Exhibit 10.1 NANOSPHERE, INC.SECOND AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT THIS SECOND AMENDED AND RESTATED
REGISTRATION RIGHTS AGREEMENT (this “Agreement”) is
made effective as of August 19, 2009 by and among Nanosphere, Inc., a
Delaware corporation (the “Company”), the Persons
listed on Schedule B of the Prior Agreement (as defined herein
below) (together with their permitted successors, assigns and transferees, the
“Series B Stockholders”), the Persons listed on
Schedule C of the Prior Agreement (as defined herein below)
(together with their permitted successors, assigns and transferees, the
“Series C Stockholders”), the Persons listed on
Schedule C-2 of the Prior Agreement (as defined herein below)
(together with their permitted successors, assigns and transferees, the
“Series C-2 Stockholders”), the Persons listed
on Schedule D of the Prior Agreement (as defined herein below)
(together with their permitted successors, assigns and transferees, the
“Series D Stockholders” and together with the
Series B Stockholders, the Series C Stockholders, the Series C-2
Stockholders, the “Investor Stockholders”) and the
Persons listed on Schedule F of the Prior Agreement (as defined
herein below) (together with their permitted successors, assigns and
transferees, the “Founder Stockholders” and, together
with the Investor Stockholders, the “Stockholders”). RECITALS A. The Company
and certain Stockholders are parties to that certain Amended and Restated
Registration Rights Agreement, dated as of April 12, 2006 (the
“Prior Agreement”). B. Simultaneously
with the execution of this Agreement, the Company is obtaining a waiver (the
“Waiver”) of certain registration rights in connection with a
proposed filing of a registration statement on Form S-3. C. Certain of the
Stockholders have required, as a condition to the Waiver, that the various
parties hereto execute this Agreement. D. For purposes
of Section 11(d) of the Prior Agreement, the Stockholders signatory hereto
collectively hold in excess of the required percentages of Company securities,
as further specified in such Section 11(d), necessary to amend or modify,
together with the Company, the Prior Agreement. Accordingly, all parties to the
Prior Agreement (or any predecessor agreement thereto) shall be deemed parties
to this Agreement as if they were original signatories hereto and the terms and
conditions of the Prior Agreement shall cease to be of any further force and
effect as of the date of this Agreement. E. Certain
capitalized terms used herein have the meanings given to them in Section 8
hereof. The parties hereto agree as follows: 1. Demand Registrations. (a)
Requests for Registration. Subject to the terms set forth herein, at any
time after the earlier to occur of (A) one hundred twenty (120) days
after the Company’s completion of an initial public offering (an
“IPO”) of its equity securities registered under the
Securities Act of 1933, as amended (the “Securities
Act”), which occurred on November 6, 2007, and
(B) April 1, 2010: (i) Investor Stockholders holding at least
twenty percent (20%) of the then outstanding Registrable Securities, having an
expected aggregate price to the market of ten million dollars ($10,000,000),
may request registration under the Securities Act of all or part of the
Registrable Securities held by such Investor Stockholders on Form S-1 or any
similar long-form registration (each, a
“Long-Form Registration”) or, if available, on
Form S-3 or any similar short-form registration (each, a
“Short-Form Registration”), on the terms and
conditions set forth in this Section 1(a) and in Section 1(b); and
(ii) Investor Stockholders holding at least ten percent (10%) of the then
outstanding Registrable Securities, having an expected aggregate price to the
market of not less than one million dollars ($1,000,000), shall, if Short-From
Registrations are then available to the Company under applicable law, be
entitled to request Short-Form Registrations, on the terms and conditions
set forth in this Section 1(a) and in Section 1(c). All registrations
requested pursuant to this Section 1(a) are referred to herein as
“Demand Registrations,” and the Investor Stockholders
requesting a Demand Registration pursuant to the terms hereof are referred to
herein as the “Initiating Holders.” Each request for
a Demand Registration shall specify the approximate number of Registrable
Securities requested to be registered and if known, the anticipated per-share
price range for such offering. Within ten (10) days after receipt of any
such request, the Company shall give written notice of such requested
registration to all other Stockholders holding Registrable Securities and,
subject to Sections 1(b), 1(c) and 1(d) below, shall include in such
registration all Registrable Securities held by such Stockholders with respect
to which the Company has received written requests for inclusion therein within
fifteen (15) days after the receipt of the Company’s notice.  1




