Free Declaration - District Court of Delaware - Delaware

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EXHIBIT A

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Filed on behalf of : Party Ni By: Jarge A. Goldstein, E q s. Eldora L. Ellison, Esq. Steme,Kessler, Goldstein & Fox, P.L.L.C. 1100 New York Avenue, N W Washington, D.C. 20005-3934 Tel: (202) 37 1-2600 Fax: (202) 371-2540

UNITED STATES PATENT AND TIIADEhOUX OFFICE

BEFORE THE BOARD OF PATENT APPEALS

AND INTERFERENCES
(Administrative Patent Judge Richard E. Schafer)

Human Genome Sciences, Inc.
Junior Party (Patent 6,872,568; Inventors: Jian Ni, Reiner L. Gentz, Guo-Liang Yu, C a g A. Rosen), ri

Immuaex Corp. Senior Party
(Application 09/378,045; Inventors: Charles Rauch, Henning Walczak).
Patent Interference No. 105,240 W

S)

NI PRIORITY STATEMENT

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-1NI PRIORITY STATEMENT Patent Interference No. 105,240

MAIL STOP INTERFERENCE
Board of Patent Appeals and Interferences U.S. Patent and Trademark Office P.O. Box 1450 Alexandria, VA. 223 13-1450 Sir: Pursuant to 37 C.F.R. Statement. 41.204(a), Party Ni respectfully submits the following Priority

I.

Date and Location of Ni's Earliest Corroborated Conception

Pursuant to 37 C.F.R. 8 4le2O4(a)(2)(i), Party Ni hereby states that the earliest corroborated conception by Party Ni of the invention defined by Count 1 took place on November 14, 1996, in the United States.

I.

Date and Location of Nits Earliest Corroborated Actual Reduction to Practice

Pursuant to 37 C.F.R. 41.204(a)(Z)(ii), Party Ni's statement of the earliest corroborated actual reduction to practice by Party Ni of the invention defined by Count 1 requires infomation believed to be in the possession of one or more third parties; such information is not currently available to Party Ni. Party Ni has filed a MISCELLANEOUS MOTION 2 UNDER 37 C.F.R.

9 4lV121(a)(3) (Requesting Authorization for Compulsion of Testimony and Production under 37
C.F.R. 9 41.156) to assist with its effort to obtain such information.
Party Ni's

MISCELLANEOUS MOTION 2 explains the reasons as to why such information is not
currently available to Party Ni. Should the MISCELLANEOUS MOTION 2 be granted, and if information is obtained fi-om one or more of the parties mentioned in that motion relating to Party Ni's actual reduction to practice, Party Ni will promptly file a request to correct its priority

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-2NI PRIORITY STATEMENT Patent Interference No. 105,240 statement under 37 C.F.R. 8 41.120(c) to include a statement of the date and location of Party

Ni's earliest corroborated actual reduction to practice.
Regardless of whether Party Ni is later able to provide a statement of the date and location of its earliest corroborated actual reduction to practice, Party Ni reserves the right to rely on the filing date of an earlier-filed application(s) to prove a constructive reduction to practice,
e.g., as detailed in NI SUBSTANTIVE

MOTION 3 (to Change Benefit Accorded for the

Contested Subject Matter). Party Ni thus reserves the right to rely on the filing date of any of U.S. Provisional Appl. No. 601040,846, filed March 17, 1997; U.S. Provisional Appl. No. 601054,021, filed July 29, 1997; U.S. Appl. No. 091042,583, filed March 17,1998;

U.S.Provisional Appl. No. 60/132,498, filed May 4, 1999;
U.S. Provisional Appl. No. 601133,238, filed May 7, 1999; and

U.S. Provisional Appl. No. 601148,939, filed August 13,1999.

III.

Statement of Earliest CorroboratedDate on which Ni's Diligence Began
Pursuant to 37 C.F.R.8 41.204(a)(2)(iii), Party Ni hereby states that the earliest

corroborated date on which diligence by Party Ni of the invention defined by Count 1 began was November 14,1996.

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-3NI PIUORITY STATEMENT Patent Interference No. 105,240

K

Copy of Earliest Documents Upon Which Ni Will R l to Show Conception ey
Pursuant to 37 C.F.R. 41.204(a)(2)(iv),Party Ni submits herewith a copy of the earliest 5

documents upon which Party Ni will rely to show conception of the invention defined by Count 1.

~ t t o r n k ~ Party Ni for Registration No. 29,021 Date: December 7.2005

STERNE, USSLER, GOLDSTEM FOX & P.L.L.C. 1100 New York Avenue, NW Washington, D.C. 20005-3934

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-4NI PRIORITY STATEMENT
Patent InterferenceNo. 105,240
CERTIFICATE OF SERVICE
I, Jorge A. Goldstein, hereby certify that a copy of the foregoing NI PRIORITY STATEMENT, filed December 7, 2005, has been served on the attorney of record of Party Rauch via Federal Express on this 7n day of Decanber, 2005, addressed as follows:

Michael J. Wise Perkins Coie LLP 1620 26thStreet 6thFloor, South Tower Santa Monica, CA 90404-4013 Tel: 310-788-3210 Fax: 310-788-3399 Respecthlly submitted,

Jorge A. Goldstein Attorney for Party Ni Registration No. 29,021 Date: December 7,2005 STERNE,KESSLER,GOLDSTEIN FOX & P.L.L.C. 1100 New York Avenue, NW Washington, D.C.20005-3934

I

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-4-

NI PRIORITY STATEMENT
Patent Interference No. 105,240
CERTIFICATE OF SERVICE

I, Jorge A. Goldstein, hereby certify that a copy of the foregoing NI PRIORITY STATEMENT, filed December 7, 2005, has been served on the at.torney of record of Party Rauch via Federal Express on this 1 4 day~ December, 2005, addressed as follows: ~ of
Michael J. Wise Perkins Coie LLP 1620 26thStreet 6thFloor, South Tower Santa Monica, CA 90404-4013 Tel: 3 10-788-3210 Fax: 310-788-3399

Attomdy for Party Ni Registration No. 29,02 1 Date: December 14,2005 STERNE, KESSLER, GOLDSTEIN FOX P.L.L.C. & 1100 New York Avenue, NW Washington, D.C. 20005-3934

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Author: Jian Nk at HGS1-HQ Date: 11/14/96 6:20 PM Normal TO: Reiner Gentz, Bob Benson at HGS-ADMIN, Craig Rosen at HGS-SCI Subject: One more TNFR-like gene ....................................... Measage Contents - . - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - One more TNFR-like gene was found today. It is not identical to TR5 (Ying-Fei) , but have a region of cDNA very close to TR5 and D R 4 . No EST was found in public EST database. bHSYAD88R

3 Nerve growth factor receptor, low affinity

-

chicken

2 Nerve growth factor receptor [Homo eapiens] >HPRCB54FP04B Length = 650

Minus Strand HSPs: Score = 177 (48.9 bits), Expect = 3.0e-18, Sum P(4) = 3.De-18 Identities = 55/81 (67%), Positives = 55/81 (67%), Strand = Minus / Plus Query: Sbjct: Query:
Sbj ct :

89 ACACACTGTGTTTCT~TCGTOE:TGCA00GACTTAGCTCCATCCTGTCACCT 30 562 A C A C A C T G T G T C T C T G G T C A T G G T G C A N G A A C T T T T A T O T 621 29 GGTGCAGCGCAAGCAGAAA74Q 9
622 T G T A ~ T G G G ~ ~ A N C 642

IIIIIIIIIII 1111111 lllllll I1111
II II I II II

I

1 1 I1111 I I l l

1111

Score = 128 (35.4 bits), Expect = 3.0e-18, Sum P(4) = 3.0e-18 Identities = 34/45 (75%), Positives = 34/45 ( 7 5 % ) , Strand = Minus / Plus Query: Sbjct: 152 TGCGGCACTTCCGGCACATCTCAGGAGAATCTTCTTCCCCGGZ4AG 108 501 TGCTACACTTCCGGCACATCTCTGGGGANTTTTCATTCCGGAAGG 545

