June 30,

 

 

2,714

 

 

$

12.96

 

 

 

 

 

2,037

 

 

$

13.71

 

   3,107   $10.93    2,714   $12.96 

Granted

 

 

715

 

 

 

4.88

 

 

 

 

 

337

 

 

 

15.53

 

   863    4.31    715    4.88 

Exercised

 

 

(5

)

 

 

0.35

 

 

 

 

 

(5

)

 

 

3.50

 

   —      —      (5   0.35 

Forfeited

 

 

(290

)

 

 

9.98

 

 

 

 

 

(12

)

 

 

19.36

 

   (166   8.08    (290   9.98 

Expired

 

 

(4

)

 

 

17.80

 

 

 

 

 

 

 

 

 

   (9   14.95    (4   17.80 
  

 

   

 

   

 

   

 

 

Outstanding at September 30,

 

 

3,130

 

 

$

11.40

 

 

 

 

 

2,357

 

 

$

13.97

 

   3,795   $9.54    3,130   $11.40 
  

 

   

 

   

 

   

 

 

Exercisable at September 30,

 

 

1,691

 

 

 

 

 

 

 

 

 

1,093

 

 

 

 

 

   2,092      1,691   
  

 

     

 

   

Weighted average fair value of options granted

during the period

 

$

3.52

 

 

 

 

 

 

 

 

$

10.62

 

 

 

 

 

  $2.81     $3.52   
  

 

     

 

   

For the three months ended September 30, 2017 and 2016,2018, share-based compensation expense related to stock options awarded to employees,non-employee directors and consultants amounted to approximately $1.2 million, compared to $1.5 million , and $1.4 million , respectively.   for the three months ended September 30, 2017.


As of September 30, 2017,2018, there was $10.4$7.0 million of unrecognized compensation expense related tonon-vested stock options. During the three months ended September 30, 2017, 715,0002018, 863,000 stock options were granted to the Company’s employees andnon-employee directors under the 2013 Equity and Incentive Plan. The fair value of each option granted is estimated on the grant date using the Black-Scholes stock option pricing model. The following assumptions were made in estimating fair value:

 

Assumption

  Three months
ended
September 30,
2018
   Three months
ended
September 30,
2017
 

Dividend yield

   0.00%    0.00% 

Expected term

   6.00 to 6.25 years    6.25 years 

Risk-free interest rate

   2.77% to 2.99%    1.83% to 1.97% 

Expected Volatility

   69.22%    83.53% 

4.

Three months ended September 30, 2017

Assumption

Dividend yield

0.00

%

Expected term

6.25 years

Risk-free interest rate

1.83%-1.97

%

Expected Volatility

83.53

%Investments:

4.

Investments:

Cash in excess of immediate requirements is invested in accordance with the Company’s investment policy that primarily seeks to maintain adequate liquidity and preserve capital.

The following table summarizes the Company’s investments by category as of September 30, 20172018 and June 30, 2017:2018:

 

In thousands

  September 30,
2018
   June 30,
2018
 

Investments - Current:

    

Certificates of deposit

  $1,869   $2,106 

Debt securities -held-to-maturity

   77,099    71,734 
  

 

 

   

 

 

 

Total investments - current

  $78,968   $73,840 
  

 

 

   

 

 

 

 

 

September 30,

 

 

June 30,

 

In thousands

 

2017

 

 

2017

 

Investments - Current:

 

 

 

 

 

 

 

 

Certificates of deposit

 

$

1,929

 

 

$

3,500

 

Debt securities - held-to-maturity

 

 

74,540

 

 

 

92,494

 

Total

 

$

76,469

 

 

$

95,994

 

Investments - Noncurrent:

 

 

 

 

 

 

 

 

Certificates of deposit

 

$

1,872

 

 

$

2,111

 

Debt securities - held-to-maturity

 

 

2,513

 

 

 

9,638

 

Total

 

$

4,385

 

 

$

11,749

 

A summary of the Company’s debt securities classified asheld-to-maturity is as follows:

 

 

 

At September 30, 2017

 

In thousands

 

Amortized Cost

 

 

Gross

Unrealized

Gains

 

 

Gross

Unrealized

Losses

 

 

Fair Value

 

Investments - Current:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

U.S. government and agency

   Obligations

 

$

72,475

 

 

$

 

 

$

(99

)

 

$

72,376

 

Corporate obligations

 

 

2,065

 

 

 

 

 

 

 

(9

)

 

 

2,056

 

 

 

$

74,540

 

 

$

 

 

$

(108

)

 

$

74,432

 

Investments - Noncurrent:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

U.S. government and agency

   Obligations

 

$

2,513

 

 

$

 

 

$

(17

)

 

$

2,496

 

Corporate obligations

 

 

-

 

 

 

 

 

 

 

 

 

 

-

 

 

 

$

2,513

 

 

$

 

 

$

(17

)

 

$

2,496

 


 

 

At June 30, 2017

 

In thousands

 

Amortized Cost

 

 

Gross

Unrealized

Gains

 

 

Gross

Unrealized

Losses

 

 

Fair Value

 

Investments - Current:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

U.S. government and agency

   Obligations

 

$

92,494

 

 

$

 

 

$

(147

)

 

$

92,347

 

Corporate obligations

 

 

-

 

 

 

 

 

 

 

 

 

-

 

 

 

$

92,494

 

 

$

 

 

$

(147

)

 

$

92,347

 

Investments - Noncurrent:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

U.S. government and agency

   Obligations

 

$

7,552

 

 

$

 

 

 

(52

)

 

$

7,500

 

Corporate obligations

 

 

2,086

 

 

 

 

 

 

(12

)

 

 

2,074

 

 

 

$

9,638

 

 

$

 

 

$

(64

)

 

$

9,574

 

   September 30, 2018 

In thousands

  Amortized
Cost
   Gross
Unrealized
Gains
   Gross
Unrealized
Losses
   Fair
Value
 

Investments - Current:

        

U.S. government and agency obligations

  $77,099   $—     $(77  $77,022 
  

 

 

   

 

 

   

 

 

   

 

 

 

Total investments - current

  $77,099   $—     $(77  $77,022 
  

 

 

   

 

 

   

 

 

   

 

 

 
   June 30, 2018 

In thousands

  Amortized
Cost
   Gross
Unrealized
Gains
   Gross
Unrealized
Losses
   Fair
Value
 

Investments - Current:

        

U.S. government and agency obligations

  $69,731   $—     $(60  $69,671 

Corporate obligations

   2,003    —      (1   2,002 
  

 

 

   

 

 

   

 

 

   

 

 

 
  $71,734   $—     $(61  $71,673 
  

 

 

   

 

 

   

 

 

   

 

 

 

The amortized cost and fair value ofheld-to-maturity debt securities as of September 30, 2017,2018, by contractual maturity, were as follows:

 

In thousands

 

Amortized Cost

 

 

Fair Value

 

Due in one year or less

 

$

74,540

 

 

$

74,432

 

Due after one year through two years

 

 

2,513

 

 

 

2,496

 

 

 

$

77,053

 

 

$

76,928

 

In thousands

  Amortized
Cost
   Fair Value 

Due in one year or less

  $77,099   $77,022 
  

 

 

   

 

 

 
  $77,099   $77,022 
  

 

 

   

 

 

 

The Company believes that the unrealized losses disclosed above were primarily driven by interest rate changes rather than by unfavorable changes in the credit ratings associated with these securities and as a result, the Company continues to expect to collect the principal and interest due on its debt securities that have an amortized cost in excess of fair value. At each reporting period, the Company evaluates securities for impairment when the fair value of the investment is less than its amortized cost. The Company evaluated the underlying credit quality and credit ratings of the issuers, noting neither a significant deterioration since purchase nor other factors leading to an other-than-temporary impairment. Therefore, the Company believes these losses to be temporary. As of September 30, 2017,2018, the Company did not have the intent to sell any of the securities that were in an unrealized loss position at that date.date.

5.

Fair Value of Financial Instruments and Investments:

Certain assets and liabilities are measured at fair value in the Company’s financial statements or have fair values disclosed in the notes to the financial statements. These assets and liabilities are classified into one of three levels of a hierarchy defined by GAAP. The Company’s assessment of the significance of a particular item to the fair value measurement in its entirety requires judgment, including the consideration of inputs specific to the asset or liability.

The following methods and assumptions were used to estimate the fair value and determine the fair value hierarchy classification of each class of financial instrument included in the table below.

Cash and Cash Equivalents. The carrying value of cash and cash equivalents approximates fair value as maturities are less than three months.