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(b)
Long-Form Registrations. The Investor Stockholders shall, in total,
be entitled to request three separate (3) Long-Form Registrations. A
registration shall not count as one of the permitted
Long-Form Registrations until it has become effective, and no registration
shall count as one of the permitted Long-Form Registrations unless the
holders of Registrable Securities are able to register and sell at least ninety
percent (90%) of the aggregate Registrable Securities requested to be included
in such registration; provided, however, any Registrable
Securities that could otherwise have been sold pursuant to an effective
Long-Form Registration but are either (i) not sold prior to the
expiration of the period during which the Company is obligated to keep such
Long-Form Registration effective or (ii) voluntarily withdrawn from
such registration, shall be deemed, for the purpose of the definition of
Registrable Securities under Section 8(d), as having been sold under an
effective registration. The Company shall pay all Registration Expenses (as
hereinafter defined) in connection with any registration initiated as one of
the Long-Form Registrations whether or not it has become effective and
whether or not such registration has counted as one of the permitted
Long-Form Registrations. The Company shall file a registration statement
in connection with any Long-Form Registration with the U.S. Securities and
Exchange Commission (the “SEC”) within forty-five
(45) days following its receipt of the Initiating Holder’s valid
notice requesting such Demand Registration. The Company agrees to use all
commercially reasonable efforts to (i) cause such registration statement
to be declared effective by the SEC as soon as possible after its filing with
the SEC; and (ii) keep such registration statement continuously effective
with the SEC for the lesser of (A) one hundred eighty (180) days
(which 180-day period shall be extended by the number of days that the sale of
Registrable Securities is suspended as described in Section 4(b)) or
(B) until all Registrable Securities covered by such registration
statement have been sold. (c)
Short-Form Registrations. In addition to the Long
Form Registrations provided pursuant to Section 1(b), the Initiating
Holders shall be entitled to request an unlimited number of Short
Form Registrations. After the Company has become subject to the reporting
requirements of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), the Company shall use all
commercially reasonable efforts to make Short-Form Registrations available
for the sale of Registrable Securities. Notwithstanding the foregoing, if
Short-Form Registrations are not available to the Company due to the
Company’s actions or omissions, then upon request of the Initiating
Holders the Company will use all commercially reasonable efforts to effect a
Demand Registration under this Section 1(c) by means of a
Long-Form Registration and such Long-Form Registration shall not
count as one of the permitted Long-Form Registrations pursuant to
Section 1(b). The Company shall pay all Registration Expenses in
connection with any registration initiated as a Short-Form Registration
whether or not it has become effective. The Company shall file a registration
statement in connection with any Short-Form Registration with the SEC as
soon as practicable and in any event within twenty (20) days following its
receipt of the Initiating Holder’s notice requesting such Demand
Registration. The Company agrees to use all commercially reasonable efforts to
cause such registration statement to be declared effective by the SEC as soon
as possible after its filing with the SEC; and (iii) keep such
registration statement continuously effective with the SEC for the lesser of:
(A) the number of days requested by the Initiating Holders, not to exceed
the maximum time period permitted by applicable law; or (B) until all
Registrable Securities covered by such registration statement have been sold. (d)
Priority on Demand Registrations. If a Demand Registration is an
underwritten offering and the managing underwriters advise the Company in
writing that, in their opinion, the number of Registrable Securities and other
securities requested to be included in such offering exceeds the number of
securities that can be sold in an orderly manner in such offering within a
price range acceptable to the holders of a majority of the Registrable
Securities requested to be included in such registration, the Company shall
include in such registration, (i) first, prior to the inclusion of any
securities which are not Registrable Securities, the number of Registrable
Securities held by the Investor Stockholders requested to be included in such
registration which, in the opinion of such underwriters, can be sold in an
orderly manner within the price range of such offering, pro rata among the
respective holders thereof on the basis of the amount of Registrable Securities
owned by each such holder, (ii) second, the number of Registrable
Securities held by other Stockholders requested to be included in such
registration which, in the opinion of such underwriters, can be sold in an
orderly manner within the price range of such offering, pro rataamong
the respective holders thereof on the basis of the amount of Registrable
Securities owned by each such holder, and (iii) third, the number of other
securities requested to be included which, in the opinion of such underwriters,
can be sold in an orderly manner within the price range of such offering,
pro rataamong the Company and the respective holders thereof on the
basis of the amount of securities requested to be included therein by each such
holder.  2




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(e)
Additional Restrictions on Demand Registrations. The Company may
postpone for up to ninety (90) days the filing or the effectiveness of a
registration statement for a Demand Registration to the extent the board of
directors of the Company in good faith determines that such postponement is
necessary in order to avoid premature disclosure of a material financing,
acquisition, recapitalization, reorganization or other material transaction,
the disclosure of which would have a materially detrimental effect on the
Company; provided, however, that the Company may not exercise
such right of postponement for more than ninety days with respect to any Demand
Registration in any period of 365 days; provided that in such
event, the holders of a majority of the Registrable Securities requested to be
included in such a Demand Registration shall be entitled to withdraw such
request and, if such request is withdrawn, such Demand Registration shall not
count as one of the permitted Demand Registrations hereunder and the Company
shall pay all Registration Expenses in connection with such registration. The
Company may delay a Demand Registration hereunder only once in any twelve
(12) month period. The Company will not be obligated to effect any Demand
Registration within the one hundred twenty (120) day period immediately
following the effective date of the Company’s IPO, which occurred on
November 6, 2007. (f)
Selection of Underwriters. The Company shall have the right to select
the investment banker(s) and manager(s) to administer any Demand Registration,
subject to the approval of the holders of Registrable Securities requested to
be included in such registration, which approval shall not be unreasonably
withheld or delayed. (g)
Other Registration Rights. The Company may grant rights to other Persons
to participate in Piggyback Registrations (defined below) so long as such
rights are subordinate to the rights of the holders of Registrable Securities
with respect to such Piggyback Registrations as provided in Sections 2(c) and
2(d) hereof. The Company shall not, without the prior written consent of the
holders of a Majority of the Registrable Securities grant rights to other
Persons to make Demand Registrations. 2. Piggyback
Registrations. (a)
Right to Piggyback. Whenever the Company proposes to register any of its
securities under the Securities Act, for its own account or for the account of
any holder of its securities other than Registrable Securities, (other than
pursuant to a Demand Registration or a registration on Form S-4 or S-8 or any
successor or similar forms) and the registration form to be used may be used
for the registration of Registrable Securities (a “Piggyback
Registration”), the Company shall give prompt written notice to
all Stockholders holding Registrable Securities of its intention to effect such
a registration and shall include in such registration all Registrable
Securities held by such Stockholders with respect to which the Company has
received written requests for inclusion therein within fifteen (15) days
after receipt of the Company’s notice. (b)
Piggyback Expenses. The Company shall pay all Registration Expenses in
all Piggyback Registrations (whether such Registration Expenses are incurred by
the Company or the holders of Registrable Securities). (c)
Priority on Primary Registration. If a Piggyback Registration is an
underwritten registration of securities for the account of the Company, and the
managing underwriters advise the Company in writing that, in their opinion, the
number of securities requested to be included in such registration exceeds the
number which can be sold in an orderly manner in such offering within a price
range acceptable to the Company, the Company shall include in such registration
(i) first, the securities the Company proposes to sell, (ii) second,
the Registrable Securities requested to be included in such registration by the
Investor Stockholders, pro rataamong the respective holders thereof on
the basis of the amount of Registrable Securities owned by each such holder,
(iii) third, the Registrable Securities requested to be included in such
registration by the other Stockholders, pro rataamong the respective
holders thereof on the basis of the amount of Registrable Securities owned by
each such holder, and (iv) fourth, any other securities eligible to be
included in such registration, pro rataamong the holders of such
securities on the basis of the number of shares owned by each such holder. (d)
Priority on Secondary Registration. If a Piggyback Registration is an
underwritten registration of securities for the account of holders of the
Company’s securities, and the managing underwriters advise the Company in
writing that, in their opinion, the number of securities requested to be
included in such registration exceeds the number which can be sold in an
orderly manner in such offering within the price range of the offering, the
Company shall include in such registration (i) first, the securities the
Company proposes to sell, (ii) second, the Registrable Securities
requested to be included in such registration by the Investor Stockholders,
pro rataamong the respective holders thereof on the basis of the amount
of Registrable Securities owned by each such holder, (iii) third, the
Registrable Securities requested to be included in such registration by the
other Stockholders, pro rataamong the respective holders thereof on the
basis of the amount of Registrable Securities owned by each such holder, and
(iv) fourth, any other securities eligible to be included in such
registration, pro rataamong the holders of such securities on the basis
of the number of shares owned by each such holder.  3




