Exhibit 10.1

*Confidential Treatment has been

requested for the marked portions

of this exhibit pursuant to Rule

24b-2 of the Securities Exchange

Act of 1934, as amended.

AMENDMENT NO. 4 TO

EXCLUSIVE SUBLICENSE AGREEMENT

THIS AMENDMENT NO. 4 (the “Amendment”) dated as of May 8, 2009 to the Exclusive
Sublicense Agreement by and between Alkermes, Inc., a Pennsylvania corporation
with its principal offices at 88 Sidney Street, Cambridge, MA 02139
(“Alkermes”), and Targeted Genetics Corporation, a Washington corporation with
its principal offices at 1100 Olive Way, Suite 100, Seattle, Washington 98101
(“Targeted”),

WITNESSETH:

WHEREAS, Alkermes and Targeted entered into an Exclusive Sublicense Agreement
dated June 9, 1999, as previously amended on March 12, 2002, May 29, 2003 and
March 9, 2007 (the “Agreement”); and

WHEREAS, Alkermes, on the one hand, and Children’s Hospital Research Foundation
and Children’s Hospital Inc., on the other hand, have entered into various
amendments to the License Agreement between these parties, dated as of April 10,
1996 (the “AAV License Agreement”), which is the license agreement underlying
the Agreement; and

WHEREAS, in accordance with the terms and conditions hereinafter set forth,
Alkermes and Targeted now wish to amend the Agreement to conform to the changes
made to the AAV License Agreement pursuant to such amendments;

NOW, THEREFORE, in consideration of the foregoing premises and the mutual
covenants and agreements set forth herein, the Parties agree as follows:

1. Definitions. Unless otherwise provide herein, all defined terms used in this
Amendment shall have the same meanings as set forth in the Agreement. The
Agreement shall be amended to add the following new definitions:

“1.18 “Customers” means research institutes, academic institutions, universities
and other organizations of higher education, and/or hospitals that contract with
Licensor for the manufacture of Licensed Products. In no event shall a Customer
be (a) a for-profit entity or (b) a not-for-profit foundation, such as the [*].
A Customer must own or control rights in the product, or use thereof, that it
desires Licensor to manufacture and supply using the rights Licensor retains
under the AAV License Agreement, which ownership or control may be evidenced
solely from a filing of a patent application regarding such Licensed Product or
its use.

1.19 “Educational and Research Purposes” means education and/or research
activities which includes clinical trials up to or consisting of Phase II
Clinical Trials.

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1.20 “Funders” means not-for-profit organizations, including not-for-profit
foundations such as the [*], and governmental entities such as the National
Institutes of Health.

1.21 “Licensor” means Children’s Hospital Research Foundation and Children’s
Hospital Inc.”

2. Section 2.2. Section 2.2 of the Agreement shall be deleted in its entirety
and replaced with a new Section 2.2 which shall read as follows:

“2.2 Reserved Rights.

(a) Alkermes reserves unto itself the personal, non-transferable right to make,
have made, and use Licensed Product(s) and Licensed Material in the Fields of
Use for internal research purposes only, and for no other purpose in the Fields
of Use.

(b) Alkermes reserves for Licensor the non-exclusive right to use and have used
the Licensed Patent Rights, Licensed Products and/or Licensed Processes, and
associated information and technology of Licensor, (i) for research and/or
educational purposes; and (ii) subject to Sections 2.2 (c) and (d), to
manufacture products containing AAV vectors for use by Licensor and Customers
for Educational and Research Purposes. The reservation of rights in this
Section 2.2(b) does not permit, in any way, any entity except Licensor from
using the Licensed Patent Rights, Licensed Products or Licensed Processes, and
associated information and technology of Licensor, to manufacture Licensed
Products.

(c) Customers may only receive funding for the manufacture by Licensor of
Licensed Products under this Section 2.2 by either self-funding or receiving
money from Funders. Licensed Products manufactured and supplied by Licensor
pursuant to this Section 2.2 shall not, in whole or in part, be funded by, owned
by, optioned or licensed for development and commercialization to a for-profit
entity at the time the Licensed Product is so manufactured by Licensor or during
the conduct of clinical trials utilizing such Licensed Product so manufactured.
A not-for-profit organization, including Licensor, may receive funding from a
Funder for the manufacture by Licensor of products pursuant to this Section 2.2;
provided however, that such funding for the manufacture by Licensor by any one
Funder shall not exceed [*] per year per Licensed Product manufactured and, in
the event that the Customer receives funding from a Funder that is a
not-for-profit foundation, the not-for-profit foundation must not own or have
licensed any patent rights necessary or useful for the Licensed Products
manufactured by Licensor, other than a non-exclusive license or option to any
inventions made during the manufacture by Licensor of Licensed Products pursuant
to Section 2.2 and funded by such not-for-profit foundation. In no instance
shall Licensor receive any funding from [*] relating to the manufacture of
Licensed Products consistent with this Section 2.2. Nothing herein shall limit
Licensor’s or a Customer’s ability to receive funding from any source for any
purpose, including Educational and Research Purposes, not related to the
manufacture of a Licensed Product under this Section 2.2.