111

11l11111111111111 1 1 I I I 1 1 1 I I I I I I

Score = 113 (31.2 bits) Expect = 3.0e-18, Sum P(4) = 3.0e-18 Identities = 25/28 (89%), Positives = 25/28 (89%), Strand = Minus / Plus Query: Sbjct: 334 CCTTCCAGGTAAGGAAGGAAGGAAGGACTTTCTTTC 307 68 CCTTTCAGGTAAGGAAOOAATTTCTTCC 95

IIII 11111111111111 IIIIII 1

Score = 100 (27.6 bits), Expect = 3.0e-18, Sum P(4) = 3.0e-18 Identities = 22/25 (88%), Positives = 22/25 (88%), Strand = Minus / Plus Query: Sbjct:
114

CCGGAAGGTGCCTTCNTCGCACTGA 90

538 CCGGAAGGTGCCTTCTTTACACTGA 562

Illlllllllltlll I 111111

~ p i r ~ ~ ~ 0 0 0 6 ~ J N 0 0 0 6growth factor receptor, low affinity - chicken nerve rspl~185191NG~~ LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR CHICK . PRECURSOR (NGF RECEPTOR) (GP80-LNOFR) Length = 416 Plus Strand HSPs:

Score = 66 (30.2 bits), Expect = 0.84, Sum P (2) = 0.57
Identities = 11/25 ( 4 4 % ) , positives = 14/25 (56%), Frame = +3 Query: Sbj ct : 15 CLRCTRCDSGEVELSPCTTTRNTVC 89 CL CT C+ EV + CT T + C 156 CLPCTICEENEVMVKECTATSDAEC 180

Score = 55 (25.2 bits) , Expect = 0.00025, Sum P ( 3 ) = 0.00025 Identities = 9/25 (36%), Positives = 15/25 (60%), Frame = +3 Query: Sbjct: 15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C C+ C+ G + PC +++TVC 114 CKECSICEVGFGLMFPCRDSQDTVC 138

Score = 47 (21.5 bits), Expect = 0.00025, Sum P ( 3 ) = 0.00025 Identities = 10/21 (47%), positives = 11/21 (52%), Frame = +2

Query:

Case 1:07-cv-00780-SLR

Sbjct:

152 TGCPRGWVKVGDCTPWSDIEC 214 T C V V +CT SD EC 160 TICEENEWKECTATSDAEC 180

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Score
Query: Sbjct:

= 45 (20.6 bits) , Expect = 0.0086, Sum P ( 3 ) = 0.0085 Identities = 8/25 ( 3 2 % ) , Positives = 12/25 (48%), Frame = +3

15 CEBCTRCDSGEVELSPCTTTRNTVC 89 C CT+C +PC + + VC 75 CKPCTQCVGLHSMSAPCVESDDAVC 99

Score = 43 (19.7 bits), Expect = 0.00025, Sum P (3) = 0.00025 Identities = 7/12 (58%), Positives = 9/12 (75%), Frame = +1
Query:
Sbjct:

76 ETQCVQCXEGTF 111 +T C +C EGTF 135 DTVCEECPEGTF 146

Score = 38 (17.4 bits), Expect = 0.093, Sum P(31 = 0.089 Identities = 6/14 (42%), Positives = 8/14 (57%), Frame = t3
Query:

Sbjct:

24 CmCDSGEVELSPC 65 C C+ GE + PC 36 CKACNLGEGWQPC 49

Score = 34 (15.6 bits) , Expect Query:
Sbjct:

= 0.024, Sum P (3) = 0.024 ,,Frame = +2 Identities = 7/17 (41%), Positives = 11/17 (64%)

191 TPWSDIECVHKESGIII 241 TP + E +H + S G I + 282 TPSPEEEKLHSDSGISV 298

Case 1:07-cv-00780-SLR
HGS Full Loctplh F j Ropnt m m

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HGS Full Length Project Report (24nov96)
Project Information
\

Project Name : Project Code : Project Status: HGS Code: Clone ID: Library: Full Length: Protein :
P a t e n t Status : PTO Serial #:

TNFR/TR7/Nerve growth factor receptor, low a f f i n i t y

Screening 1760054 HSYAD88 Human Thymus Stromal Cells N o N o No

Map Location: Collaborator: Created by : Modified by:

Jian Ni, 1 1 / 1 4 / 9 6 Jian Ni, 1 1 / 1 4 / 9 6

General Comments
It is a novel TNFR/NGFR. It is not identical to TR5, but have a region o f cDNA very close t o TR5. No EST i n public EST database.

>HSYAD88R

3 Nerve growth factor receptor, low affinity Length = 410

-

chicken

Plus Strand HSPs:

Score = 2003 (553.5 bits), Expect = 1.5e-161, P = 1.Se-161 Identities = 403/409 ( g o % ) , Positives = 403/409 (9891, Strand
Q u e r y:

=

Plus / Plus

1 ATmCCTCCTTTTCTGCTTGCGCTGCACCAGGTGTGATTCAGGTGAAGTGGAGCTAAGTC 60

Illllllll~lllllIIIIII1IIlltllt~lllllllllll1t111ll11l111111l1
Sbjct :
Query:
Sbjct :

1 ATGACCTCCTTTTCTGCTTGCGCTGCACCAGGTGTGATTCAGGTGTAGCTGTC 60

61 CCTGCACCACGACCAGAZlACACAGTGTGfTCAGTGCGANGAAGGCACCTTCCGGGGAAGA120 IIIIlIIIIIIIIIIIIIIIIIlIIII11111111111 lIIlIIIIIIIIIIIIIl1Il 61 CCTGCACCACGACCAGAAACACAGTGTGTGTTCAGTGCGANGAAGGCACCTTCCGGGGAAGA 1 2 0
121 AGATTCTCCTGAGATGTGCCGGAAGTGCCGCACAGGGTGTCCGAGGATGGGTCGGT 180

Query:
Sbjct:

1111111111111111111l11~ll1ft1l111111t1l11111ll11111111111ll1
1 2 1 AGATTCTCCTGAGATGTGCCGGAAGTGCCGCACAGGGTGTCCCAGAGGATGGGTCGG 180

Query: Sbjct: Query:
Sbjct:

1 8 1 CGGTGA'STGTACACCCTGGAGTGACATCGAATGTGTCCAGTGGCATCATCAT 240

II1tIItlI1IIIIIIIIIIlllllllllllll~lltlIIIIIIIIII1II1IIIII1t1 181 C G G T G A T T C T A C A C C C T G G A G T G A C A T C G A A T G T G T C C A C T 240
241 AGGAGTCACAGTTGCCAGCCGTAGTCTTGATTGTGNGCTGTGTTTGTTTGCTTCTTTT 300 111111111111111111lllllllllllll111l 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 l 1 1 1 1 1 1 241 AGGAGTCACAGTTGCCAGCCGTAGTCTTGATTGTGNGCTGTGTTTGTTTGCAATTCTTTT 300
3 0 1 ACTGTGGAAAGAAAGTCCTTCCTTACCTGGAAGGCATCTGCTCGTGTGGTGGGGAN 360

Query:

Case 1:07-cv-00780-SLR
HGS Full Lmgfh Pmjal R p om

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Sbjct:

111l11111l11l111t1l11111111111tllllllltlllllt I l l l l l t l l l l l l 301 ACTGTGGAAaGAAAGTCCTTCCTTACCTGGAAGGCATCTGCCAGTGGTGGTGGGGAN 360
361 CCGNAGCTGTGGGACAGAAGCTCACAACGACNTCEGECTGAAGACAAGT 409 Ill I l l l l l l l l l l l l l l l l l l I l l t l l l l lIIII1IIIIIIIIIII 361 CCGNAGCTGTGGGACAGAAGCTCACAACGACNTGGGGCTGGT 409

Query:

Sbjct:

>HPRCB54FPO4B 2 Nerve growth factor receptor [Homo sapiensl Length = 650
Minus Strand HSPs: Score = 177 ( 4 8 . 9 bits), Expect = 3.0e-18, Sum P ( 4 1 = 3.0e-18 Identities = 55/81 [67%), Positives = 55/81 ( 6 7 % ) , Strand = Minus / Plus

Query:
Sbjct:
Query :
Shjct :

89 ACACACTGTGTTTCTGGTCGTGGTGCAGGGACTTAGCTCCACTTCACCTGAATCACACCT 30 I I I I I I I I I I I l l l i l l l I11IllI 1 1 1 1 1 1 II I1111 I I l l 562 ACACACTGTETCTCTGGTCATGGTGCANGAACTTTTATGTTTTTGATCTGATTTACAAAC 621
2 9 GGTGCAGCGCAAGCAGAAAAG 9 II II I !I II 1 1 1 1 622 TGTACATGGGAANCAANAAAG 642

Score 128 (35.4 bits), Expect = 3.0e-18, Sum P ( 4 ) = 3.0e-18 Identities = 34/45 (75%), Positives = 34/45 (75%), Strand = Minus / Plus
Query:
Sbjct:
Score

-

152 TGCGGCACTTCCGGCACATCTCAGGAGAATCTTCTTCCCCG 108 1 1 1 I l l t l l l l l f I I I I I I l I1 I I I i l l I ! I I I I 501 TGCTACACTTCCGGCACATCTCTGGGGANTTTTCATTCCGGAAGG 545

113 (31.2 bits), Expect = 3.0e-18, Sum P (4) = 3.0e-18 Identities = 25/28 (89%), Positives 25/28 (89%), Strand = Minus / Plus 334 CCTTCCAGGTAAGGAAGGACTTTCTTTC 307 1 1 1 1 Illlllllllllll IIIIII 1 68 CCTTTCAGGTAAGGAAGGAATTTCTTCC 95

-

Query:
Sbjct:

Scare = 100 (27.6 hits), Expect = 3.W-18, Sum P (4) = 3.0e-18 Identities = 22/25 (88%), Positives = 22/25 (88%), Strand = Minus / Plus

Query: Sbjct:

114 CCGGAAGGTGCCTTCNTCGCACTGA 90 ltlllllltllllll 1 111111 . 538 CCGGAAGGTGCCTTCTTTACACTGA 562
2 Nerve growth factor receptor [Homo sapiensl

>HPRCB54X

Length
p l u s Strand HSPs:

-

1392

Score = 180 (49.7 bits), Expect = 5.6e-17, Sum P(4) = 5,6e-17 Identities = 56/81 (69%), Positives = 56/81 (6911, Strand = Plus / Plus

Query :
Sbjct:

9 C T T T T C T G C T T G C G C T G C A C C A G E T G T G A T T C A G G T G A A C 68

I I1
Query:

11111 I

I I II

1 1 1 1 1 1 1 1 1 It

1

IIII 11111111
488

429 CCTTCTTGCTTCCCATGTACAGTTTGTAAATCAGATCUCATAAAAGTTCCTGCACC

6 9 ACGACCAGAAACACAGTGTGT 89

1 1 1 1 1 1 1 1 11111111~Il

Case 1:07-cv-00780-SLR
HGS FIIIILcnglb Pmjm Rcpml

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Sbjct:

489 ATGACCAGAGACACAGTGTGT 509

Score = 126 (34 - 8 b i t s ) , Expect = 5.6e-17, Sum P ( 4 ) a 5.6e-17 Identities = 34/45 (75%), P o s i t i v e s = 34/45 ( 7 5 % ) , Strand = Plus / Plus

Query:
Sbjct:

108 CTTCCGGGGaAGAAGATTCTCCTGAGATETGCCGTGCCGC 152

I I I I1 1 111 1 II 11 11111111111111111

111

526 CCTTCCGGAATGAAAACTCCCCAGAGATGTGCCGGAAGTGTAGCA 570

Score = 113 ( 3 1 . 2 b i t s ) , Expect = 5.6e-17, Sum P ( 4 ) = 5.6e-17 I d e n t i t i e s = 25/28 ( 8 9 % ) , P o s i t i v e s = 25/28 t a g % ) , Strand = Plus / Plus
Query: Sbjct:
307 GAAAGAAAGTCCTTCCTTACCTGGAAGG 334

1 IIIIII Illlllll~lflll 1111
976 GGAAGAAATTCCTTCCTTACCTGAAAGG 1003

Score

= 100 ( 2 7 . 6 b i t s ) , Expect = 5.6e-17, Sum P (4) = 5.6e-17 I d e n t i t i e s = 22/25 ( 8 8 5 ) , P o s i t i v e s = 22/25 ( 8 8 % ) , Strand = Plus / Plus

Query: Sbjct:

90 TCAGTGCGANGAAGGCACCTTCCGE 114

111111

I 111111111111111

509 TCAGTGTAAAGAAGGCACCTTCCGG 533

Protein BLAST Analysis
> p i r 1 JNOOO6 [JN0006 nerve growth f a c t o r r e c e p t o r , low affinity - chicken >splP185191NGFR_CHICK LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR PRECURSOR (NGF RECEPTOR) (GPO0-LNGFR) . Length 416

-

Plus Strand HSPs:
Score = 66 (30.2 bits) , Expect = 0.84, Sum P (2) = 0.57 Identities = 11/25 ( 4 4 % ) , P o s i t i v e s = 14/25 ( 5 6 % ) , Frame = +3

Query: Sbjct:

15 CLRCTRCDSGEVELSPCTTTRNTVC 8 9 CL CT C+ EV + CT T + C 156 CLPCTICEENEVMVKECTATSDAEC 180

Score = 55 ( 2 5 . 2 bits) , Expect = 0 . 0 0 0 2 5 , Sum P ( 3 ) = 0.00025 Identities = 9/25 ( 3 6 % ) , P o s i t i v e s = 15/25 (60%), Frame +3
Query:
Sbjct: 15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C C+ CC G + PC +++TVC 1 1 4 CKECSICEVGFGLMFPCRDSQDTVC 138

-

Score = 47 ( 2 1 . 5 bits), Expect = 0.00025, Sum P ( 3 ) = 0.00025 I d e n t i t i e s = 10/21 ( 4 7 % ) , P o s i t i v e s 11/21 ( 5 2 % ) , Frame = +2

-

Query:
sbjct:

152 TGCPRGWVKVGDCTPWSDIEC 214 T C V V +CT SD EC 160 TICEENEVMVKECTATSDA~Ci a o

Score = 4 5 ( 2 0 . 6 bits), Expect = 0 . 0 0 8 6 , Sum P(3) = 0 . 0 0 8 5 I d e n t i t i e s = 8 / 2 5 (32%), P o s i t i v e s 12/25 (48%), Frame = +3
Query:
Sbjct :

-

15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C CT+C +PC + + VC 75 CKPCTQCVGLHSMSAPCVESDDAVC 99

Case 1:07-cv-00780-SLR
HGS Full t a g t h Pmjcct R p cm

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Score = 43 (19.7 b i t s ) , Expect = 0.00025, Sum P ( 3 ) = 0.00025 I d e n t i t i e s = 7/12 { 5 8 % ) , P o s i t i v e s = 9/12 ( 7 5 % ) , Frame = +1
Query: Sbjct:
'

76 ETQCVQCXEGTF 311

+T C +C EGTF 135 DTVCEECPEGTF 146

Score = 38 ( 1 7 . 4 b i t s ) , Expect = 0.093, Sum P ( 3 ) = 0 . 0 8 9 Identities = 6/14 ( 4 2 % ) , P o s i t i v e s = 8/14 ( 5 7 % ) , Frame = t3
Query:

Sbjct:

24 CTRCDSGEVELSPC 65 C C+ GE + PC 36 CKACNLGEGWQPC 4 9

Score = 34 (15.6 bits), Expect = 0.024, Sum ~ ( 3 )=' 0 . 0 2 4 Identities 7/17 (41%), Positives = 11/17 ( 6 4 % ) , Frame = t2
Quexy:

-

Sbjct :

191 TPWSDXECVHKESGIII 241 TP + E +H tSGI + 282 TPSPEGEKLRSDSGISV 298

>gi 1339760 TNF receptor [Homo s a p i e n s ] Length = 453

Plus Strand HSPs:

Score = 66 ( 3 0 . 2 b i t s ) , Expect = 0 . 0 2 5 , Sum P ( 3 ) = 0.025 Identities = 12/23 (52%), Positives = 16/23 (69%), Frame = +3 Query:
Sbjct :

30 RCDSGEWLSPCTTTRNTVCSVR 98 R + G+VE+S CT R+TVC R 106 RKEMGQVEISSCTVDRDTVCGCR 128

Score = 34 (15.6 b i t s ) , Expect = 0 . 0 2 5 , Sum P ( 3 ) 0.025 Identities = 5/10 ( 5 0 % ) , Positives = 7/10 (70%), Frame = t3

-

Query:
Sbjct:

6 LLFCLRCTRC 35 L CL C++C 96 LRHCLSCSKC 105

Score = 33 (15.1 b i t s ) , Expect = 0 . 0 2 5 , Sum Y ( 3 ) = 0.025 I d e n t i t i e s = 6/18 ( 3 3 % ) , Positives = 9/18 ( 5 0 % ) , Frame = +3
Query:
Sbjct:

285 CLQFFYCGKKVLPYLEGI 330 C + C K LP+E+ 185 CKKSZECTKLCLPQIENV 202

>gi 1904969 55 kD TNF-BP [unidentified] >qi 1579600 TNF alpha gene gene product [Homo sapiens] >g11339745 tumor necrosis factor receptor [Homo sapiens] pgi1339754 tumor necrosis factor r e c e p t o r [Homo sapiens] >gi1339756 tumor necxosis factor receptor [Homo sapiens] >gi1339750 tumor n e c r o s i s factor r e c e p t o r 1 [Homo s a p i e n s l >gi 137224 tumor necrosis f a c t o r receptor type 1 [Homo sapiens] rpirlA382081GQHUTl tumor necrosis factor receptor type 1 precursor - human >splP194381TNRl_HUMAN TUMOR NECROSIS FACTOR RECEPTOR 1 PRECURSOR (TUMOR NECROSIS FACTOR BINDING PROTEIN 1) (TBPI) (P60) ( T N F - R l ) (P55) (CD120A).

Case 1:07-cv-00780-SLR
NOS Full Length Pmjac R f p a ~ l

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Length = 4 5 5 Plus Strand HSPs:
Score = 66 130.2 bits), Expect = 0.026, Sum P ( 3 ) = 0.025 Identities = 12/23 [ 5 2 % ) , positives = 16/23 (69%), Frame = t3

Query:
Sbjct :

30 RCDSGEVELSPCTTTMTVCSVR 9 8 R + GSVEtS CT R+TVC R 106 RKEMGQm TSSCTmRDTVCGCR 128

Score * 34 ( 1 5 . 6 bits), Expect = 0.026, Sum P ( 3 ) = 0.025 I d e n t i t i e s = 5/10 ( 5 0 % ) , P o s i t i v e s = 7/10 (70%), Frame = + 3

Query:
Sbjct:

6 LLFCLRCTRC 35 L CL C++C 96 LRHCLSCSKC 105

Score = 33 ( 1 5 . 1 bits), Expect 0.026, Sum P(3) = 0.025 Identities = 6/18 (33%), Positives = 9/18 ( 5 0 % ) , Flame = t3

-

Query:
Sbjct:
>gi t 56756

285 CLQFFYCGKKVLPYLEGI 338 C + C K LP+EC 1 8 5 CKKSLECTKLCLPQIENV 202

precursor (AA -29 to 396) [Rattus norvegicus] >pirlA26431la26431 nerve g r o w t h factor receptor precursor, low affinity - rat >splPD71741WEFR_RAT LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR PRECURSOR (NGB RECEPTOR) (GP80-LNGFR)
Length = 425

.

Plus Strand HSPs: Score = 54 ( 2 4 . 7 bits), Expect = 0.23, Sum PI21 = 0.21 Identities 7/10 (70%), Positives = 9/10 ( g o % ) , Frame = +2

-

Query:
Sbjct: Score

185 DCTPWSDIEC 214 +CTPW+D EC 180 ECTPWADAEC 189

= 50 (22.9 bits), Expect = 0.23, Sum P(2) = 0.21 I d e n t i t i e s = 9/25 (368), Positives 13/25 ( 5 2 % ) , Frame = +3

-

Query:
Sbjct:

15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C C+ C+ G + C tNTVC 123 CEACSVCEVGSGLVFSCQDKQNTVC 147

Score = 44 (20.2 bits), Expect = 1.6, Sum P ( 2 ) = 0.81 Identities = 8/25 (32%), P o s i t i v e s 11/25 ( 4 4 % ) , Frame
Query:
15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C CT C + +PC + VC 84 CKPCTECLELQSMSAPCVEADDAVC 108

-

=

+3

Sbjct:

Score = 39 (17.9 bits), E x p e c t = 0.070, Sum P(3) = 0.068 Identities 6 / 1 4 ( 4 2 % ) , Positives 9/14 ( 6 4 % ) , Frame = tl
Query:

-

-

70 RPETQCVQCXEGTF 113. + T C +C EGT+

Case 1:07-cv-00780-SLR
HGS Full Length Pmjar Report

Document 24-2

Filed 02/29/2008

Page 15 of 84

Sbjct :

142 KQNTVCEECPEGTY 155

Score = 36 (16.5 bits), Expect = 0.070, Sum P(3) = 0.068 Identities = 6/14 ( 4 2 % ) , Positives = 7/14 (50%), Frame = +3
Query:

Sbjct:

24 CTRCDSGEVELSPC 65 C C+ GE PC 45 CKACNLGEGVAQPC 58

>gi 1440374 PC6B [Mus musculus] >pir 1 S34583 IS34583 serine proteinase (EC 3.4.21.-) PCGB mouse Length 1548

-

-

Plus Strand HSPs:
Score = 44 (20.2 bits), Expect = 0.077, Sum P ( 4 ) = 0.074 Identities = 9/22 (40%), Positives = 12/22 (54%), Frame = t3
Query:

Sbjct :

24 CTRCDSGEVELSPCTTTRNTVC 89 C+RC SG V + P T + C 674 CSRCMSGYVIIPPNHTCQKLEC 695

Score = 42 (19.2 bits), Expect = 0.077, Sum ~ ( 4 = 0.074 ) Identities = 7 / 1 3 (53%), Positives = 7/13 {53%), Frame = t2
Query: Sbjct:

Score 37 (17.0 bits), Expect = 0.077, Sum P ( 4 ) = 0.074 Identities = 5/38 (27%], Positives = 9/18 ( 5 0 % ) , Frame = t1
Query:
205 HRMCPQRIRHHHRSBSCQ 258

-

119 EDSPEMCMCRTG 157 ED P C C TG 720 EDDPGACTSCATG 732

Sbjct :

HR CP+ t +C+ 1298 HRACPEHYYADQHAQTCE 1315

Score = 34 (15.6 bits), Expect = 1.3, Sum P ( 4 ) = 0.72 51'8 ( 6 2 % ) , Frame = t2 Identities = 5/8 (62%), Positives
Query:
137 CRKCRTGC 160

-

Sbjct:

CRCTC 755 CRACGTNC 762

Score = 34 (15.6 bits), Expect = 1.3, Sum P ( 4 ) = 0.72 Identities = 5/15 ( 3 3 % ) , Positives = 7/15 ( 4 6 % ] , Frame = +2

Query: Sbjct:

116 EEDSPEMCRKCRTGC 160 tt E C C GC 701 QDSEYEECMPCEEGC 715

Score = 34 (15.6 bits), Expect = 1.3, Sum P ( 4 ) = 0.72 Identities 5/15 ( 3 3 % ) , Positives = 8/15 ( 5 3 % ) , Frame = t2