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(e)
Selection of Underwriters. If any Piggyback Registration is an
underwritten offering, the selection of investment banker(s) and manager(s) for
the offering shall be made by the Company. 3. Restrictions on Certain
Distributions. (a) The
Company (i) shall not effect any public sale or distribution of its equity
securities, or any securities convertible into or exchangeable or exercisable
for such securities, during the seven (7) days prior to, and during the
one-hundred-eighty (180) day period in the case of an IPO, or the ninety
(90) day period in the case of any other underwritten offering beginning
on, the effective date of any underwritten Demand Registration or any
underwritten Piggyback Registration (except as part of such underwritten
registration or pursuant to registrations on Form S-8 or any successor form),
unless the underwriters managing the registered public offering otherwise
agree, and (ii) shall use all commercially reasonable efforts to cause
each director or officer of the Company to agree not to effect any public sale
or distribution (including sales pursuant to Rule 144 under the Securities
Act) of any such securities during such period (except as part of such
underwritten registration, if otherwise permitted), unless the underwriters
managing the registered public offering otherwise agree. 4. Additional Registration
Procedures. (a) In
connection with any Demand Registration, the Company shall use all reasonable
commercially reasonable efforts to effect the sale of such Registrable
Securities in accordance with the intended method of disposition thereof. The
registration statement filed in connection therewith shall (i) be
available for the sale of the Registrable Securities in accordance with the
intended method or methods of distribution by the selling holders thereof and
(ii) comply as to form in all material respects with the requirements of
the applicable form and include all financial statements required by the SEC to
be included therein or if permitted by the rules and forms of the SEC,
incorporate such financial statements therein by reference. Before filing a
registration statement or prospectus or any amendments or supplements thereto
relating to a Demand Registration, the Company shall furnish to the counsel
selected by the holders of a majority of the Registrable Securities requested
to be included in such Demand Registration copies of all such documents
proposed to be filed, which documents shall be subject to the review and
comment of such counsel. Additionally, the Company shall, as
expeditiously as possible: (b) notify
each holder of Registrable Securities of the effectiveness of each registration
statement filed hereunder and subject to the last three sentences of this
Section 4(b) hereof, (i) prepare and file with the SEC such amendments to
any registration statement as may be necessary to keep any such registration
statement effective for the period specified in Section 1(b) or 1(c) hereof;
(ii) cause the prospectus to such registration statement to be amended or
supplemented as required and to be filed as required by Rule 424 or any
similar rule that may be adopted under the Securities Act; (iii) respond
as promptly as practicable to any comments received from the SEC with respect
to any Long-Form or Short-Form Registration statement or any amendment
thereto; and (iv) comply with the provisions of the Securities Act with
respect to the disposition of all securities covered by such registration
statement during the applicable period in accordance with the intended method
or methods of distribution by the selling holders thereof. Notwithstanding
anything to the contrary contained herein, the Company may delay taking any of
the actions described in clauses (i), (ii) or (iii) in this
Section 4(b), with respect to each holder of Registrable Securities
(x) to the extent that the board of directors of the Company in good faith
determines that such delay is necessary in order to avoid premature disclosure
of a material financing, acquisition, recapitalization, reorganization or other
material transaction, the disclosure of which would have a materially
detrimental effect on the Company; provided, however, that the
Company may not exercise such right of delay for more than sixty days, less the
number of days if any such registration statement may have been postponed
pursuant to Section 1(e) above, with respect to any Demand Registration in any
period of 365 days and it delivers written notice to each such holder of
Registrable Securities to such effect or (y) unless and until the Company
has received a written notice (a “Registration
Notice”) from such holder that such holder intends to make offers
or sales under the registration as specified in such Registration Notice;
provided, however, that the Company shall have ten
(10) business days to prepare and file any such amendment or supplement
after receipt of the Registration Notice or such longer period as is reasonably
necessary if such preparation and filing are not commercially practicable
within ten (10) business days. Once a holder has delivered a Registration
Notice to the Company, such holder shall promptly provide to the Company such
information as the Company reasonably requests in order to identify such holder
and the method of distribution in a post-effective amendment to such
registration statement or a supplement to its prospectus. Such holder also
shall notify the Company in writing upon completion of such offer or sale or at
such time as such holder no longer intends to make offers or sales under such
registration statement;  4