Certificates of Deposit. The Company’s certificates of deposit are placed through an account registry service. The fair value measurement of the Company’s certificates of deposit is considered Level 2 of the fair value hierarchy as the inputs are based on quoted pricesrates currently offered for identical assets in markets that are not active.  deposits of similar remaining maturities. The carrying amounts of the Company’s certificates of deposit reported in the unaudited condensed balance sheets approximate fair value.

Debt securities –held-to-maturity. The Company’s investments in debt securities classified asheld-to-maturity generally include U.S. Treasury Securities, government agency obligations, and corporate obligations. U.S. Treasury Securities and U.S. government agency obligations are valued using quoted market prices. Valuation adjustments are not applied. Accordingly, U.S. Treasury Securities are

considered Level 1 of the fair value hierarchy. The fair values of U.S. government agency obligations and corporate obligations are generally determined using recently executed transactions, broker quotes, market price quotations where these are available or other observable market inputs for the same or similar securities. As such, the Company classifies its investments in U.S. government agency obligations and corporate obligations within Level 1 or Level 2 of the hierarchy.  hierarchy, depending on the information used to determine the fair values.


The following fair value hierarchy table presents information about each major category of the Company’s financial assets and liabilities measured at fair value on a recurring basis:

 

In thousands

 

Quoted prices

in active

markets

(Level 1)

 

 

Significant

other observable inputs

(Level 2)

 

 

Significant unobservable

inputs

(Level 3)

 

 

Total Fair

Value

 

 

Total

Carrying

Value

 

  Quoted prices
in active
markets
(Level 1)
   Significant
other observable
inputs

(Level 2)
   Significant
unobservable
inputs

(Level 3)
   Total Fair
Value
   Total
Carrying
Value
 

September 30, 2017

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

September 30, 2018

          

Cash and cash equivalents

 

$

48,734

 

 

$

 

 

$

 

 

$

48,734

 

 

$

48,734

 

  $26,472    —      —     $26,472   $26,472 

Certificates of deposit

 

 

 

 

 

3,793

 

 

 

 

 

 

3,793

 

 

 

3,801

 

   —      1,868    —      1,868    1,869 

Held-to-maturity investments:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

          

Corporate obligations

 

 

 

 

 

2,056

 

 

 

 

 

 

2,056

 

 

 

2,065

 

   —      —      —      —      —   

U.S. government and agency obligations

 

 

62,984

 

 

 

11,887

 

 

 

 

 

 

74,871

 

 

 

74,988

 

   77,022    —      —      77,022    77,099 
  

 

   

 

   

 

   

 

   

 

 

Total assets

 

$

111,718

 

 

$

17,736

 

 

$

 

 

$

129,454

 

 

$

129,588

 

  $103,494   $1,868   $—     $105,362   $105,440 

June 30, 2017

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  

 

   

 

   

 

   

 

   

 

 

June 30, 2018

          

Cash and cash equivalents

 

$

30,706

 

 

$

 

 

$

 

 

$

30,706

 

 

$

30,706

 

  $31,065   $—     $—     $31,065   $31,065 

Certificates of deposit

 

 

 

 

 

5,601

 

 

 

 

 

 

5,601

 

 

 

5,610

 

   —      2,100    —      2,100    2,106 

Held-to-maturity investments:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

          

Corporate obligations

 

 

 

 

 

2,074

 

 

 

 

 

 

2,074

 

 

 

2,086

 

   —      2,002    —      2,002    2,003 

U.S. government and agency obligations

 

 

79,476

 

 

 

20,372

 

 

 

 

 

 

99,848

 

 

 

100,046

 

   69,671    —      —      69,671    69,731 
  

 

   

 

   

 

   

 

   

 

 

Total assets

 

$

110,182

 

 

$

28,047

 

 

$

 

 

$

138,229

 

 

$

138,448

 

  $100,736   $4,102   $—     $104,838   $104,905 
  

 

   

 

   

 

   

 

   

 

 

 

(6)

6.

Collaboration AgreementsAgreement

Biogen

On July 1, 2015, the Company entered into a Collaboration Agreement (the “Collaboration Agreement”), a Manufacturing License and Technology Transfer Agreement (the “Manufacturing Agreement”), and the Common Stock Purchase Agreement (the “Equity Agreement”) with Biogen (collectively, the “Biogen Agreement”), pursuant to which the Company and Biogen will collaborate to develop, seek regulatory approval for and commercialize gene therapy products to treat XLRS, XLRP, and discovery programs targeting three indications based on the Company’s adeno-associated virus vector technologies.  The Collaboration Agreement became effective on August 14, 2015.

Under the Collaboration Agreement, the Company will conduct all development activities through regulatory approval in the United States for the XLRS program (with activities through Phase 1/2 completion being pre-funded under the agreement and any further activities subject to incremental consideration), and all development activities through the completion of the first in human clinical trial for the XLRP program (with activities through filing the IND being pre-funded under the agreement and any further activities subject to incremental consideration).  In addition, the Collaboration Agreement provides for discovery programs targeting three indications whereby the Company will conduct discovery, research and development activities for those additional drug candidates through the stage of clinical candidate designation, after which, Biogen may exercise an option to continue to develop, seek regulatory approval for and commercialize the designated clinical candidate.  In February 2016, the Company announced Biogen’s selection of adrenoleukodystrophy as the non-ophthalmic indication of the discovery programs.  Under the terms of the Collaboration Agreement, the Company, in part through its participation in joint committees with Biogen, will participate in overseeing the development and commercialization of these specific programs.

The Company has granted to Biogen with respect to the XLRS and XLRP programs, and upon exercise of the option for the applicable discovery program, an exclusive, royalty-bearing license, with the right to grant sublicenses, to use adeno-associated virus vector technology and other technology controlled by the Company for the licensed products or discovery programs developed under the Collaboration Agreement.Agreements. Biogen and the Company have also granted each other worldwide licenses, with the right to grant sublicenses, of their respective interests in other intellectual property developed under the collaboration outside the licensed products or discovery programs.

Activities under Biogen has pre-funded the Collaboration Agreement were evaluated under ASC 605-25, Revenue Recognition—Multiple Element Arrangements, as amended by ASU 2009-13, Revenue Recognition ("ASC 605-25"),Company to determine if they representedconduct all development activities through the completion of a multiple element revenue arrangement.  The Collaboration Agreement includes the following significant deliverables:

(1)first in human trial for each of the XLRS program and all development activities through the date that the Investigational New Drug Application (“IND”) becomes effective and the completion of a natural history study for the XLRP programs, exclusive, royalty-bearing licenses, with the right to grant sublicenses, to use adeno-associated virus vector technology and other technology controlled byprogram. In addition, Biogen has pre-funded the Company to conduct discovery, research and development activities for additional drug candidates through the purposestage of researching,


developing, manufacturing and commercializing licensed products developed under the arrangement (the “License Deliverables”);

(2)clinical candidate designation for each of the discovery programs exercisable optionstargeting three indications (of which one indication has two development plans at contract inception), after which, Biogen may exercise an option to obtain exclusive licensescontinue to develop, seek regulatory approval for and commercialize any of the designated clinical candidates under such discovery programs (the “Option Deliverables”); and

(3) the performance obligations to conductcandidate. The pre-funded research and development activities through (a) regulatory approval in the United States, in the case of the XLRS program; (b) completion of the first in human clinical trial, in the case of the XLRP program; and (c) the stage of clinical candidate designation, in the case of each of the discovery programs (the “R&D Activity Deliverables”).  

The R&D Activity Deliverables for each program are further segmented by those that arereferred to as “Pre-Funded Activities” and those that are “Post-Funding Development Activities”. Pre-Funded Activities are those R&D activities for whichBiogen will reimburse the Company has primary responsibility and the consideration to be received under the agreement was received at the inception of the arrangement.  Post-Funding Development Activities are thoseon an FTE basis for any additional development activities that may occur after the Pre-Funded Activities and for whichit requests the Company is entitled to additional compensation underperform (“Post-Funded Activities”).

In February 2016, the agreement from Biogen.  Biogen has final decision-making authority for all matters related toCompany announced Biogen’s selection of adrenoleukodystrophy as the conduct of the Post-Funding Development Activities.  Because Biogen is not contractually obligated to continue the programs beyond the Pre-Funded Activities, and due to the uncertain outcomenon-ophthalmic indication of the discovery research and development activities,programs. Under the Post-Funding Development Activities are not considered deliverables at the inceptionterms of the arrangement and the associated fees and milestones are not included in the allocable arrangement consideration.  The Company has determined that the additional fees it could receive under the arrangement for Post-Funding Development Activities are not priced at a significant and incremental discount.