-

Query:
Sbjct:

116 EEDSPEMCRKCRTGC 160 +Et -I- CR C C 1109 KEEENDECRDCPESC 1123

Score = 33 (15.1 bits), Expect 0.077, Sum P ( 4 ) 0.074 Identities = 7/17 { 4 1 % ) , Positives = 11/17 ( 6 4 % ) , Frame = +2
5

-

Case 1:07-cv-00780-SLR
HGS Full h g l h hjccr Rcpnt

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Query:
Sbjct:

278 LCLIFAILLLWKESPSLP 328
L L A

++WttS S

P

1451 LLLGAAAWWRKSRSRP 1467

Score = 33 ( 1 5 . 1 b i t s ) , Expect = 1 . 4 , Sum f (4) = 0 . 7 6 Identities 5/11 (45%1, Positives = 7/11 ( 6 3 % ) , Frame = + 1
Query:
Sbjct:

-

82 QCVQCXEGTFR 114 QC+ C G F+
1231 QCLSCRPGWFQ 1241
= t2

Score = 33 ( 1 5 . 1 b i t s ) , Expect = 6.8, Sum P ( 4 ) = 1.0 Identities = 4/8 ( 5 0 % ) , Positives = 5 / 8 ( 6 2 % ) , Frame
Query:
137 CRKCRTGC 160

C+KC

C

Sbjct:

1365 CKKCHESC 1372

>pirlJC2404IJC2404 tumor necrosis factor alpha inhibitor Length = 161
Plus Strand HSPs:

- human

Score = 66 ( 3 0 . 2 b i t s ) , Expect = 0 . 1 7 , Sum P ( 2 ) 0.16 Identities = 12/23 (52%), Positives = 16/23 ( 6 9 % ) , Frame = +3

-

Query:
Sbj c t :

30 RCDSGEVELSPCTTTRNTVCSVR 98 R GtVEtS CT RtTVC R 66 RKEMGQVEISSCTVDRDTVCGCR 88

+

Score = 34 ( 1 5 . 6 bits), Expect = 0 . 1 7 , Sum P(2) = 0 . 1 6 Identities 5/10 ( 5 0 % ) "Positives = 7/10 ( 7 0 % ) , Frame Query:
Sbjct :
6 LLFCLRCTRC 35

-

-

t3

L

CL

C++C

56 LRHCLSCSKC 65

>gi 11167929 or£ UL144 [Human cytomegalovirus]
Length

-

176

Plus Strand HSPs:
Score = 75 (34.4 bits), Expect = 0.18, P = 0 . 1 7 Identities = 12/26 (46%), Positives = 18/26 (69%1, Frame
=

+3

Query :
Sbjct :

15 CLRCTRCDSGEVELSPCTTTRNTVCS 92 C CT+C+ +V + CT+T NTVC+ 71 CTDCTQCNVTQVMIRNCTSTNNTVCA 9 6

>gi 11280119 coded for by C. elegans cDNA cmlOd3 [Ceenorhabditis elegans] L e n g t h = 392

Plus S t r a n d HSPs:

Score = 74 (33.9 b i t s ) , Expect 0.32, P = 0.28 I d e n t i t i e s = 13/25 ( 5 2 % ) , Positives = 15/25 (602), Frame = +3

-

Case 1:07-cv-00780-SLR
HGS Fl~ll Lcngh PmjffiiREpml

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Query:
Sbjct:

15 CLRCTRCDSGEVELS PCTTTWTVC 89 C +CT C EL+ CT T NTVC 41 CFQCTPCGDFMYELAKCTDTSNTVC 65

>gi1207362 tumor necrosis factor receptor [Rattus norvegicus] >pirlB365551GQRTTl tumor necrosis factor receptor type 1 precursor rat >splP229341TNR1 RAT TUMOR NECROSIS FACTOR RECEPTOR 1 PRECURSOR . (P60) (TNF-R1) ( ~ 5 5 ) . Length = 461

-

Plus Strand HSPs:

Score

= 51 (23.4 bits), Expect 0.67, Sum P ( 3 ) = 0.58 Identities = 9/17 ( 5 2 % ) , P o s i t i v e s = 11/17 L64%), Frame = +1

-

Query:

Sbjct:

61 PAPRPETQCVQCXEGTF 11 1 PtP ET C C +GTP 73 PSPGQETVCEVCDKGTF 89

Score = 38 (17.4 bits), Expect 0.87, Sum P(3) = 0.58 Identities = 6/14 (42%), Positives = 8/14 ( 5 7 % ) , Frame = +3 Query:
Sbjct:

-

Score 33 (15.1 bits), Expect = 0.87, Sum P(3) 0.58 Identities = 6/14 ( 4 2 % ) , Positives 9 / 1 4 ( 6 4 % ) , Frame
Query :
264 VLIVXCVCLQFFYC 305 ++I +CL FF C 216 LVXFLGLCLLFPIC 229

-

24 CTRCDSGEVELSPC 65 CT+C G +S C 59 CTKCHKGTYLVSDC 72

-

= +3

Sbjct :

>gi1342385 metallothionein I [Monkey sp.] >gi138124 metallothionein (1) [Cercopithecidae gen sp. I >pir l A03273 ( SMMK1 metallothionein 1

.

-

green monkey ;l~plP02797lMTl_CERAE METALLOTHIONEIN-1 (MT-I). Length = 61
Plus Strand HSPs:

Score = 43 (19.7 bits), Expect = 0.97, Sum P(2) = 0.62 Identities = 8/23 ( 3 4 % ) , Positives = 13/23 ( 5 6 % ) , Frame
Query:
24 CTRCDSGEmLSPCTTTRNTVCS 92 CT DS + + CT+ + + CS 13 CTCADSCKCKECKCTSCKKSCCS 35

=

I-3

Sbjct:

Score = 37 (17.0 bits), Expect = 0.97, Sum ~ ( 2 ) 0.62 = Identities = 6/11 ( 5 4 % ) , Positives = 6/11 ( 5 4 % ) , Frame = +2
Query:
Sbjct: 128 PEMCRKCRTGC 160 P C KC GC 38 PVGCAKCAQGC 48

>gill141753 p55 TNF receptor [Sus scrofal >pirlJC43021JC4302 tumor necrosis factor receptor p55 pig Length = 461

-

Case 1:07-cv-00780-SLR
HCS Full Lcnah Pmjccr Repmi

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Page 18 of 84

Plus Strand HSPs: Score = 70 (32.1 bits), Expect = 1.2, P = 0.71 Identities = 12/23 ( 5 2 % ) , Positives = 16/23 (69%), Frame = $3
Query: Sbj ct :

30 RCDSGEVELSPCTTTRNTVCSVR 9 8 R + +VE+SPCT R+TVC R 106 RSEMSQIEISPCTVDRDTVCGCR 128

>gi1904971 75kD TNF-BP [unidentified] Length = 392

Plus Strand HSPs: Score = 62 (28.4 bits) Expect = 1.8, Sum P(2) = 0.84 I d e n t i t i e s = 10/24 (41%), Positives = 15/24 (62%), Frame = +3
I

Query: Sbjcr:

Score 35 (16.0 bits), Expect = 1.8, Sum P ( 2 ) 0.84 Identities = 7/18 (38%), Positives = 8/18 ( 4 4 % ) , Frame = +1 Query: 85 CVQCXEGTFRGRRFSXDV 138 C C GTF S D+ 91 CKPCAPGTFSNTTSSTDI 108
+2

-

27 TRCDSGEVELSPCTTTRNTVCSVR 98 +RC S +VE CT + N + C + R 28 SRCSSDQVETQACTREQNRIC!fCR 51

-

Sbjct:

Score = 35 (16.0 bits), Expect = 2 .l, Sum P(2) = 0.87 Identities = 7/18 ( 3 8 % ) , Positives = 9/18 (50%), Frame

Query:
Sbjct:

104 APSGEEDSPEMCRKCRTG 157 A G E S +C+C G 80 ARPGTETSDWCKPCAPG 97

>gi1339758 tumor necrosis factor receptor [Homo sapiens] >splP203331TNR2_HUMAN TUMOR NECROSIS FACTOR RECEPTOR 2 PRECURSOR (TUMOR NECROSIS FACTOR BINDING PROTEIN 2) (TBPII) (P80) (TNF-R2) (P75) (CDIPOB). Length = 461
Plus Strand HSPs:
Score = 62 (28.4 bits) , Expect = 2.2, Sum P (2) = 0 . 8 9 Identities = 10/24 ( 4 1 % ) , Positives = 15/24 ( 6 2 % ) , Frame = +3

Query:
Sbjct:

27 TRCDSGEVELSPCTTTIWTVCSVR 98 +RC S +VE CT +N +C+ R 98 SRCSSDQVETQACTREQNRICTCR 121

Score = 35 (16.0 bits), Expect = 2.2, Sum P(2) = 0 . 8 9 Identities = 7/18 (36%), Positives = 8/18 (44%), Frame = +I
Query:

Sbjct:

85 CVQCXEGTE'RGRRFS*DV 138 C C GTF S D+ 161 CKPCAPGTFSNTTSSTDT 178

Score = 35 (16.0 bits)# Expect = 2.5, Sum P ( 2 ) = 0.92

I

Case 1:07-cv-00780-SLR

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HOS Full Lcnglh P j RcpM mm

I d e n t i t i e s = 7/18 ( 3 8 % ) , p o s i t i v e s = 9/18 (50%) Frame = +2

Query:

104 APSGEEDSPEMCRKCRTG 157

Sbj ct :

A G E S +C+C G 150 ARPGTETSDWCKPCAPG 167

>gi 1189186 tumor necrosis f a c t o r r e c e p t o r [Homo sapiens] >gi 11469541 tumor n e c r o s i s f a c t o r receptor [Homo s a p i e n s l >pirlA353561A35356 tumor necrosis f a c t o r r e c e p t o r type 2 precursor - human >gi1235649 tumor n e c r o s i s f a c t o r receptor, TNF receptor=75-kda [human, P e p t i d e , 439 aa] (SUB 23-461) > g i ) 8 2 5 7 0 1 p75 TNF r e c e p t o r [Homo s a p i e n s ] {SUB 1-37) Length = 461

Plus Strand BSPs:
S c o r e = 62 ( 2 8 . 4 bits), Expect = 2.2, Sum P(2) = 0.89 Identities = 10/24 ( 4 1 % ) , P o s i t i v e s = 15/24 (62%), Ftame = +3

Query:
Sbjct:

Score 35 (16.0 bits), Expect = 2 . 2 , Sum P(2) = 0.89 Identities = 7/18 ( 3 8 % ) , Positives = 8/18 [ 4 4 % ) , Frame = + 1

-

27 TRCDSGEWLSPCTTTRNTVCSVR 9 8 +RC S +VE CT +N +C+ R 98 SRCSSDQVETQACTREQNRICTCR 1 2 1

Query:
Sbjct:

85 CVQCXEGTFRGRRFS*DV 138
C

C

GTF

'

S D+

Score 35 (16 .O bits), Expect = 2.5, Sum P (2) = 0.92 I d e n t i t i e s = 7/18 L38%), Positives 9/18 (50%), Frame = +2 Query:
Sbjct:
104 APSGEEDSPEMCRKCRTG 157

-

1 6 1 CXPCAPETFSNTTSSTDI 178

-

A G E S +C+C G 150 ARPGTETSDVVCKPCAPG 1 6 7

>gi1333519 crmB [unidentified poxvirus]

Length = 355 Plus Strand WSPs:

Score = 68 (31.2 bits), Expect 2.3, P = 0.90 I d e n t i t i e s = 1 1 / 2 0 ( 5 5 % ) , Positives = 13/20 ( 6 5 % ) , Frame = +3

-

Query:
Sbj ct :

30 RCDSGEVELSPCTTTRNTVC 89 RCDS +VE C TT N +C 89 RCDSNQVETRSCNTTHNRIC 108

>gi/642392 ORP Cl [Banana bunchy top v i r u s ] >gi1642395 ORF C1 [Banana bunchy top v i r u s 1 Length = 4 8

Minus Strand HSPs:
S c o r e = 3 4 (15.6 bits), Expect = 2.8, Sum ~ ( 2 = 0.94 ) I d e n t i t i e s = 5 / 1 1 ( 4 5 % ) , P o s i t i v e s = 6 / 1 1 (54%), Frame = -2

,
HCS

Case 1:07-cv-00780-SLR
I1 Lcngth Pmjccr Rcparl

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Filed 02/29/2008

Page 20 of 84

Query:
Sbjct:

358 PHHWXKQMPSR 326 PHtH P R 9 PHYHSDHRPRR 19

Score = 33 1 1 5 . 1 bits], Expect = 2.8, Sum PI21 = 0.94 Identities = 6/13 ( 4 6 % ) , Positives = 11/13 ( 8 4 % ) , Frame

-

-1

Query:
Sbjct:

134 SQENUPRKVPSS 96 S ++L+PR+tP S 20 SFDHLVPRQLPPS 32

>gill89205 nerve growth f a c t o r receptor [Homo sapiens] >pirlA25218IGQHUN nerve growth factor receptor precursor, low affinity - human >spIP08138INGFR_WUMAN LOW-AFFINITY NERVE GROWTH FACTOR RECEPTOR PRECURSOR (NGF RECEPTOR) (GP80-LNGFR). >gi 1 189207 nerve growth factor receptor protein [Homo sapiens] {SUB 1-22} Length = 427

Plus Strand RSPs:
Score = 51 (23.4 b i t s ) , Expect = 3 . 2 , S m P(2) = 0.96 u Identities = 9/25 (36%), Positives = 13/25 {52%), Frame = +3
Query: 15 CLRCTRCDSGEVELSPCTTTRNTVC 89 C C C++G + C tNTVC 122 CEACRVCEAGSGLVFSCQDKQNTVC 1 4 6

Sbjct:

Score = 45 (20.6 bits), Expect = 3.2, Sum P ( 2 ) = 0.96
Identities
Query:

-

6/10 (60%), Positives = 8/10 (80%), Frame = +2

Sbjct:

185 DCTPWSDIEC 214 +CT W+D EC 179 ECTRWADAEC 188
(42%), Positives = 7/14 { S O % ) , Frame = +3

Score = 36 (16.5 bits), Expect = 3.7, Sum P (3) = 0.98

Identities = 6/14

Query:
Sbjct :

24 CTRCDSGEVELSPC 65 C C+ GE PC
44 CKACNLGEGVAQPC 57

Score = 36 (16.5 b i t s ) , E x p e c t = 3.7, Sum P ( 3 ) = 0 . 9 8 Identities = 5/14 (35%), Positives = 9/14 ( 6 4 % ) , Frame = +1

Query:
Sbjet :

70 RPETQCVQCXEGTF 111 + T C +C +GT+ 141 XQNTVCEECPDGTY 154

Thu May 29 15:23:24 EDT 2003
Gearge Komatsoulis 05/29/2003 15:23:24
~ e s R ~ U 0N~ ~e ? ? u Z 1 t

PI

%$ I% :

In

[~Evz'I%?~inefl

H t S Proteln PmJscts Version 2.0

Case 1:07-cv-00780-SLR

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P Dism'bution Lia for Onobar 18.1995 Team M d n s w
SB
Edward R Appelbaum

S

B

.

M.Burke E Dul Fdupard G M R Don E Grimold
Jeremy A Hacrop Yen Stn Ho-1 Mark R Hurle John CLet S W . D Lw - ... ,. .Gordou P Moon Terence Porter Mmjula P Reddy

-

Sherin S Abdcl-MtNd Christine hrl Debauck Giora ZF e u m i n George I Glover MaxineGowm C Preston Henslc)i Zdenka L Jon& Krisry KWy-1 Loretta C McCauley

. .. .. . - .. . b ~ ~ ~ M = k .e y . -.. ....
Andrew J Nichols Martin Roscnberg ~ l l a R ~hauman' n Theodore J Torphy

.- .