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(c) furnish
to each seller of Registrable Securities such number of copies of such
registration statement, each amendment and supplement thereto, the prospectus
included in such registration statement (including each preliminary prospectus
or supplement), such documents incorporated by reference in such registration
statement, and such other documents as such seller may reasonably request in
order to facilitate the disposition of the Registrable Securities owned by such
seller; (d) use
all commercially reasonable efforts to register or qualify such Registrable
Securities, and to keep such registration or qualification effective during the
period such registration statement is to be kept effective, under such other
securities or blue sky laws or such jurisdictions as any seller reasonably
requests and do any and all other acts and things which may be reasonably
necessary or advisable to enable such seller to consummate the disposition in
such jurisdictions of the Registrable Securities owned by such seller (provided
that the Company shall not be required to (i) qualify generally to do
business in any jurisdiction where it would not otherwise be required to
qualify but for this Section 4(d), (ii) subject itself to taxation in
any such jurisdiction or (iii) consent to general service of process in
any such jurisdiction); (e) immediately
notify each seller of such Registrable Securities (i) when any amendment
or supplement to the prospectus relating to a Demand Registration has been
filed with the SEC, (ii) of the issuance by the SEC or any state
securities authority of any stop order suspending the effectiveness of the
registration statement or any part thereof or the initiation of any proceedings
for that purpose, (iii) if the Company receives any notification with
respect to the suspension of the qualification of the Registrable Securities
for offer or sale in any jurisdiction or the initiation of any proceeding for
such purpose, and (iv) of the happening of any event during the period the
registration statement is effective as a result of which (A) such
registration statement contains any untrue statement of a material fact or
omits to state any material fact required to be stated therein or necessary to
make the statements therein not misleading or (B) such prospectus as then
amended or supplemented contains any untrue statement of a material fact or
omits to state any material fact necessary in order to make the statements
therein, in light of the circumstances under which they were made, not
misleading; and, the Company shall prepare a supplement or amendment to such
prospectus so that, as thereafter delivered to the purchasers of such
Registrable Securities, such registration statement or prospectus shall not
contain an untrue statement of a material fact or omit to state any fact
necessary to make the statements therein not misleading; (f) cooperate
with the selling holders of Registrable Securities to facilitate the timely
preparation and delivery of certificates representing Registrable Securities to
be sold, and enable certificates for such Registrable Securities to be issued
for such numbers of shares and registered in such names as the selling holders
may reasonably request at least two (2) business days prior to any sale of
Registrable Securities; (g) use
all commercially reasonable efforts to cause all such Registrable Securities to
be listed on each securities exchange on which similar securities issued by the
Company are then listed and, if not so listed, use all commercially reasonable
efforts to be listed on the National Association of Securities Dealers
(“NASD”) automated quotation system, or any successor
system or exchange (“NASDAQ”), and if listed on the
NASD automated quotation system, or any such successor system or exchange, use
all commercially reasonable efforts to secure designation of all such
Registrable Securities covered by such registration statement as a NASDAQ
“national market system security” within the meaning of
Rule 11Aa2-1 of the SEC (or equivalent designation under any successor
rule or provision) or, failing that, to use all commercially reasonable efforts
to secure NASDAQ authorization for such Registrable Securities and, without
limiting the generality of the foregoing, to use all commercially reasonable
efforts to arrange for at least two (2) market makers to register as such
with respect to such Registrable Securities with the NASD; (h) provide
a transfer agent and registrar for all such Registrable Securities and a CUSIP
number for all such Registrable Securities not later than the effective date of
such registration statement; (i) enter
into such customary agreements (including underwriting agreements in customary
form) and take all such other actions as the holders of a majority of the
Registered Securities requested to be included in the registration statement or
the underwriters, if any, reasonably request in order to expedite or facilitate
the disposition of such Registrable Securities (including effecting a stock
split or a combination of shares); (j) subject
to the receipt of a confidentiality agreement, make available for inspection by
any seller of Registrable Securities, any underwriter participating in any
disposition pursuant to such registration statement and any attorney,
accountant or other agent retained by any such seller or underwriter, all
financial and other records, pertinent corporate documents and properties of
the Company, and cause the Company’s officers, directors, employees and
independent accountants to supply all information reasonably requested by any
such seller, underwriter attorney, accountant or agent in connection with such
registration statement;  5