The Company determined that both the License Deliverables and Option Deliverables do not have stand-alone value and do not meet the criteria to be accounted for as separate units of accounting under ASC 605-25.  The factors considered byCollaboration Agreement, the Company, in making this determination included, among other things, the unique and specialized nature ofpart through its proprietary technology and intellectual property, andparticipation in joint committees with Biogen, will participate in overseeing the development stagesand commercialization of each ofthese specific programs.

Pursuant to the XLRS, XLRPManufacturing Agreement, Biogen may elect an option to receive a manufacturing license for up to six genes for a fixed fee per gene elected. If exercised, the Company becomes eligible to receive certain event milestones and the discovery programs targeting three indications.  Accordingly, the License Deliverables under each of the XLRS and XLRP programs and the Option Deliverables under each of the discovery programs have been combined with the initial, Pre-Funded Activities deliverables associated with each related program and as a result, the Company’s separate units of accounting under its collaboration with Biogen, comprise the XLRS program, the XLRP program, and each of the discovery programs.royalties.

Under the Collaboration Agreement, the Company received a non-refundablewas paid an upfront paymentnonrefundable fee of $94.0 million in August 2015of which it recorded as deferred revenue.  This upfront payment$58.4 million related to the Pre-Funded Activities (“Pre-Funded Amounts”) and $35.6 million related to the access of $94.0 million was allocated among the separate units of accounting discussed above using the relative selling price method.licenses. In addition, to the Collaboration Agreement, on July 1, 2015, the Company also entered into an equity agreement with Biogen.  Underunder the terms of this equity agreement,the Equity Agreement, Biogen purchased 1,453,957 shares of the Company’s common stock at a price of $20.63 per share, for an aggregate cash purchase price of $30.0 million which the Company also received in August 2015.million. The shares issued to Biogen represented approximately 8.1% of the Company’s outstanding common stock on a post-issuance basis, calculated on the number of shares that were outstanding at June 30, 2015, and constitute restricted securities that may not be resold by Biogen other than in a transaction registered under, or pursuant to an exemption from the registration requirements of, the Securities Act of 1933, as amended.

Accounting standards for multiple element arrangements contain a presumption that separate contracts negotiated or entered into at or near to the same time with the same entity were likely negotiated as a package and should be evaluated as a single agreement.  The Company determined that the price of $20.63 paid by Biogen included a premium of $7.45 per share over the fair value of the company’s stock price, calculated based upon the stock price on the date of close of the agreement and adjusted for lack of marketability due to restrictions.  Accordingly, the total premium of $10.8 million was also recorded as deferred revenue and, together with the $94.0 million, allocated to the separate units of accounting identified above using the relative selling price method as discussed in Note 2 to these financial statements.  The Company will record revenue based on the revenue recognition criteria applicable to each separate unit of accounting.  For amounts received up-front and initially deferred, the Company will recognize the deferred revenue on a straight-line basis over the estimated service periods in which it is required to perform the research and development activities associated with each unit of accounting. At the inception of the Collaboration Agreement, the Company initially estimate the service periods to range between 2 and 3 years.  However, due to certain delays which have extended our estimated period of performance, the estimated service periods are currently anticipated to be between 2 and 4 years from the inception of the Collaboration Agreement.

During the three months ended September 30, 2017 and 2016, the Company recognized revenue of approximately $10.3 million and $11.8 million, respectively from its collaboration with Biogen.  Below is a summary of the components of the collaboration revenue:


 

 

For the Three Months Ended September 30,

 

 

 

2017

 

 

2016

 

 

 

(dollars in thousands)

 

Amortization of non-refundable upfront fees

 

$

9,754

 

 

$

11,725

 

Other

 

 

554

 

 

 

47

 

Total collaboration revenue

 

$

10,308

 

 

$

11,772

 

 As a result of the upfront payment of $94.0 million made by Biogen and achievement of the $5.0 million milestone as discussed above, the Company became liable to various research partner institutions for sub-license and other payments under existing agreements with such institutions.  These agreements obligate the Company to pay to each research partner institution, amounts that range from 5% to 10% of certain proceeds received from collaboration and other arrangements, including any milestone payments received under such arrangements.  Accordingly, the Company recorded total collaboration costs of approximately $12.0 million associated with such obligations, including $636,000 of expense that was settled during fiscal year 2016 by the issuance of 40,000 shares of the Company’s common stock to a research partner institution, pursuant to the terms of the existing agreement with that institution.  The remainder of these sub-license and milestone fees were fully paid in cash during the fiscal year ended June 30, 2016.

The Company is also eligible to receive total payments of up to $467.5$472.5 million based on the successful achievement of future milestones under its XLRS and XLRP programs. For XLRS, the Company is eligible to receive up to: (i) $40$45.0 million in milestone payments based upon the successful achievement of clinical milestones (relating to dosing in specified trials), (ii) $155$155.0 million in milestone payments based upon the achievement of regulatory approvals and first commercial sale in specified territories and (iii) $65$65.0 million in milestone payments based upon the achievement of worldwide sales targets. For the XLRS program, the Company has an option to share development costs and profits after the initial clinical trial data are available instead of receiving milestone payments. For XLRP, the Company is eligible to receive up to: (i) $42.5 million in milestone payments based upon successful achievement of clinical milestones (relating to dosing in specified trials), (ii) $102.5 million in milestone payments based upon the achievement of regulatory approvals and first commercial sale in specified territories and (iii) $62.5 million in milestone payments based upon the achievement of worldwide sales targets. For the XLRP program, the Company has an option to share development costs and profits after the initial clinical trial data are available instead of receiving milestone payments. In addition, the Company is eligible to receive payments of up to $592.5 million based on the exercise of the option for and the successful achievement of future milestones under its discovery programs. Each discovery program is categorized as Category A, Category B or Category C depending on the nature of the indication it seeks to address. For Category A, the Company is eligible to receive payments of up to: (i) $20$20.0 million based upon the successful achievement of clinical milestones (relating to dosing in specified trials) and (ii) $70$70.0 million in milestone payments based upon the achievement of regulatory approvals and first commercial sale in specified territories. For Category B, the Company is eligible to receive payments of up to: (i) $27.5 million based upon the successful achievement of clinical milestones (relating to dosing in specified trials) and (ii) $105$105.0 million in milestone payments based upon the achievement of regulatory approvals and first commercial sale in specified territories. For Category C, the Company is eligible to receive payments of up to: (i) $40$40.0 million based upon the successful achievement of clinical milestones (relating to dosing in specified trials) and (ii) $140$140.0 million in milestone payments based upon the achievement of regulatory approvals and first commercial sale in specified territories. Under certain limited circumstances, if there are discovery products from more than one discovery program in any of Category A, Category B or Category C, then the milestone payments under the applicable category shall be payable for the applicable discovery product from each such discovery program to achieve the specified milestones.

Biogen will also pay revenue-based royalties for each licensed product at tiered rates ranging from high singlehigh-single digit to mid-teen percentages of annual net sales of the XLRS or XLRP products and at rates ranging from mid-single digit to low-teen percentages of annual net sales for the discovery products.  The

Prior to 2018, the Company received a $5.0 million milestone payment related to initial dosing of a XLRS patient. In April 2018, the Company triggered a $2.5 million milestone payment related to the initial dosing of a XLRP patient. In July 2018, the Company triggered a $10.0 million milestone payment related to the treatment of a first patient of second cohort in a Phase 1/2 Clinical XLRP Study.

Accounting Analysis

For the periods prior to July 1, 2018, the Company applied the provisions of ASC 605 in accounting for this arrangement. Refer to the Company’s Annual Report on Form 10-K for the year ended June 30, 2018, filed with the Securities and Exchange Commission on September 11, 2018, for the accounting analysis under these provisions.

Under ASC 605 and Topic 606, the Company has elected to applyconcluded that the guidance in ASC 605-28 toCollaboration Agreement, the milestones. These milestones, if achieved,Manufacturing Agreement and the Equity Agreement should be accounted for as one arrangement as the agreements were with the same party and were negotiated and executed contemporaneously.

The performance obligations and the allocated transaction price as of the date of initial application of Topic 606 are substantive as they relate solely to past performance, are commensurate with estimated enhancement of valuefollows (in thousands):

Performance Obligations:  Allocated
Transaction Price
 

XLRS License andPre-Funded Activities

  $52,060

XLRP License andPre-Funded Activities

   43,570 

Pre-Funded Activities associated with the Discovery Programs

   16,700 
  

 

 

 
  $112,330 
  

 

 

 

ThePre-Funded Activities associated with the achievementDiscovery Programs amount is comprised of each milestonefour distinct performance obligations based on the separate development plans for discovery candidates at contract inception. The Company concluded that the delivered license was not distinct from thePre-Funded Activities as a resultBiogen cannot obtain the benefit of the Company’slicense without the related services. Further, each of the license and relatedPre-Funded Activities performance obligation is considered a distinct performance obligation as each development plan is pursued independent of every other development plan.