-.- ._

..

.,

Carol Silv-

Kong B Tan Ping Tmi-1 X.Wmg Perm R Young T.L.Yuc

Documwtt Management UW 2309

HGS
Reiner Genn Jian N i
Guo-Liang Yu S s Lackey um

Case 1:07-cv-00780-SLR

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h
W *
F

c

19

Attendee:

SB: E.Appclbaurn, M.Burke, E.Dul, J. H m p , M.Hurle, Z Jonak, L Krikly, J. Lee, S Lyn, G.Moore, M.Reddy, K3.Tan, P Tsui, A. Truneh, P Young, X . . . Rfang,T L Yue i HGS: R.Gentz, J. N ,G-L Yu,

P.Young presented a critical path depicting key components a stratem for identification ofgene function for T F Nrtlatcd gens (overhead P I . Y)
., , ... .. .,. . .
, ,.

h'l. Hwle reviewed thc sequences of 8 navel T h l like and 3 TNF Illrt gmes :. (o\lerhea& mid); .. - .. --. .- . - .. . - . -- .. . - ----.,. --- .-- ... . . . -... ....

-

.-..

..

- .. .

J. Y reviewed for the p u p the current members of known TNF and TNFR i supedamily*a well as the recently described associated proreins. Mimy of thc s known proteins are present in tho HGS database as full length geaes. The rat Fas ligand like molecule has been expressed in E. coli and polyclmal &tibody is generated. The second TNF like Iigand, termed ThFy or EDAP, is being pursued by HGS as a novel antiviral agent This molecule has been expressed and pmified at HGS. The third TNF U e ligand has been shown to be expressed ia most tissues with tbc highest expression in the hcah O the eight novel bER like pro* f one appears to be a soluble q t o r to w i h antibody has bca made. HGS is mart hc interested in working on the ligands than the receptors.

RE, revtiwed the tissuelccU distribution of the 5 5 hostiattresting TNFfMER Tan genes. The resulrs art summarized in overbeads K 1-8. Mosl of this genes E TR3 and TL1)appear to be primarily expressed in hunatopoietic cells while TRl message was found in ari osttoclast d line. A larger size message for TR1 was l also found in a hwnatopoieticprecursor and a T cell line.

m,

P. Young/S. Lynn provided an update on the efforts of cloning aud otpressing wha is now hown as TR2. Expression of the human IgGl Wsjon protein mammalianells is successful. Monoclonal antibody production has been initiated

E Applebaum f t p t d the expression of the rat Fas ligand homolog i two fusion . n
conmcrs as tpitope tag@ proteins.

Case 1:07-cv-00780-SLR

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A number of issues surfaced during the ensuing discussion period and they w listed below with solutions and& action plans:
1 N-Iniure . Given that t m art multiple designations of the original EST6 by HGS and h subsequent nameslnurnbers given by SBlATG and the increasing number of interesting rnolecuks, it has become apparent&at an mXed nomenclature s h d d be established. It was aged a11the novel TNFRKTFR relattd I k , genes will l n4 l have T as the hm prefix ro denote their homology to these supufmilics, foUowed by L or R to denote membership to the ligand or fcceptor superfamily,followtd by P unique number for each unique full lcngrh noveI squcnce. S p h variantswill be sub-classifred with m alphabet; e.g. TR2a for -49 (see also post meeting .~~a~lcsl~~~d2iqAT1-~for.det~Is)- - . . . ....-.-.-.---... -----,.-.---+-- -.-.--.-,..-....-. ..... ....I....

_ . . .. ....

f

--.-

'

2. Focus HGS will focus on ptitativs ligands and SB on tht receptors

3. Sequrnn emrdd~erences benvien HGS and SB Consultationamong the two pascis is recommcn&tcd befon any work is to be done. Any discrtpdes in sequence that may have impact on patents must seek Icgal input.
4. Spliced variants

Whether spliced variants are meaningful targets would rtq& by PCR of the in- and TNT mts should be conducted
5. Retaganfor u~thunge Ctlmntly,the followiug tool reagtnu arc availahlc:

~

ec o rn f j n

SB:TEU-18
HGS: 7L1 and TRI pmtcb and autiscra to TL2 and TR1 .
6. Coordination o expressione . m f

w expressing all TR moloeulcs and same TL pro* HGS will express all TL proteins
SB will con=-

Established h u ~ HGS; h

Case 1:07-cv-00780-SLR

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a Alan Porter (U. i p a p e ) on TRZ (signal transduction) and TRAP dopes (2 S hybrid screen)
b. Kwon (Jhdiana U) on T2 (genomic cloning and spliced variant) . I2

I

Anderson) an TRI, TL1 etc (biologid effects, functions and effect on tumor ctlls)
a. Aggwal &ID

b. D o m (Lndiana U.)on novel TRAP moltcules
Ue nd

...._._. ,^.",...._. _..__ ...

.I

.I.._..... I

..

. . -. .. .... .... .-... ..
f

l-

......l-l-.,

.

--

a. Beutler (UTSX3 on navel TRs (signaling mechmfsms)

Case 1:07-cv-00780-SLR

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Critical path

a

IIn vitro biology I{ proteincellcellprotein + cell + + clone rodent cDNAs
if human tools do

Checkknown ligds/receptom Novel ligand

not cross-species

Case 1:07-cv-00780-SLR

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- .r-(

, o 2 s Qr N g z eg ~ $ g ~9 v o o o k tt -3.? -3 5 3 z e s E
%L*.

nnh

-

U P I W

r v w u

$ 3 ~ & 3 =

E

Case 1:07-cv-00780-SLR

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Case 1:07-cv-00780-SLR

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Case 1:07-cv-00780-SLR

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Novel TN R Receptor- Related Molecules

TNFR-L 1

TNFR-L2

HITEN6 1 23 1556

HTXEI33 5 10304

-

HSAVO# 664257

(41BB splice)

Case 1:07-cv-00780-SLR

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HLHAB4B HTOAU65 HT1S 852 HTOBH42

HHFFi79 (HBNA731) (HT4S 180)

HMS8259

(HROAQ75)

(HFNBH3]

All solid lines have sequence in common Sizes of splIce insens are shown inside oval-shaped symbol Project IDS for full length sequences or (individual ESTs) are shown

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Novel TNF-Relabed M6lecules

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I

' S ~ ~ aofr Receptor y Expression
Sequenced HTOAU65 (103902)

.

Named this TNFRL2 - TNFRL2 differs from patent
Position 41 (Ser to Phe)
. -. .

.-..

.- . . - .

t. .l?~si.timl? (Ly$ ~~.sQw.EsTs).*-. &.kg _.-. one silent change -

....-.. .-.,.,

.-

-,.-.

Cloned into mammalian expression vector COSFc - Re-engineered start codon

Expressed Human IgGl Fc-fusion TNFRL2
- COS cells

Monoclonal antibody production initiated
Sequenced HSABH13(195 197)

-

Named this TNFRCl
Sequence different from patent C 1077 missing Altered C-terminus and an I I aa longer protein

..

-.

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Case 1:07-cv-00780-SLR

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TRWSIATP of; t f ? . e n:lsq cleck: 9389 f m n : 9 to: 857 grclerrted symbcls L to: 203. TNF receptor like 2 sequence as copied Lron HGS full l-gth reporc filename 103902.000, KGS code 203902, Projecr I?:WlSB52 1SFORS.T of: Tphlfr2.Seq check: -1 fzom: 1 to: $81 M y 16, 1995 13:54 a

(No d;oczxiencacion)

...

to: T-,5rlZfclink.?egr check: 9981 f x a : 1 to: 432 W S L Z I T E of: mfrl2felink.seq check: 768 &on: 665 t : 1960 o generated symbols 1 to: 432. Tnfrl2iclink is se-enccd 103902fc (ECOFU Asp718 o i Tafrl2f ceoatigl. set$ i n Casfcia. coS?clhik is sPcrlcos4 with Ehe a g e C a O U redon of. hum^ X* irse-:& h place of the r?eR eDNA and a 27bp l i n k e r b m o d ugstztm

...