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(k) otherwise
use all commercially reasonable efforts to comply with the Securities Acts and
the Exchange Act and all applicable rules and regulations of the SEC, and make
available to its security holders, as soon as reasonably practicable, an
earnings statement covering the period of at least twelve (12) months
beginning with the first day of the Company’s first full calendar quarter
after the effective date of the registration statement, which earnings
statement shall satisfy the provisions of Section 11(a) of the Securities Act
and Rule 158 promulgated thereunder; (l) permit
any holder of Registrable Securities which holder, in its sole and exclusive
judgment, might be deemed to be an underwriter or a controlling person of the
Company, to participate in the preparation of such registration or comparable
statement and to require the insertion therein of material, furnished to the
Company in writing, which in the reasonable judgment of such holder and its
counsel should be included; (m) in
the event of the issuance of any stop order suspending the effectiveness of a
registration statement, or of any order suspending or preventing the use of any
related prospectus or suspending the qualification of any Common Stock included
in such registration statement for sale in any jurisdiction, the Company shall
use all commercially reasonable efforts promptly to obtain the withdrawal of
such order; and (n) use
all commercially reasonable efforts to obtain all legal opinions, auditors
consents and comfort letters and experts cooperation as may be required,
including furnishing to each underwriter of Registrable Securities on the date
the registration statement with respect to such Registrable Securities becomes
effective, (i) an opinion, dated as of the such date, of counsel for the
Company and (ii) a “cold comfort” letter, dated as of such
date, signed by the independent public accountants of the Company, in each case
in form and substance as is customarily given to underwriters in an
underwritten public offering. 5. Registration Expenses. (a) All
expenses incident to the Company’s performance of or compliance with this
Agreement, including without limitation all registration and filing fees,
expenses and fees of compliance with securities or blue sky laws, printing
expenses, messenger and delivery expenses, fees and disbursements of
custodians, and fees and disbursements of counsel for the Company and all
independent certified public accounts, underwriters (excluding discounts and
commissions) and other Persons retained by the Company (all such expenses being
herein called “Registration Expenses”), shall be
borne by the Company, and the Company shall, in any event, pay its internal
expenses (including, without limitation, all salaries and expenses of its
officers and employees performing legal or accounting duties), the expense of
any annual audit or quarterly review, the expense of any liability insurance
and the expenses and fees for listing the securities to be registered on each
securities exchange on which similar securities issued by the Company are then
listed or on the NASDAQ. (b) In
connection with each Demand Registration and each Piggyback Registration, the
Company shall pay the reasonable fees and disbursements of one counsel chosen
by the holders of Registrable Securities holding a majority of the Registrable
Securities requested to be included in such Demand Registration or Piggyback
Registration. (c) To
the extent Registration Expenses are not required to be paid by the Company
hereunder, each holder of securities included in any registration hereunder
shall pay those Registration Expenses allocable to the registration of such
holder’s securities so included, and any Registration Expenses not so
allocable shall be borne by all sellers of securities included in such
registration in proportion to the aggregate selling price of the securities to
be so registered. 6. Indemnification;
Contribution. (a)
Indemnification by the Company. The Company agrees to indemnify and hold
harmless each Stockholder selling securities in connection with the exercise of
rights under this Agreement and their respective officers, directors,
stockholders, members, representatives on the Board of Directors of the
Company, and each Person, if any, who controls or is alleged to control any
such holder within the meaning of Section 15 of the Securities Act (each
such Person referenced to herein as a “Covered
Person”) as follows: (i)against
any and all loss, liability, claim, damage and expense whatsoever to which such
Covered Person may become subject under the Securities Act or otherwise (or
actions or proceedings in respect thereof) (A) that arise out of or are
based upon any untrue statement or alleged untrue statement of a material fact
contained or incorporated by reference in any registration statement relating
to the holder’s Registrable Securities or any amendment thereto, and any
other disclosure document produced by or on behalf of the Company or any of its
subsidiaries, including, without limitation, reports required to be filed under
the Exchange Act or the omission or alleged omission to state therein a
material fact required to be stated therein or necessary to make the statements
therein not misleading, (B) that arise out of or are based upon any untrue
statement or alleged untrue statement of a material fact contained or
incorporated by reference in any prospectus or any amendment or supplement
thereto, or the omission or alleged omission to state therein a material fact
necessary in order to make the statements therein, in the light of the
circumstances under which they were made, not misleading;  6




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(ii)
against any and all loss, liability, claim, damage and expense whatsoever to
the extent of the aggregate amount paid in settlement of any litigation, or
incurred in connection with any investigation or proceeding by any governmental
agency or body, commenced or threatened, or of any claim whatsoever based upon
any such untrue statement or alleged untrue statement or any omission or
alleged omission contained or incorporated by reference in any registration
statement relating to the holder’s Registrable Securities, if such
settlement is effected with the written consent of the Company, which shall not
be unreasonably withheld, conditioned or delayed; (iii)
against any and all expense whatsoever (including reasonable fees and
disbursements of counsel), reasonably incurred in investigating, preparing or
defending against any litigation, or investigation or proceeding by any
governmental agency or body, commenced or threatened, in each case whether or
not a party, or any claim whatsoever based upon any such untrue statement or
alleged untrue statement or omission or alleged omission, to the extent that
any such expense is not paid under Section 6(a)(i) or
Section 6(a)(ii) above; and (iv)
against any and all loss, liability, claim, damage and expense whatsoever to
which such Covered Person may become subject as a result of any violation by
the Company of any rule or regulation promulgated under the Securities Act, the
Exchange Act, or any state securities law applicable to the Company in
connection with any registration, qualification, or compliance of the
Registrable Securities or any other capital stock of the Company or otherwise; provided, however, that
the indemnity provided pursuant to this Section 6(a) shall not apply with
respect to any loss, liability, claim, damage or expense that arises out of or
is based upon any untrue statement or alleged untrue statement or omission or
alleged omission made in reliance upon and in conformity with written
information furnished to the Company by such holder expressly for use in any
registration statement relating to the holder’s status as a selling
security holder or any amendment thereto or the prospectus or any amendment or
supplement thereto. (b)
Indemnification by Holders. Each holder of Registrable Securities
severally agrees to indemnify and hold harmless the Company, and each of its
directors and officers who have signed the registration statement, and each
Person, if any, who controls the Company or any other selling holder within the
meaning of Section 15 of the Securities Act, to the same extent as the
indemnity contained in Section 6(a) hereof, but only insofar as such loss,
liability, claim, damage or expense arises out of or is based upon any untrue
statement or alleged untrue statement or omission or alleged omission made in
any registration statement relating to Registrable Securities or any amendment
thereto or the prospectus or any amendment or supplement thereto in reliance
upon and in conformity with written information furnished to the Company by
such selling holder expressly for use therein relating to the holder’s
status as a selling security holder. Notwithstanding the foregoing, the
indemnification obligations under this Section 6(b), and the contribution
obligations under Section 6(d), of an indemnifying holder of Registrable
Securities shall be limited to the amount of net proceeds received by such
holder upon the sale of Registrable Securities under the registration statement
to which the indemnification obligations relate. (c)
Conduct of Indemnification Proceedings. Each indemnified party shall
give reasonably prompt notice to each indemnifying party of any action or
proceeding commenced against it in respect of which indemnity may be sought
under this Section 6, but failure to so notify an indemnifying party
(i) shall not relieve it from any liability which it may have under the
indemnity agreement provided in Section 6(a) or (b) above, unless and to
the extent it did not otherwise learn of such action and the lack of notice by
the indemnified party materially prejudices the indemnifying party or results
in the forfeiture by the indemnifying party of substantial rights and defenses
and (ii) shall not, in any event, relieve the indemnifying party from any
obligations to such indemnified party other than the indemnification obligation
provided under Section 6(a) or (b) above. After receipt of such notice,
the indemnifying party shall be entitled to participate in and, at its option,
jointly with any other indemnifying party so notified, to assume the defense of
such action or proceeding at such indemnifying party’s own expense with
counsel chosen by such indemnifying party and approved by the indemnified
party, which approval shall not be unreasonably withheld; provided, however,
that, if the defendants in any such action or proceeding include both the
indemnified party and the indemnifying party and the indemnified party
reasonably determines, upon advice of counsel, that a conflict of interest
exists or that there may be legal defenses available to it or other indemnified
parties that are different from or in addition to those available to the
indemnifying party, then the indemnified party shall be entitled to one
separate counsel, the reasonable fees and expenses of which shall be paid by
the indemnifying party. If the indemnifying party does not assume the defense
of any such action or proceeding, after having received the notice referred to
in the first sentence of this Section 6(c), the indemnifying party will
pay the reasonable fees and expenses of counsel (which shall be limited to a
single law firm) for the indemnified party. In such event, however, the
indemnifying party will not be liable for any settlement effected without the
written consent of such indemnifying party, which consent shall not be
unreasonably withheld, conditioned or delayed. If the indemnifying party
assumes the defense of any such action or proceeding in accordance with this
Section 6(c), such indemnifying party shall not be liable for any fees and
expenses of counsel for the indemnified party incurred thereafter in connection
with such action or proceeding except as set forth in the proviso in the second
sentence of this Section 6(c).  7