The Company concluded that Post-Funded Activities represent customer options that are not material rights as any services requested by Biogen and provided by the Company are reasonable when compared to other consideration amounts payable underreimbursed at a rate that reflects the Collaboration Agreement; however, there can be no assurance thatestimated standalone selling price for the services. As such, the Company will achieverecognize revenue related to Post-Funded Activities as the milestones orservices are provided. Through the date of adoption of ASC 606, the Company has recognized revenue of $4.7 million for Post-Funded Activities. The Company recorded revenue of $1.1 million in the three months period ended September 30, 2018 related to Post-Funded Activities.

The Company concluded that the Company willoption to receive i) commercial licenses for the related revenue.  Due to the uncertainty surrounding the achievement of the future milestones, such payments were not considered fixed or determinable at the inception ofDiscovery Programs that achieve clinical candidate designation, as defined in the Collaboration Agreement and accordingly,ii) manufacturing licenses for up to six genes pursuant to the Manufacturing Agreement represent customer options that are not material rights as the exercise price for such options reflects the estimated standalone selling price for such option. As such, the Company will not be recognized as revenue unless and until they become earned.  The Company is not able to reasonably predictaccount for such option if and when the remaining milestones will be achieved. options are exercised.

Bionic Sight

On February 2, 2017,As of the Company entered into a strategic research and development collaboration agreement with Bionic Sight, LLC (“Bionic Sight”), to develop therapies for patients with visual deficits and blindness due to retinal disease. Through the AGTC-Bionic Sight collaboration, the companies seek to develop a new optogenetic therapy that leverages AGTC’s deep experience in gene therapy and ophthalmology and Bionic Sight’s innovative neuro-prosthetic device and algorithm for retinal coding.


Under the agreement, AGTC made an initial $2.0 million payment to Bionic Sight for an equity interest in that company. This initial investment represents an approximate 5% equity interest in Bionic Sight. In addition todate of the initial investment, AGTC will contributeapplication of Topic 606, the total transaction price for the Biogen Agreement was $112.3 million which included a $5.0 million milestone payment for initiation of dosing of XLRS and a $2.5 million milestone payment for initiation of dosing of XLRP. The Company used the most-likely method to ongoing researchdetermine the amount of variable consideration in the Biogen Agreement. The Company believes that any estimated amount of variable consideration related to clinical and development support costs through additionalregulatory milestone payments or other in-kind contributions (“AGTC Ongoing R&D Support”).  The AGTC Ongoing R&D Support payments and in-kind contributions willshould be made over time, upfully constrained as the achievement of such milestones is highly susceptible to the date that Bionic Sight has received both IND clearance from the FDA and receipt of written approval from an internal review board to conduct clinical trials from at least one clinical site for that product (the “IND Trigger”.)  

If the IND Trigger is attained, AGTC will receive additional equity, based on the valuation in place at the beginningfactors outside of the agreement, for the AGTC Ongoing R&D Support payments and in-kind contributions, and will be obligated to purchase additional equity in Bionic Sight for $4.0 million, at a pre-determined valuation. Due to the uncertainty of achieving the IND Trigger, the Company is expensing the AGTC Ongoing R&D Support payments and in-kind contributions made under the collaboration agreement. Such amounts are included as a component of research and development expenses in the Company’s financial statements.

control. The Company recorded its initial $2.0 million investment in Bionic Sight using the cost method of accounting for investments, which is recorded as its own line item on the Company’s balance sheet. The ongoing research and development costs and contributions will be recorded as a periodic cost until such time when or if the IND Trigger is achieved.

The collaboration agreement grants to AGTC, subject to achievement by Bionic Sight of certain development milestones, an option to exclusively negotiate for a limited period of time to acquire (i) a majority equity interest in Bionic Sight, (ii) the Bionic Sight assets to which the collaboration agreement relates, or (iii) an exclusive license with respect to the product to which the collaboration agreement relates.

(7)

Revision of Prior Period Financial Statements

In the fourth quarter of fiscal 2017, we became aware of an immaterial error regarding the calculation of our income tax provision. An assessment concluded that the error was not material to any prior period financial statements. As such, in accordance with ASC 250 (SAB No. 108, Considering Effects of Prior Year Misstatements when Quantifying Misstatements in Current Year Financial Statements), the prior period financial statements have been revised (the "Revision") in the applicable financial statements. Periods not presented herein will be revised, as applicable, in future filings. Although management has determined that the errorcommercial milestones and sales-based royalties will be recognized when the related sales occur as they were deemed to relate predominately to the license granted and therefore have also been excluded from the transaction price. The Company willre-evaluate the transaction price in each reporting period and as uncertain events are resolved or other changes in circumstances occur.

In the quarter ended September 30, 2018, the Company received a $10.0 million milestone payment related to XLRP which increased the transaction price. Based on an understanding between the parties in the quarter ended September 30, 2018, the Company also reallocated $1.1 million ofPre-Funded Amounts to cover Post-Funded Activities which resulted in a decrease to the transaction price and deferred revenue of $1.1 million in the quarter ended September 30, 2018. Additionally, the Company reallocated $1.8 million of variable consideration betweenPre-Funded Activities associated with Discovery program performance obligations based on changes to the underlying development plans of the product candidates. The reallocation between Discovery Programs generated an insignificant cumulative catch up adjustment to revenue in the quarter ended September 30, 2018. The cumulativecatch-up adjustment to revenue that relate to changes or reallocations of the transaction price are further discussed in theSummary of Contract Assets and Liabilities section below.

The transaction price was not materialallocated to prior periods, the financial statementsperformance obligations based on the relative estimated standalone selling price of each performance obligation or, in the case of certain variable consideration, to one or more performance obligations. The estimated standalone selling prices for performance obligations, that include a license andPre-Funded Activities, were developed using the estimated selling price of the license and an estimate of the overall effort to perform thePre-Funded Activities. The estimated selling price of the licenses were determined using a discounted cash flow valuation utilizing forecasted revenues and costs for the Company’s product candidate licenses.

The Company will recognize revenue related to the performance obligations which include a license andPre-Funded Activities over the estimated period of the research and development services using a proportional performance model. The Company measures proportional performance based on the costs incurred relative to the total costs expected to be incurred to satisfy the performance obligation. Management believes that recognizing revenue on a proportional performance basis based on costs incurred faithfully depicts the transfer of goods and services to the customer because the customer consumes the Company’s services as such services are performed.

During the three months ended September 30, 2016, included herein, have been revised2018 and 2017, the Company recorded revenue of $14.0 million, and $10.3 million, respectively, related to correct forits efforts under the impact of this item. Unless otherwise indicated, the financial informationBiogen Agreement. The Company has accounts receivable balances with Biogen as of September 30, 2018 and forJune 30, 2018 of $0.7 million and $1.7 million, respectively, related to the Biogen Agreement. As of September 30, 2018, the Company had recorded $25.4 million in deferred revenue related to the Biogen Agreement that will be recognized over the remaining performance period. The Company expects to satisfy its remaining performance obligations under the Biogen Agreement within the next three years.

The company’s revenue is comprised of the following related to the Biogen Agreement:

   For the three months
ended September 30,
 
   2018   2017 

Collaboration revenue

    

Licenses and related services

  $4,619   $9,754 

Development services

   1,058    554 

Milestone revenue

   8,348    —   
  

 

 

   

 

 

 

Total collaboration revenue

  $14,025   $10,308 
  

 

 

   

 

 

 

License and related services revenue is comprised of revenue related to the Company’s completion of performance obligations that contain the delivery of licenses and Pre-Funded Activities. Development services revenue relates to the delivery of Post Funded Activities. Milestone revenue relates to the portion of milestone payments received that are recognized as revenue based on the proportional performance of the underlying performance obligation.

Summary of Contract Assets and Liabilities

The following table presents changes in the balances of our contract assets and liabilities during the three months ended September 30, 2016 presented in this Quarterly Report on Form 10-Q reflects this revision.2018 (in thousands):

 

   Balance at
Beginning
of Period
   Additions   Deductions   Balance at
End of
Period
 

Three months ended September 30, 2018

        

Contract assets

  $—    $—    $—    $—  

Contract liabilities:

        

Deferred revenue

  $29,521   $10,000   $14,096   $25,425 

The following table summarizeCompany recorded an entry to increase deferred revenue and accumulated deficit for $22.6 million as of July 1, 2018 related to the effectadoption of Topic 606. The impact of the Revision onadoption of Topic 606 is reflected within the statementsbeginning of operations forperiod balance. Additions include the three months ended September 30, 2016:$10.0 million milestone payment received associated with the XLRP program. Deductions from deferred revenue include revenue recognized related to the deferred revenue balance at the beginning of the period of $4.6 million, revenue recognized related to additions to deferred revenue in the quarter of $8.3 million (of which $7.8 million relates to performance in prior quarters) and $1.1 million of variable consideration that was constrained in the quarter.