 

  2   *Confidential Treatment Requested.

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(d) Restrictions on Manufacturing. In no event shall Licensor manufacture and
supply any Licensed Products pursuant to this Section 2.2 for Educational and
Research Purposes on the following without the prior written consent of
Alkermes, which consent shall be provided on behalf of Alkermes by its
sublicensee Targeted: [*]. Alkermes shall be informed by Licensor of any such
consent provided by Alkermes’ sublicensee, Targeted. Licensor will not grant the
right to use Licensed Products manufactured and supplied to Customers by
Licensor pursuant to this Section 2.2 by for-profit entities (excluding those
conducting the clinical trials, e.g. hospitals, and the CROs administering
them).”

3. Section 2.4. The penultimate sentence of Section 2.4 of the Agreement shall
be deleted in its entirety and replaced with a new penultimate sentence which
shall read as follows:

“Targeted shall keep Alkermes apprised of all ongoing sublicensing negotiations
and the general nature of same in a timely manner; Targeted shall also give
Alkermes prompt notification of the identity and address of each Sublicensee
with whom it concludes a Sublicense Agreement and shall supply Alkermes with a
copy of each such Sublicense Agreement.”

4. Section 2.6. Section 2.6 of the Agreement shall be deleted in its entirety
and replaced with a new Section 2.6 which shall read as follows:

“2.6 At any time after the date which is the [*] anniversary of the Effective
Date, Targeted shall, upon receipt of notice from Alkermes to such effect, enter
into good faith negotiations to enter into a sublicense agreement with a
proposed sublicensee designated by Alkermes in such notice, with respect to any
of the Additional Fields of Use for which Targeted, its Affiliates or
Sublicensee(s) have not initiated Phase I Clinical Trials; provided that
entering into such negotiations is not inconsistent with obligations of Targeted
to any Sublicensee. Targeted shall consider a request from Alkermes to conduct
good faith negotiations to enter into a sublicense agreement with a proposed
sublicensee, prior to the [*] anniversary, in fields in which Targeted does not
have any ongoing research efforts, but shall have no obligation to enter into
such a sublicense agreement. Any such sublicense agreement described in this
Section 2.6, if entered into, shall be subject to Section 2.4 above.”

5. Sections 2.7 and 2.8. The Agreement shall be amended to add the following new
Sections 2.7 and 2.8:

“2.7 Development Efforts. Targeted shall keep Alkermes reasonably informed of
Targeted’s efforts in any particular Field of Use, including Targeted’s
development and commercialization of Licensed Products or Licensed Processes,
and provide written status reports at least annually regarding same; provided,
however, that if Licensor requires Alkermes to provide written status reports
semi-annually, then Targeted shall, upon receipt of written notice from
Alkermes, provide such status reports to Alkermes on

 

  3   *Confidential Treatment Requested.

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a semi-annual basis. If at any time Targeted elects not to pursue any particular
Field of Use or elects not to diligently pursue development or sublicensing of
Licensed Products or Licensed Processes for commercial use, Targeted shall
promptly inform Alkermes in writing of same. Thereafter, Targeted shall release
its rights therein, and Alkermes shall be free to grant any and all such rights
to any third party.

2.8 Government Funding. Targeted acknowledges that the U.S. Government retains a
none-exclusive, non-transferable, irrevocable, paid-up license to practice and
have practiced any government-funded invention claimed in the Licensed Patent
Rights as set forth in 35 U.S.C. §§200-211 and shall cause any Licensed Products
or Licensed Processes to be substantially manufactured in the United States in
accordance with 35 U.S.C. §204, as applicable and unless waived.”