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(d)
Contribution. In order to provide for just and equitable contribution in
circumstances in which the indemnity agreement provided for in this
Section 6 is for any reason held to be unenforceable although applicable
in accordance with its terms, the Company and the selling holders of
Registrable Securities shall contribute to the aggregate losses, liabilities,
claims, damages and expenses of the nature contemplated by such indemnity
agreement incurred by the Company and the selling holders of Registrable
Securities, in such proportion as is appropriate to reflect the relative fault
of and benefits to the Company on the one hand and such selling holders on the
other (in such proportions that the selling holders are severally, not jointly,
responsible for the balance), in connection with the statements or omissions
which resulted in such losses, claims, damages, liabilities or expenses, as
well as any other relevant equitable considerations; provided, that in no event
shall any contribution by a selling holder of Registrable Securities under this
Section 6(d) exceed the net proceeds from the offering received by such selling
holder. The relative benefits to the indemnifying party and indemnified parties
shall be determined by reference to, among other things, the total proceeds
received by the indemnifying party and indemnified parties in connection with
the offering to which such losses, claims, damages, liabilities or expenses
relate. The relative fault of the indemnifying party and indemnified parties
shall be determined by reference to, among other things, whether the action in
question, including any untrue or alleged untrue statement of a material fact
or omission or alleged omission to state a material fact, has been made by, or
relates to information supplied by, such indemnifying party or the indemnified
parties, and the parties’ relative intent, knowledge, access to
information and opportunity to correct or prevent such action. The parties
hereto agree that it would not be just or equitable if contribution pursuant to
this Section 6(d) were determined by pro rataallocation or by any other
method of allocation which does not take account of the equitable
considerations referred to this Section 6(d). Notwithstanding the foregoing, no
Person guilty of fraudulent misrepresentation (within the meaning of Section
11(f) of the Securities Act) shall be entitled to contribution from any Person
who was not guilty of such fraudulent misrepresentation. For purposes of this
Section 6(d), each Person, if any, who controls a holder of Registrable
Securities within the meaning of Section 15 of the Securities Act and
directors and officers of such holder shall have the same rights to
contribution as such holder, and each director of the Company, each officer of
the Company who signed the registration statement and each Person, if any, who
controls the Company within the meaning of Section 15 of the Securities
Act shall have the same rights to contribution as the Company. 7. Participation in
Underwritten Registrations. No Person may participate in any registration
hereunder which is underwritten unless such Person (i) agrees to sell such
Person’s securities on the basis provided in any underwriting
arrangements approved by the Person or Persons entitled hereunder to approve
such arrangements and (ii) completes and executes all questionnaires,
powers of attorney, indemnities, underwriting agreements and other documents
required under the terms of such underwriting arrangements; provided that no
holder of Registrable Securities included in any underwritten registration
shall be required to make any representations or warranties to the Company or
the underwriters (other than representations and warranties regarding such
holder, such holder’s title to and authority to sell the Registrable
Securities and such holder’s intended method of distribution) or to
undertake any indemnification obligations to the Company or the underwriters
with respect thereto, except as otherwise provided in Section 6 hereof. 8. Definitions. (a)
“Common Stock” means the Company’s Common
Stock, $0.01 par value per share. (b)
“Person” includes any legal person, including,
without limitation, any natural person, corporation, partnership, limited
liability company or trust. (c)
“Registrable Securities” means: (i) any shares
of Common Stock issued or issuable upon conversion of the Series B
Preferred, the Series C Preferred, the Series C-2 Preferred or the
Series D Preferred owned by the Stockholders, including upon conversion of
shares issued as dividends thereon and upon conversion of any shares acquired
upon exercise of any warrant issued under the Series D Purchase Agreement
and (ii) other shares of Common Stock now or hereafter owned by any
Stockholder. Notwithstanding the foregoing, the term “Registrable
Securities” shall exclude: (i) Common Stock that has been disposed
of under any effective registration statement; (ii) Common Stock sold or
otherwise transferred pursuant to Rule 144 under the Securities Act;
(iii) Common Stock that is held by holders who are not affiliates of the
Company that are eligible for sale pursuant to Rule 144(k) under the Securities
Act; and (iv) Common Stock that is held by any Stockholder whose aggregate
stockholdings represent less than one percent (1%) of the total then
outstanding Common Stock (considered on an as-converted,
“fully-diluted” basis). Additionally, for purposes of this
Agreement, a Person shall be deemed to be a holder of Registrable Securities
whenever such Person is known by the Company to have the right to acquire such
Registrable Securities (upon conversion or exercise in connection with a
transfer of securities or otherwise, but disregarding any restrictions or
limitations upon the exercise of such right), whether or not such acquisition
has actually been effected, and such Person shall be entitled to exercise the
rights of a holder of Registrable Securities hereunder.  8