 

 

For the three months ended September 30,

 

In thousands

 

2016

 

 

Adjustment

 

 

2016

 

Income (loss) before provision for income taxes

 

$

3,625

 

 

 

 

 

 

$

3,625

 

Provision for Income Taxes

 

 

-

 

 

 

600

 

 

 

600

 

Net income (loss)

 

$

3,625

 

 

 

 

 

 

$

3,025

 

Net earnings per share, basic

 

$

0.20

 

 

 

 

 

 

$

0.17

 

Net earnings per share, diluted

 

$

0.20

 

 

 

 

 

 

$

0.16

 


ITEM 2. MANAGEMENT’SMANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis provides an overview of our financial condition as of September 30, 2017,2018, and results of operations for the three months ended September 30, 20172018 and 2016.2017. This discussion should be read in conjunction with the accompanying Unaudited Condensed Financial Statements and accompanying notes, as well as our Annual Report on Form10-K for the year ended June 30, 2017, as amended2018 (“June 20172018 Form10-K”). In addition to historical financial information, the following discussion contains forward-looking statements that reflect our plans, estimates, assumptions and beliefs. Our actual results could differ materially from those discussed in the forward-looking statements. Factors that could cause or contribute to these differences include those discussed below and elsewhere in this report as well as those set forth in Part I, Item 1A, “Risk Factors” of the June 20172018 Form10-K. Forward-looking statements include information concerning our possible or assumed future results of operations, business strategies and operations, financing plans, potential growth opportunities, potential market opportunities and the effects of competition. Forward-looking statements include all statements that are not historical facts and can be identified by terms such as “anticipates,” “believes,” “could,” “seeks,” “estimates,” “expects,” “intends,” “may,” “plans,” “potential,” “predicts,” “projects,” “should,” “will,” “would” or similar expressions and the negatives of those terms. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Also, forward-looking statements represent our management’s plans, estimates, assumptions and beliefs only as of the date of this report. Except as required by law, we assume no obligation to update these forward-looking statements publicly or to update the reasons actual results could differ materially from those anticipated in these forward-looking statements, even if new information becomes available in the future.

As used herein, except as otherwise indicated by context, references to “we,” “us,” “our,” or the “Company” refer to Applied Genetic Technologies Corporation.

Overview

Overview

We are a clinical-stage biotechnology company that uses a proprietary gene therapy platform to develop transformational genetic therapies for patients suffering from rare and debilitating diseases. Our initial focus is in the field of ophthalmology, where we have active clinical programs inX-linked retinoschisis (XLRS), achromatopsia (ACHM) andX-linked retinitis pigmentosa (XLRP), and achromatopsia (ACHM) and a preclinical program in optogenetics. In addition to ophthalmology, we have recently initiated preclinical programs in adrenoleukodystrophy (ALD) and otology. With a number of important clinical milestones on the horizon, we believe we are well positioned to advance multiple programs towards pivotal studies. In addition to our product pipeline, we have also developed broad technological capabilities through our collaborations with 4D Molecular Therapeutics (4DMT), Synpromics Limited (Synpromics), and the University of Florida, which provide us with expertise in vector design and manufacturing as well as synthetic promoter development and optimization. Finally, our partnership with Biogen, which includes our clinical XLRS and XLRP programs, a discovery program in ALD and two ophthalmology programs, validates our approach and technology, and provides us with a significant cash runway to advance our wholly-owned candidates.technology.

Since our inception in 1999, we have devoted substantially all of our resources to development efforts relating to ourproof-of-concept programs in ophthalmology andalpha-1 antitrypsin deficiency, or AAT deficiency, an inherited orphan lung disease, including activities to manufacture product in compliance with good manufacturing practices, preparing to conduct and conducting clinical trials of our product candidates, providing general and administrative support for these operations and protecting our intellectual property. We do not have any products approved for sale and have not generated any revenue from product sales. To date, weWe have funded our operations to date primarily through thepublic offerings of our common stock, private placementplacements of our preferred stock, common stock, convertible notes and warrants to purchase preferred stock, through our public offerings consummated in April 2014 and July/August 2014, and through upfront and milestone payments from our partners.collaborations. We have also been the recipient, either independently or with our collaborators, of grant funding administered through federal, state, and local governments and agencies, including the United States Food and Drug Administration, or FDA, and by patient advocacy groups such as The Foundation Fighting Blindness, or FFB, and theAlpha-1 Foundation.


Although we recorded incomeWe have incurred losses from operations of $1.9in each year since inception except for fiscal 2017. Our net income for the three-month period ended September 30, 2018 was $1.2 million while the net loss for the fiscal year ended June 30, 2017 due in part to the amortization of revenue associated with our collaboration agreement with Biogen, we have incurred losses from operations in each other year since inception. Our net income for the fiscal year ended June 30, 20172018 was $0.4$21.3 million, compared to net lossesincome of $1.4$0.4 million and $24.3net loss of $1.4 million for each of the fiscal years ended June 30, 20162017 and 2015,2016, respectively. Substantially all our net losses resulted from costs incurred in connection with our research and development programs and from general and administrative costs associated with our operations. We expect to continue to incur significant operating expenses for at least the next several years and anticipate that such expenses will increase substantially in connection with our ongoing activities, as we:

conduct preclinical studies and clinical trials for our XLRS, ACHM and XLRP product candidates;

continue our research and development efforts, including exploration through early preclinical studies of potential applications of our gene therapy platform in:

orphan ophthalmology indications;

non-orphan ophthalmology indications including wet AMD and other inherited retinal diseases; and

other inherited diseases, such as otology and CNS indications.

 

o

orphan ophthalmology indications;

o

non-orphan ophthalmology indications including wet AMD and other inherited retinal diseases; and

o

other inherited diseases, such as otology and CNS indications.  

manufacture clinical trial materials and develop larger-scale manufacturing capabilities;

seek regulatory approval for our product candidates;

further develop our gene therapy platform;

add personnel to support our collaboration, product development and commercialization efforts; and

continue to operate as a public company.

As of September 30, 2017,2018, we had cash and cash equivalents and investments totaling $129.6$105.4 million.

We do not expect to generate revenue from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years and which we believe is subject to significant uncertainty. We believe that our existing cash and cash equivalents and investments at September 30, 2017,2018, will be sufficient to allow us to generate data from our ongoing clinical programs, to move ourpre-clinical optogenetic program in collaboration with Bionic Sight into the clinic and to fund our currently planned research and discovery programs for at least the next two years. In order to complete the process of obtaining regulatory approval for our lead product candidates and to build the sales, marketing and distribution infrastructure that we believe will be necessary to commercialize our lead product candidates, if approved, we will require substantial additional funding. Also, our current operating plan may change as a result of many factors currently unknown to us, and we may need to seek additional funds sooner than planned, through public or private equity or debt financings, government or other third-party funding, marketing and distribution arrangements and other collaborations, strategic alliances and licensing arrangements or a combination of these approaches. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. Our failure to raise capital or enter into such other arrangements as and when needed would have a negative impact on our financial condition and our ability to develop our products.

Critical Accounting Policies

Our management’s discussion and analysis of our financial condition and results of operations are based on our financial statements, which have been prepared in accordance with U.S. generally accepted accounting principles. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenue and expenses and the disclosure of contingent assets and liabilities in our financial statements. On an ongoing basis, we evaluate our estimates and judgments, including those related to accrued expenses and share-based compensation. We base our estimates on historical experience, known trends and events, and various other factors that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

For a description of our accounting policies that, in our opinion, involve the most significant application of judgment or involve complex estimation and which could, if different judgments or estimates were made, materially affect our reported results of operations, see “Management’s Discussion and Analysis of Financial Condition and Results of Operations—Critical Accounting Policies and Estimates” in our June 2017 2018Form 10-K. In addition, refer to Note 2 “Revenue Recognition” included in this quarterly report for further information regarding the adoption of ASC 606.


The Company adopted Topic 606 on July 1, 2018. See Note 2 to the condensed financial statements included in this Quarterly Report on Form 10-Q for a description of our revenue recognition accounting policies.