6. Section 3.4. The Agreement shall be amended to add the following new
Section 3.4:

“3.4 Waiver. Alkermes hereby waives any applicable milestone and royalty
obligations set forth in this Article 3, if: (a) such obligations arise solely
from activities of [*] (to the extent [*] is a sublicensee under the Licensed
Patent Rights at the time such activities occur) in furtherance of developing
and selling a Licensed Product in only [*], as that term is defined in
Attachment A annexed hereto and incorporated herein by reference (which shall be
amended from time to time as necessary to reflect [*]); and (b) consideration is
not paid to Targeted for any such milestone or royalty, including consideration
received in lieu of cash payments therefor. On an annual basis, Targeted shall
certify in writing to Alkermes that no payments were received that, absent this
waiver, would have been due Alkermes. Nothing in the foregoing shall be
interpreted as a waiver, or otherwise to prevent Alkermes from receiving
milestones and royalties pursuant to this Agreement for any Licensed Product
(even a Licensed Product of [*]): (i) if such Licensed Product is sold outside
of [*]; or (ii) if the activity triggering such milestone payment corresponds
with or is relied on to support (A) development of a Licensed Product for sale
outside of [*] or (B) sale of a Licensed Product outside of [*]. For example, if
a Licensed Product is commercialized for [*] and Targeted then starts
development of a Licensed Product for sale outside [*] and regulatory bodies in
[*] allow, based on review of previous data generated on the Licensed Product
for [*], a Phase III Clinical Trial to begin in [*], then Targeted shall pay all
milestones related to earlier development achievements.”

7. Section 15.1. Section 15.1 of the Agreement shall be deleted in its entirety
and replaced with a new Section 15.1 which shall read as follows:

“15.1 Targeted agrees to indemnify, hold harmless and defend Alkermes, Licensor,
its Affiliates and sublicensees and their respective trustees, directors,
officers, employees and agents, against any and all claims, suits, losses,
damages, costs, fees and expenses, including reasonable attorneys’ fees,
resulting from or arising out of Targeted’s exercise of its rights granted under
this Agreement including, but not limited to, product liability, and damages,
losses or liabilities whatsoever with respect to death or injury to any person

 

  4   *Confidential Treatment Requested.

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and damage to any property arising from the development, production,
manufacture, import, sale, lease, consumption, advertisement, possession, use or
operation of Licensed Products by Targeted, its Affiliates or its Sublicensees
or their customers in any manner whatsoever.”

8. Section 15.3. Section 15.3 of the Agreement shall be deleted in its entirety
and replaced with a new Section 15.3 which shall read as follows:

“In the event of any claim for which indemnification will be sought pursuant to
Sections 15.1 or 15.2, the indemnified party will give the indemnifying party
prompt written notice of such claim. The indemnifying party shall have the sole
right to control the defense and settlement of any such claim and shall not be
liable for any settlement that the indemnifying party does not approve in
writing in advance; provided, however, that the indemnifying party shall not
settle any such claim, if such settlement may have an adverse effect on the
indemnified parties or admit the fault thereof, without the prior written
consent of the same, which consent shall not be unreasonably withheld. The
indemnified party will cooperate fully with the indemnifying party, at the
indemnifying party’s expense, in connection with the defense and settlement of
any such claim and may, at its option and expense, be represented in any such
action or proceeding.”

9. Section 15.4. The words “and Licensor, its Affiliates and sublicensees” shall
be added after the word “Alkermes” each time it appears in the second sentence
of Section 15.4 of the Agreement.

10. Miscellaneous. Except as specifically modified or amended hereby, the
Agreement shall remain in full force and effect in accordance with its terms. No
oral promise, covenant or representation of any character or nature has been
made to induce any Party to enter into this Amendment. No provision of this
Amendment may be modified or amended except expressly in a writing signed by
both Parties and referencing this Amendment. In addition, no term of this
Amendment shall be waived except expressly in a writing referencing this
Amendment that is signed by the Party making such waiver.

11. Counterparts. This Amendment may be executed in two or more counterparts,
each of which shall be deemed an original but all of which taken together shall
constitute one and the same instrument. A Party’s signature may be transmitted
by facsimile or electronically, thereby constituting a signed and delivered
document.

[signature page follows]

 

  5   *Confidential Treatment Requested.

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IN WITNESS WHEREOF, the Parties have executed and delivered this Amendment by
their duly authorized officers and representatives, effective as of the day and
year first above written.

 

Targeted Genetics Corporation     Alkermes, Inc. By:  

/s/    B.G. Susan Robinson

    By:  

/s/    Michael Landine

Name:   B.G. Susan Robinson     Name:   Michael Landine Title:   President & CEO
    Title:   Senior Vice President

 

  6   *Confidential Treatment Requested.

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ATTACHMENT A

[*]

[*]

 

  7   *Confidential Treatment Requested.