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(d)
“Series B Preferred” means shares of the
Company’s Series B Preferred Stock, $0.01 par value per share. (e)
“Series C Preferred” means shares of the
Company’s Series C Preferred Stock, $0.01 par value per share. (f)
“Series C-2 Preferred” means shares of the
Company’s Series C-2 Preferred Stock, $0.01 par value per share. (g)
“Series D Preferred” means shares of the
Company’s Series D Preferred Stock, $0.01 par value per share. 9. Reports Under Securities
Exchange Act of 1934; Transfer of Restricted Securities. (a) With a
view to making available to the holders of Registrable Securities the benefits
of Rule 144 promulgated under the Securities Act and any other rule or
regulation of the SEC that may at any time permit a holder of Registrable
Securities to sell securities of the Company to the public without registration
or pursuant to a registration on Form S-2 or S-3, the Company agrees to: (i) make
and keep public information available, as those terms are understood and
defined in Rule 144, or such other similar information required by any
similar rule or regulation hereafter adopted by the SEC, at all times after
ninety (90) days after the effective date of the first registration
statement filed by the Company for the offering of its securities to the
general public so long as the Company remains subject to the periodic reporting
requirements under Sections 13 or 15(d) of the Exchange Act; (ii) take
such action, including the voluntary registration of its Common Stock under
Section 12 of the Exchange Act, as is necessary to enable the holders of
Registrable Securities to utilize Form S-2 or S-3 for the sale of their
Registrable Securities, such action to be taken as soon as practicable after
the end of the fiscal year in which the first registration statement filed by
the Company for the offering of its securities to the general public is
declared effective; (iii) file
with the SEC in a timely manner all reports and other documents required of the
Company under the Securities Act and the Exchange Act; and (iv) furnish
to any holder of Registrable Securities, so long as such holder owns any
Registrable Securities, forthwith upon request (A) a written statement by
the Company that it has complied with the reporting requirements of
Rule 144 or any similar rule or regulation hereafter adopted by the SEC
(at any time after ninety (90) days after the effective date of the first
registration statement filed by the Company), the Securities Act and the
Exchange Act (at any time after it has become subject to such reporting
requirements), or that it qualifies as a registrant whose securities may be
resold pursuant to Form S-2 or S-3 (at any time after it so qualifies),
(B) a copy of the most recent annual or quarterly report of the Company
and such other reports and documents so filed by the Company, and (C) such
other information as may be reasonably requested in availing any holder of
Registrable Securities of any rule or regulation of the SEC which permits the
selling of any such securities without registration or pursuant to any such
form. (a) If
any Registrable Securities become eligible for sale pursuant to
Rule 144(k), the Company shall, upon the request of the holder of such
Registrable Securities, remove any applicable legend from the certificate(s)
representing such securities. 10. Directed Share
Programs. The Company and Stockholders agree that, with respect to only the
Series C-2 Preferred or Series D Preferred owned by a Stockholder,
such Stockholder shall have the right to purchase that number of shares of
Common Stock issuable as directed shares in connection with an IPO of the
Company’s Common Stock equal to not less than the product of (x) the
total number of such directed shares, times (y) ten percent (10%), times
(z) the percentage of the total number of shares of Common Stock issued or
issuable on conversion of the Series C-2 Preferred or Series D
Preferred owned by such holder. No Stockholders other than the holders of
Series C-2 Preferred or Series D Preferred shall have the right to
purchase such directed shares. 11. General Provisions;
Termination (a)
No Inconsistent Agreements. Without the written consent of Stockholders
holding a majority of the then outstanding Registrable Securities, the Company
shall not hereafter enter into any agreement with respect to its securities
which is inconsistent with or violates or limits the rights granted to the
holders of Registrable Securities in this Agreement, including without
limitation with respect to priority on cutback in an underwritten public
offering as specified in Sections 1(d), 2(c) and 2(d). (b)
Adjustments Affecting Registrable Securities. The Company shall not take
any action, or permit any change to occur, with respect to its securities which
would materially adversely affect the ability of the holders of Registrable
Securities to include such Registrable Securities in a registration undertaken
pursuant to this Agreement or which would materially adversely affect the
marketability of such Registrable Securities in any such registration (which
might include, without limitation, effecting a stock split or a combination of
shares).  9