New Accounting Pronouncements

Refer to Note 2 to the condensed financial statements included in this quarterly report for further information on recently issued accounting standards.

Financial operations overviewreview

Revenue

We primarily generate revenue through collaboration agreements, sponsored research arrangements with nonprofit organizations for the development and commercialization of product candidates and from federal research and development grant programs. In the future, we may generate revenue from a combination of: product sales, license fees, milestone payments, development services, research and development grants, and from collaboration and royalty payments for the sales of products developed under licenses of our intellectual property.

We expect that any revenue we generate will fluctuate from quarter to quarter as a result of the timing and amount of license fees, research and development programs, manufacturing efforts and reimbursements, collaboration milestone payments, and the sale of our products, to the extent any are successfully commercialized. We do not expect to generate revenue from product sales for the foreseeable future, if at all. If we or our collaborators fail to complete the development of our product candidates in a timely manner or obtain regulatory approval for them, our ability to generate future revenue, our results of operations and financial position would be materially adversely affected.

We expect in fiscal year 2018 that revenues from our Biogen collaboration associated with amortization of non-refundable upfront fees will decrease approximately $17 million compared to fiscal year 2017.  This decrease is primarily due to reaching the end of the XLRP service period in the first quarter of fiscal year 2018, and to a much lesser extent, due to changes in estimates associated with the period of performance under the XLRS and preclinical programs.

Research and development expenses

Research and development expenses consist primarily of costs incurred for the development of our product candidates, which include:

employee-related expenses, including salaries, benefits, travel and share-based compensation expense;

expenses incurred under agreements with academic research centers, contract research organizations, or CROs, and investigative sites that conduct our clinical trials;

license and sublicense fees and collaboration expenses;

the cost of acquiring, developing, and manufacturing clinical trial materials; and

facilities, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, insurance, and other supplies.

Research and development costs are expensed as incurred. Costs for certain development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and our clinical sites.


We cannot determine with certainty the duration and completion costs of the current or future clinical trials of our product candidates or if, when, or to what extent we will generate revenues from the commercialization and sale of any of our product candidates that obtain regulatory approval. We may never succeed in achieving regulatory approval for any of our product candidates. The duration, costs, and timing of clinical trials and development of our product candidates will depend on a variety of factors, including:

the scope, rate of progress, and expense of our ongoing as well as any additional clinical trials and other research and development activities;

the timing and level of activity as determined by us or jointly with our partners;

the level of funding received from our partners;

whether or not we elect to cost share with our partners;

the countries in which trials are conducted;

future clinical trial results;

uncertainties in clinical trial enrollment rates ordrop-out or discontinuation rates of patients;

potential additional safety monitoring or other studies requested by regulatory agencies or elected as best practice by us;

increased cost and delay associated with manufacturing or testing issues, including ongoing quality assurance, qualifying new vendors and developingin-house capabilities;

significant and changing government regulation; and

the timing and receipt of any regulatory approvals.

A change in the outcome of any of these variables with respect to the development of a product candidate could mean a significant change in the costs and timing associated with the development of that product candidate. For example, if the FDA, or another regulatory authority were to require us to conduct clinical trials beyond those that we currently anticipate will be required for the completion of clinical development of a product candidate or if we experience significant delays in enrollment in or execution of any of our clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

From inception through September 30, 2017,2018, we have incurred approximately $145.3$179.3 million in research and development expenses. We expect our research and development expenses to increase for the foreseeable future as we continue the development of our product candidates and explore potential applications of our gene therapy platform in other indications. We expect sublicensing fees will fluctuate from quarter to quarter as a result of the timing of Biogen milestone payments.

General and administrative expenses

General and administrative expenses consist primarily of salaries and related costs for personnel, including share-based compensation and travel expenses for our employees in executive, operational, legal, business development, finance and human resource functions. Other general and administrative expenses include costs to support employee training and development, board of directors’ costs, depreciation, insurance expenses, facility-related costs not otherwise included in research and development expense, professional fees for legal services, including patent-related expenses, and accounting, investor relations, corporate communications and information technology services. We anticipate that our general and administrative expenses will continue to increase in the future as we hire additional employees to support our continued research and development efforts, collaboration arrangements, and the potential commercialization of our product candidates. Additionally, if and when we believe a regulatory approval of the first product candidate appears likely, we anticipate an increase in payroll and related expenses as a result of our preparation for commercial operations, especially as it relates to the sales and marketing of our product candidates.

Other income (expense), net

Other income and expense consists primarily of interest earned on cash and cash equivalents and ourheld-to-maturity investments.

Provision for income taxes

Income tax expense (benefit) for the three months ended September 30, 2018 was $19,000 compared to $0 for the three months ended September 30, 2017. The income tax expense for the three months ended September 30, 2018, was primarily driven by interest expense related to the Company’s uncertain tax position.


Results of Operations

Comparison of the three months ended September 30, 20172018 to the three months ended September 30, 20162017

Revenue

 

   For the Three Months
Ended September 30,
   Increase   % Increase 
   2018   2017   (Decrease)   (Decrease) 
   (dollars in thousands) 

Collaboration revenue

        

Licenses and related services

  $4,619   $9,754   $(5,135   (53)% 

Development services

   1,058    554    504    91

Milestone revenue

   8,348    —      8,348    nm
  

 

 

   

 

 

   

 

 

   

 

 

 

Total collaboration revenue

   14,025    10,308    3,717    36

Grant revenue

   9    7    2    29
  

 

 

   

 

 

   

 

 

   

 

 

 

Total revenue

  $14,034   $10,315   $3,719    36
  

 

 

   

 

 

   

 

 

   

 

 

 

 

 

For the Three Months Ended September 30,

 

 

Increase

 

 

% Increase

 

 

 

2017

 

 

2016

 

 

(Decrease)

 

 

(Decrease)

 

 

 

(dollars in thousands)

 

Collaboration revenue

 

$

10,308

 

 

$

11,772

 

 

$

(1,464

)

 

 

(12

)%

Grant revenue

 

 

7

 

 

 

34

 

 

 

(27

)

 

 

(79

)%

Total revenue

 

$

10,315

 

 

$

11,806

 

 

$

(1,491

)

 

 

(13

)%

Total revenue for the three months ended September 30, 20172018 was $10.3$14.0 million, compared to $11.8$10.3 million generated duringfor the same periodthree months ended September 30, 2017. The increase was primarily due to increased milestone revenue of $8.3 million and increased development services revenue of $0.5 million, partially offset by decreased license and related services revenue of $5.1 million. The increase in 2016.milestone revenue was primarily due to recognizing revenue of $8.3 million associated with the receipt of a $10.0 million milestone payment from Biogen. Effective July 1, 2018, the Company adopted Topic 606. Based on the Company’s Topic 606 revenue recognition methodology, milestone payments are recognized based on the proportional performance of the underlying performance obligation for which the milestone payment relates. The increase in development services revenue was primarily due to additional Phase 1/2 study activities related to the Company’s XLRP program. The decrease in license and related service revenue was due to decreased Pre-Funded XLRP activities and due to the Company’s revised pattern of revenue recognition under Topic 606. For the three months ended September 30, 2018, license and related services, which includes the Pre-Funded Activities associated with each program under the Biogen Collaboration, revenue recorded duringare recognized on a proportional performance basis under Topic 606. For the three months ended September 30, 2017, license and 2016 resulted primarily from the amortization of upfront fees received under our collaboration agreement with Biogen which began in August 2015. Non-refundable upfront fees are amortized to collaborationrelated services revenue was recognized based on a straight-line basis over the estimated service period. Extensions toperiod under the length of time for the estimated service periods resulted in a decrease in non-refundable upfront fees recognized asCompany’s prior revenue during the three months ended September 30, 2017 versus the three months ended September 30, 2016. Grant revenue decreased $27 thousand during the three months ended September 30, 2017 compared to the same period in 2016, largely attributable to reduced research and development activities on grant-funded projects.recognition methodology.