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(c)
Remedies. Any Person having rights under any provision of this Agreement
shall be entitled to enforce such rights specifically to recover damages caused
by reason of any breach of any provision of this Agreement and to exercise all
other rights granted by law. The parties hereto agree and acknowledge that
money damages may not be an adequate remedy for any breach of the provisions of
this Agreement and that any party may in its sole discretion apply to any court
of law or equity of competent jurisdiction (without posting any bond or other
security) for specific performance and for other injunctive relief in order to
enforce or prevent violation of the provisions of this Agreement. (d)
Amendment and Waivers. Except as otherwise provided herein, the
provisions of this Agreement may be amended or waived only upon the prior
written consent of (i) the Company, (ii) holders of at least
fifty-one percent (51%) of the then outstanding shares of Common Stock issued
or issuable upon conversion of the Series C-2 Preferred and
(iii) holders of at least 51% of the then outstanding Series D
Preferred; provided that if such amendment or waiver would materially
adversely affect a holder or group of holders of Registrable Securities in a
manner materially different than any other holder or group of holders of
Registrable Securities, then such amendment or waiver will require the consent
of such holder of Registrable Securities or a majority of the Registrable
Securities held by such group of holders materially adversely affected. The
failure of any party to enforce any of the provisions of this Agreement shall
in no way be construed as a waiver of such provisions and shall not affect the
right of such party thereafter to enforce each and every provision of this
Agreement in accordance with its terms. (e)
Successors and Assigns. All covenants and agreements in this Agreement
by or on behalf of any of the parties hereto shall bind and inure to the
benefit of the respective successors and assigns of the parties hereto whether
so expressed or not. In addition, whether or not any express assignment has
been made, the provisions of this Agreement which are for the benefit of
purchasers or holders of Registrable Securities are also for the benefit of,
and enforceable by, any subsequent holder of Registrable Securities. (f)
Severability. If any provision of this Agreement is held to be
prohibited by or invalid, illegal or unenforceable in any respect under
applicable law by the SEC or by a court of competent jurisdiction, such
provision shall be ineffective only to the extent of such prohibition,
invalidity, illegality or unenforceability without invalidating the remainder
of this Agreement. (g)
Counterparts. This Agreement may be executed simultaneously in one or
more counterparts (any one of which may be by facsimile), any one of which need
not contain the signatures of more than one party, but all such counterparts
taken together shall constitute one and the same Agreement. (h)
Descriptive Headings. The descriptive headings of this Agreement are
inserted for convenience only and do not constitute a part of this Agreement. (i)
Governing Law. This Agreement shall be governed by and construed in
accordance with the laws of the State of New York. (j)
Notices. All notices, demands or other communications to be given or
delivered under or by reason of the provisions of this Agreement shall be in
writing and shall be deemed to have been given when delivered personally to the
recipient or one day after being sent to the recipient by reputable overnight
courier service (charges prepaid). Such notices, demands and other
communications shall be sent to each Stockholder at the address and to the
attention of such person as the Stockholder has specified to the Company, and
to the Company at the address and to the attention of such person indicated
below: Nanosphere, Inc. 
4088 Commercial
Avenue 
Northbrook, Illinois 60062 
Attention: President 
 

with a copy to: 
  
Seyfarth Shaw LLP 
620 Eighth Avenue

New York, NY 10018 
Attention: Esteban A. Ferrer, Esq. 
 

or to such other address or to the attention of such other person as the
recipient party has specified by prior written notice to the sending party.  10




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(k) Aggregation of
Stock. All shares of Registrable Securities held or acquired by affiliated
entities or Persons shall be aggregated together for the purpose of determining
the availability of any rights under this Agreement. (l) Prior Agreement and
Entire Agreement. This Agreement hereby amends and restates the Prior
Agreement in its entirety, and upon execution and delivery of this Agreement,
the Prior Agreement shall be of no further force of effect. Additionally,
except as otherwise expressly set forth herein, this Agreement and the
agreements and instruments referred to herein embody the complete agreement and
understanding among the parties hereto with respect to the subject matter
hereof and supercede and preempt any prior understandings, agreements or
representations by or among the parties, written or oral, which may have
related to the subject matter hereof in any way. [Signature pages follow.]   11




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IN WITNESS WHEREOF, the parties have executed this Second Amended and Restated Registration Rights Agreement as of
the date first written above. NANOSPHERE, INC. By: /s/ William P. Moffitt, III 
 AOQ TRUST By: /s/ Mark Slezak 
 LFT PARTNERSHIP By: /s/ Mark Slezak 
 ALFA-TECH, LLC By: /s/ Mark Slezak 
 LURIE INVESTMENT FUND, L.L.C. By: /s/ Mark Slezak 
 LURIE INVESTMENTS, INC. By: /s/ Mark Slezak 
 EAGLE CAPITAL MANAGEMENT, LLC By: /s/ Mark Slezak 
 WASK INVESTMENTS, L.L.C. By: /s/ Mark Slezak 
 [SIGNATURE PAGE TO SECOND AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT]  12




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ANN AND ROBERT H. LURIE FOUNDATION By: /s/ Mark Slezak 
 /s/ William P. Moffitt, III  /s/ Mark Slezak  /s/ Chad A. Mirkin  BAIN CAPITAL VENTURE FUND 2005, L.P. By: Bain Capital Venture Partners, L.P.,  By: Bain Capital Investors, LLC  By: /s/ James Nahirny 
 BCIP ASSOCIATES III, LLC By: BCIP Associates, III,  By: Bain Capital Investors, LLC  By: /s/ James Nahirny 
 BCIP ASSOCIATES III-B, LLC By: BCIP Associates, III-B,  By: Bain Capital Investors, LLC  By: /s/ James Nahirny 
 [SIGNATURE PAGE TO SECOND AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT]  13