Research and development expense

The following table summarizes our research and development expenses by product candidate or program for the three months ended September 30, 20172018 and 2016:  2017:

 

 

 

For the Three Months Ended September 30,

 

 

Increase

 

 

% Increase

 

 

 

2017

 

 

2016

 

 

(Decrease)

 

 

(Decrease)

 

 

 

(dollars in thousands)

 

External research and development expenses

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ACHM

 

$

1,079

 

 

$

904

 

 

$

175

 

 

 

19

%

XLRS

 

 

818

 

 

 

418

 

 

 

400

 

 

 

96

%

XLRP

 

 

700

 

 

 

258

 

 

 

442

 

 

 

171

%

Research and discovery programs

 

 

1,763

 

 

 

740

 

 

 

1,023

 

 

 

138

%

Total external research and development expenses

 

 

4,360

 

 

 

2,320

 

 

 

2,040

 

 

 

88

%

Internal research and development expenses

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Employee-related costs

 

 

2,092

 

 

 

1,603

 

 

 

489

 

 

 

31

%

Share-based compensation

 

 

542

 

 

 

634

 

 

 

(92

)

 

 

(15

)%

Other

 

 

1,282

 

 

 

1,014

 

 

 

268

 

 

 

26

%

Total internal research and development expense

 

 

3,916

 

 

 

3,251

 

 

 

665

 

 

 

20

%

Total research and development expense

 

$

8,276

 

 

$

5,571

 

 

$

2,705

 

 

 

49

%

   For the Three Months
Ended September 30,
   Increase   % Increase 
   2018   2017   (Decrease)   (Decrease) 
   (dollars in thousands) 

External research and development expenses

        

ACHM

  $1,042   $1,079   $(37   (3)% 

XLRS

   431    818    (387   (47)% 

XLRP

   2,759    700    2,059    294

Research and discovery programs

   877    1,763    (886   (50)% 
  

 

 

   

 

 

   

 

 

   

 

 

 

Total external research and development expenses

   5,109    4,360    749    17
  

 

 

   

 

 

   

 

 

   

 

 

 

Internal research and development expenses

        

Employee-related costs

   2,589    2,092    497    24

Share-based compensation

   484    542    (58   (11)% 

Other

   1,883    1,282    601    47
  

 

 

   

 

 

   

 

 

   

 

 

 

Total internal research and development expenses

   4,956    3,916    1,040    27
  

 

 

   

 

 

   

 

 

   

 

 

 

Total research and development expense

  $10,065   $8,276   $1,789    22
  

 

 

   

 

 

   

 

 

   

 

 

 

External research and development costs consist of collaboration, licensing, manufacturing, testing, and other miscellaneous expenses that are directly attributable to our most advanced product candidates and discovery programs. We do not allocate personnel-related costs, including stock-based compensation, costs associated with broad technology platform improvements or other indirect costs, to specific programs, as they are deployed across multiple projects under development and, as such, are separately classified as internal research and development expenses in the table above.

Research and development expenses for the three months ended September 30, 20172018 were $8.3$10.1 million, compared to $5.6$8.3 million for the three months ended September 30, 2016,2017, an increase of $2.7$1.8 million, or 49%22%. This increase was primarily attributable to:

 

$1.00.7 million of increased external spending on generalwhich was primarily due to incurring sublicense expense of $2.3 million associated with receiving a $10.0 million XLRP milestone payment from Biogen, partially offset by decreased XLRS and research and discovery programs primarily due to increased spending on the optogenetics, otology, and adrenoleukodystrophy (ALD) preclinical programs and increased spending on general research activities in ophthalmology to support ongoing clinical programs;program spending;


$0.4 million of increased external spending on the XLRP program primarily associated with filing an Investigational New Drug application with the U.S. Food and Drug Administration in August 2017 and activities associated with preparing to conduct a Phase1/2 clinical trial;

$0.4 million of increased external spending on the XLRS program primarily related to increased patient enrollment in the ongoing Phase 1/2 clinical trial; and

$0.5 million of increased employee-related expenses associated with the hiring of additional employees to support clinical trial execution and research and development activities.  activities; and

 

$0.6 million of increased general research and development expenses including training fees, equipment rental fees, dues and conference fees.

General and administrative expense

 

 

For the Three Months Ended September 30,

 

 

Increase

 

 

% Increase

 

  For the Three Months
Ended September 30,
   Increase   % Increase 

 

2017

 

 

2016

 

 

(Decrease)

 

 

(Decrease)

 

  2018   2017   (Decrease)   (Decrease) 

 

(dollars in thousands)

 

  (dollars in thousands) 

Employee-related costs

 

$

1,381

 

 

$

1,021

 

 

$

360

 

 

 

35

%

  $1,277   $1,381   $(104   (8)% 

Share-based compensation

 

 

927

 

 

 

786

 

 

 

141

 

 

 

18

%

   697    927    (230   (25)% 

Legal and professional fees

 

 

264

 

 

 

285

 

 

 

(21

)

 

 

(7

)%

   159    264    (105   (40)% 

Other

 

 

1,134

 

 

 

754

 

 

 

380

 

 

 

50

%

   1,080    1,134    (54   (5)% 
  

 

   

 

   

 

   

 

 

Total general and administrative

expense

 

$

3,706

 

 

$

2,846

 

 

$

860

 

 

 

30

%

  $3,213   $3,706   $(493   (13)% 
  

 

   

 

   

 

   

 

 

General and administrative expense for the three months ended September 30, 2017 increased2018 decreased by $0.9$0.5 million to $3.7$3.2 million compared to the same period in 2016.2017. The increasedecrease was primarily driven by increased corporate infrastructure,lower employee-related costs and sharedshare based compensation expenses associated with our continued expansioncompensation. Legal and hiring of additional employees.  

Other income (expense), net

Forprofessional fees also decreased by $0.1 million during the three months ended September 30, 2017, other income (expense), net, which was primarily comprised of investment income, increased2018 compared to $0.3 million from $0.2 million generated in 2016 due to modestly better investment performance.

Provision for income taxes

There was no income tax expense for the three months ended September 30, 2017 compared to $600,000 in the three months ended September 30, 2016.  The income tax expense results from the recognition of revenue related to the Biogen agreement for tax purposes, which is accelerated compared to our GAAP revenue, resulting in significantly more taxable income than GAAP net income.  While our taxable income is largely offset by the use of NOLs, our income tax expense is primarily due to federal alternative minimum tax expense, the apportionment of income to certain state jurisdictions where we do not have NOLs and the recognition of a reserve for uncertain tax positions.2017.

Liquidity and capital resources

We have incurred cumulative losses and negative cash flows from operations since our inception in 1999, and as of September 30, 2017,2018, we had an accumulated deficit of $91.0 million.$132.3 million. It will be several years, if ever, before we have a product candidate ready for commercialization. We expect that our research and development and general and administrative expenses will continue to increase and as a result, we anticipate that we will require additional capital to fund our operations, which we may raise through a combination of equity offerings, debt financings, other third-party funding, marketing and distribution arrangements and other collaborations, strategic alliances and licensing arrangements.

As of September 30, 2017,2018, we had cash, cash equivalents, and investments totaling $129.6$105.4 million. We believe that our existing cash, cash equivalents, and investments at September 30, 20172018 will be sufficient to enable us to advance planned preclinical studies and clinical trials for our lead product candidates and currently planned discovery programs for at least the next two years.

Cash in excess of immediate requirements is invested in accordance with our investment policy which primarily seeks to maintain adequate liquidity and preserve capital by generally limiting investments to certificates of deposit and investment-grade debt securities that mature within 2412 months. As of September 30, 2017,2018, our cash and cash equivalents were held in bank accounts and money market funds, while our short and long-term investments consisted of certificates of deposit and corporate and government bonds, none of which mature more than 2412 months after the balance sheet date.  date, consistent with our investment policy that seeks to maintain adequate liquidity and preserve capital.


Cash flows

The following table sets forth the primary sources and uses of cash for each of the periods set forth below:

 

 

For the Three Months Ended September 30,

 

  For the Three Months
Ended September 30,
   Increase   % Increase 

 

2017

 

 

2016

 

  2018   2017   (Decrease)   (Decrease) 

 

(in thousands)

 

  (dollars in thousands) 

Net cash provided by (used in):

 

 

 

 

 

 

 

 

        

Operating activities

 

$

(8,651

)

 

$

(5,795

)

   583   $(8,651   9,234    107

Investing activities

 

 

26,677

 

 

 

32,888

 

   (5,050   26,677    (31,727   (119)% 

Financing activities

 

 

2

 

 

 

19

 

   (126   2    (128   nm

Net increase in cash and cash equivalents

 

$

18,028

 

 

$

27,112

 

  

 

   

 

   

 

   

 

 

Net increase (decrease) in cash and cash equivalents:

  $(4,593  $18,028   $(22,621   (125)% 
  

 

   

 

   

 

   

 

 

Operating activities.For the three months ended September 30, 2017 and 2016,2018, net cash used inprovided by operating activities was primarily the result of cash payments made forreceived from the collaboration with Biogen, partially offset by research and development and general and administrative expenses incurred in conducting normal business operations, and the impact of changes in our working capital accounts. For the three months ended September 30, 2017, net cash used in operating activities was primarily the result of cash received from the collaboration with Biogen, offset by the impact of operating losses which included research and development and general and administrative expenses incurred in conducting normal business operations, and the impact of changes in our working capital accounts.

Investing activities.Net cash provided byused in investing activities for the three months ended September 30, 2018 consisted primarily of cash proceeds of $24.7 million from the maturity of investments, net of investment repurchases of $29.7 million. For the three months ended September 30, 2017, net cash provided by investing activities consisted primarily of cash proceeds of $26.8 million from the maturity of investments.  For

Financing activities.Net cash used in financing activities during the three months ended September 30, 2016, net cash provided by investing activities2018 consisted primarily cash proceeds of $35.4 million from the maturity of investments, partially offset by cash outflows of $2.4 million related to the purchase of investments securities. 

Financing activities.  payments for deferred offering costs. Net cash provided by financing activities during the three months ended September 30, 2017 and 2016 was associated with the exercise of common stock options.  options and restricted stock awards.

Operating capital requirements

To date, we have not generated any revenue from product sales. We do not know when, or if, we will generate any revenue from product sales. We do not expect to generate significant revenue from product sales unless and until we obtain regulatory approval of and commercialize one of our current or future product candidates. We anticipate that we will continue to generate losses for the foreseeable future as we continue the development of, and seek regulatory approvals for, our product candidates, and begin to commercialize any approved products. We are subject to all of the risks incident in the development of new gene therapy products, and we may encounter unforeseen expenses, difficulties, complications, delays and other unknown factors that may adversely affect our business.

We believe that our existing cash and cash equivalents and investments at September 30, 2017, will be2018, will be sufficient to allow us to generate data from our ongoing clinical programs, to move ourpre-clinical optogenetic program in collaboration with Bionic Sight into the clinic and to fund our currently planned research and discovery programs for at least the next two years. In order to complete the process of obtaining regulatory approval for our lead product candidates and to build the sales, marketing and distribution infrastructure that we believe will be necessary to commercialize our lead product candidates, if approved, we will require substantial additional funding.


ITEM 3. QUANTITATIVEQUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Refer to Part II, Item 7A, “Quantitative and Qualitative Disclosures About Market Risk” in our Annual Report on Form10-K for the year ended June 30, 2017, Form 10-K, which is incorporated by reference herein, for a description of our market risks.

ITEM 4. CONTROLS AND PROCEDURES

Material Weakness

a)

Conclusions Regarding the Effectiveness of Disclosure Controls and Procedures

Our management, with the participation of the Chief Executive Officer and Chief Financial Officer, has evaluated the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Internal Control overRules 13a-15e and 15d-15e under the Securities Exchange Act of 1934, as amended as of the end of the period covered by this quarterly report). Based on this evaluation the Chief Executive Officer and Chief Financial Reporting

As discussedOfficer concluded that these disclosure controls and procedures are effective and designed to ensure that the information required to be disclosed in our June 2017 Form 10-K, our management has determined that we have a material weaknessreports filed or submitted under the Exchange Act is recorded, summarized and reported within the requisite time periods.

b)

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting which relates to(as defined in Rules 13a-15f and 15d-15f under the design and operationExchange Act) identified in connection with the evaluation of our closing and financial reporting processes.  Referinternal control performed during the last fiscal quarter that has materially affected, or is reasonably likely to Part II, Item 9A, “Controls and Procedures,” in our June 2017 Form 10-K for a discussion of the actions that we have previously undertaken to remediate this material weakness.

Notwithstanding the material weaknesses, each of our Chief Executive Officer, Chief Financial Officer, and Corporate Controller concluded that the consolidated financial statements included in this report present fairly, in all material respects, our financial position, results of operations, and cash flows as of the dates and for the periods presented, in conformity with U.S. GAAP.

Changes in Internal Control over Financial Reporting

As discussed in Item 9A of our Annual Report on Form 10-K for the year ended June 30, 2017, we have undertaken actions to redesign processes and controls to address all of the material weaknesses. We have engaged specialists to assist us with reviewing, documenting, and (as needed) supplementing our controls, with a goal of providing controls that not only better address both the accuracy and precision of management’s review, but also enhance our ability to manage our business as it has evolved. We continue to evaluate our financial team and organizational structure, and have begun to make changes to roles and responsibilities to enhance controls and compliance. We expect to make further changes as our specialists deliver recommendations from their reviews. As we implement these plans, management may determine that additional steps may be necessary to remediate the material weaknesses.

Although we intend to resolve all of the material control deficiencies discussed in Item 9A of our Annual Report on Form 10-K for the year ended June 30, 2017, we cannot provide any assurance that these remediation efforts will be successful, will be completed quickly, or thatmaterially affect our internal control over financial reporting will be effective as a result of these efforts by any particular date. Our remediation plan will last through 2018 due to the number of controls involved, the need for new risk assessments and control design implementation, and ultimately testing of such controls.reporting.

Inherent Limitation of the Effectiveness of Internal Control

The effectiveness of any system of internal control over financial reporting is subject to inherent limitations, including the exercise of judgment in designing, implementing, operating, and evaluating the controls and procedures, and the inability to eliminate misconduct completely. Accordingly, any system of internal control over financial reporting can only provide reasonable, not absolute, assurances. In addition, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. We intend to continue to monitor and upgrade our internal controls as necessary or appropriate for our business, but cannot assure that such improvements will be sufficient to provide us with effective internal control over financial reporting.


PARTPART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

We are not a party to any pending legal proceedings. However, because of the nature of our business, we may be subject at any particular time to lawsuits or other claims arising in the ordinary course of our business, and we expect that this will continue to be the case in the future.

ITEM 1A. RISK FACTORS

Information regarding risk factors appears inRefer to Part I, Item 1A, of“Risk Factors,” in our Annual Report on Form10-K for the year ended June 30, 2017, which was filed with the SEC on September 13, 2017.2018 for a listing of our risk factors. There havehas been no material changes from thechange in such risk factors previously disclosed in that Annual Report on Form 10-K.since June 30, 2018.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

The following table provides certain information with respect to our purchases of shares of the Company’s common stock during the first fiscal quarter of 2019:

Issuer Purchases of Equity Securities

 

Period

  Total Number of
Shares
Purchased(a)
   Average Price
Paid per Share(a)
   Total Number of Shares
Purchased as Part of
Publicly Announced Plan
   Approximate Dollar Value
of Shares That May Yet Be
Purchased Under the Plan
 

July 1, 2018 through July 31, 2018

   685   $4.15    —     $—   

August 1, 2018 through August 31, 2018

   592   $4.00    —     $—   

September 1, 2018 through September 30, 2018

   685   $3.93    —     $—   
  

 

 

     

 

 

   

Total

   1,962   $4.03    —     
  

 

 

   

 

 

   

 

 

   

 

 

 

(a)

These columns reflect the surrender to the Company of an aggregate of 1,962 shares of common stock to satisfy tax withholding obligations in connection with the vesting of restricted stock issued to an employee during the first fiscal quarter of 2019.

ITEM 6. EXHIBITS

 

Exhibit

Number

Exhibit
Number

Description

  3.1

Fifth Amended and Restated Certificate of Incorporation of Applied Genetic Technologies Corporation (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form8-K, event date March 26, 2014, filed on April 1, 2014)

  3.2

Amended and Restated Bylaws of Applied Genetic Technologies Corporation (incorporated by reference to Exhibit 3.2 to the Company’s Current Report on Form8-K, event date March 26, 2014, filed on April 1, 2014)

10.1

31.1*

Employment Letter Agreement, effective as of July 27, 2017 by and between Applied Genetic Technologies Corporation and William A. Sullivan (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, event date July 27, 2017, filed on August 2, 2017)

10.2

Separation Agreement, dated as of July 27, 2017 by and between Applied Genetic Technologies Corporation and Lawrence E. Bullock (incorporated by reference to Exhibit 10.2 to the Company’s Current Report on Form 8-K, event date July 27, 2017, filed on August 2, 2017)

31.1*

Rule13a-14(a)/15d-14(a) Certification of Principal Executive Officer of Applied Genetic Technologies Corporation

31.2*

Rule13a-14(a)/15d-14(a) Certification of Principal Financial Officer of Applied Genetic Technologies Corporation

32.1**

Section 1350 Certification of Principal Executive Officer and Principal Financial Officer of Applied Genetic Technologies Corporation

101*

Interactive Data Files pursuant to Rule 405 of RegulationS-T (XBRL)

 

*

Filed herewith.

**

Furnished herewith.


SIGNATURESIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

 

APPLIED GENETIC TECHNOLOGIES CORPORATION

(Registrant)

By:

/s/ William Sullivan

William Sullivan, Chief Financial Officer

Date: November 7, 2017

9, 2018

 

27