1
c-heck:

c ~ ~ l l p a t i s o table: Geneoredisk: fGcgcore.Data.Ehm8ata]Nwsga~ep.~ r. 1254 *.
Gap Weigh=:

-

3.000

........

Lezsc'n Weigkt: 0.100

.....

. I

...........
ZlS.8 L.L16

Average ~atch: 0 .5i0 Ave-zzge Mimat&: -0 3 9 6
.--1

..........

.-3 1-.-.

Quality:

Satlo:

?ercex Sidlaricy: 8C.IC5

?e:cat

L e ~ l e : 439 Gaps : 6 fbenticy: 76.812

..... .....-.. -..-.. *_.._ ........... ........ ... .... b..

-

-

_

_. . .

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 35 of 84

Case 1:07-cv-00780-SLR

Document 24-2

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Page 36 of 84

Receptor-IgFc fusions

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 37 of 84

COOMA&

ST-D SDS-PAGE GEL ANAL'YSIS OF 8UG TNFRL2Fc UNDER REDUCING AND NON-REDUCING
uan

-. .,..---.. ..

I . .

-

,_

..-.-..- . ..- .

--.-*

-

- - . --. -..-.- . . &&'ed..--. .... : ...- ....,.-..-.. .,..... -.. .. .. .." . m
.-,

-

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 38 of 84

B

~ of: T Stnfrll.Seq check: 8473

from: 1 to: 1173

RDFoF(L~AT of: ~tnfrlikel-Sep check: -1 from: 1 t o : ,3173 k y 9, 1995 10:ZB k Co&ing resfon of soluble TNFEI gulled from ATG f u l l leagth report 80245.000, gr0je~C H W U 3 ( f u l l length clme = 195197)

m:

w: 195197contigedtext.Se~ check:

4750

ton: 1 to: 1850

..

. -. -

Qurlicy: 1L66.7 Rztio: 0.935

Petrceat SWlcrity: 100.000

1173 Gaps t 1 Percent Identiry: 100.000

Length:

-

U70 A

I i l l l l l l l l l I I l l l t l l l l l l t l llll1lllllllllltllIlltll
* ] ) .

1418

Case 1:07-cv-00780-SLR

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Filed 02/29/2008

Page 39 of 84

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 40 of 84

g-eracad

SLAT^ of: srafrlikal.seq symbols 1 t o : 391.
(Na bocmentation)

.eck: 8473 4rm: 1 t : 1173 o
9, 1995 10:28

REFO~T of: Smfrlikel-Seq check: -1 from: i to: 1173 May

Stafrlikel.pep L n * : eg.
1 HEZLCCRLV

351 May 9. 1995 16:13

-8:

P check: 8773

..

FmrSim QETPPPKYLR IIEVSH~IJ. ~ X P P G I I I .

51 KQIICTAS;WXT VCAPCPDHYY !PDSWXTSDEC Lye-

QnrPQ-

wSmlZ

of: 195197co~tigedtaxt.seq check: 4750 fro~:320 to: 152j
1 to: 402.

generated - 1 0s

195197coari~edtext.F Length: C02 Ocfobex 17, 1995 1 : 1 70

T p : P check: S l a t ye

..

3c&~t'

B

E5N'EZLCCRLV EZDISIh7kTT QET??PPKXLR YD%ETSIiQLLCDKCPFGTfL VCAPCPJNYY TD!~QH&EC

51 KQ:EC?!?'T

LYCSIVCP;EL QYVKQMNRT

Case 1:07-cv-00780-SLR

Document 24-2

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Page 41 of 84

BESTPIT of: Stnfrll.Pep
~ ~ S W T E of:

check: 6773

from: 1 to: 391

stnlrlikel.sep check: 8473 from: 1 to: 1173 check: -1 ixora: 1
to: I173

ge~~eratrsd symbols 1 to: 391. IEEWX~P of: stnfr1ikel.Seq [NO 60cmentatic4

My 9, 1995 1 0 : 2 8 e

t : 195197contigedtext.Pep thackr 5187 o

era:

1 to: 402

m S L A T E 01: 195197ccntigedtext.r~check: 4750 from: 320 to: 1525 generatea symbols 1 to: 402.

Gep Weight : 3,000 Length Weights 0 .I00

Average Match:
Average

0.540

k&smatch: -0.396 Lens&:

Quality:

543.8

Ratio: 1.424 Fem~entS h i l a x i t y : 95.812

400 Gcgs : 1 Percent Z d a n t i t y : 94.764

2sl F

251 F Q U K L W R H ~ D N K K X I P D T O M : E N S V q R H I G 00~ 3~

Ill llllllllllllllllllt llllllllllf IIIII1IIIIIIIIIlI

Q

~

~

~

~

~

M

P

M

~

~

D

~

V

R

R ~ O O .~ I

Q

D

~

~

S

V

~

~

X

G

~

351 USKWdPPTIXZSESKED.

.................HQVPSQLNNVQIVS 382 .X I..E U T I = L ~ S ~ Y Q . U , ~ ~ C N W:Q 400 ; C S C :..!::.l.l 351 ~ S K ~ F P ~ S I 4 SW
Il1Il1II..-

Case 1:07-cv-00780-SLR

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Ligands
1. Fas lipand-like
I, Protein
v*as purified from

HTPAN08
E coli. expression system. .

11, Potyclonal antibody
*..,..
*

was made.

. . - -

III, Expression and purification .. ._......... ,... - - from baculdvirus-... in .. . . . ...-. of protein is ...., .. . _ ... ..... ... ....-.. -.- ...-.. -..--..-...... progress.
,_

*

11.111..

VI, Expression in COS and CEO cells is in progress.

V, Functional study is in progress,

Case 1:07-cv-00780-SLR

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I, Two new constructs with different El-terminal sequences [no tag) were

made, and expressed in E coU. Protein was puriffed. .

1 1 Polyclonal and monoclonal antibodies are not available a t present. 1,

aress. VI, Expression in COS and CHO cells is i pro, n

V, Expression level of protein in bacu'fovirus is low.

Case 1:07-cv-00780-SLR

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TNF Ligand, Receptor and Receptor . ..... A-is.6kiaite'd" SE'c'-t-6 GF6ffgg ".,....,..ds
*.
fd;r.

"

-

.".,

I, Overview
11, Class I TlYF Ligand, Receptor and Receptor Associated Factor Superfamily Members in HGS Database

III, Novel TNF Ltgand, Receptor and Receptor Associated Factor Superfamily Members in HGS Database

Case 1:07-cv-00780-SLR

Document 24-2

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Page 45 of 84

r;iPands
1 TNFa :

Receptots

h c e p tor Associated Factors

-

TNFRl

FADD (MORTI), TRADD, TRAP-I, TRAP-2, TRAK, RIP,

2,

LTa

TNFR2

EB16 (TRAFIX TRAF2 (TRAP-3).
TRAF3 (CD40bp, LAP-1, CRAF-I,

CAP-I)

4,' FasL

Fas (APO-I)

FADD (MORTI), TRADD, RIP, FAP-I, FAST

5, CD40L

CD40

TRAR (CDlObp, LAP-1, CRAF-I,

CAP-1)
TMF2 (TRAP-31, EB16 (TRAFl )

CD30 CD27
4-1BB

OX40
NGFR PV-T2 (MyxomaT2) PV-AS3R ECPl Cowpox CrmB

VVsalFl9R
SFVT2

G4R C22/B28R G2R

Case 1:07-cv-00780-SLR

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Page 46 of 84

TNF Signal transducers
I, Receptor Associated Factors:
I, EB16 (TRAFl),
2, TRAPS(TRAF2),

3, TRAF3 (CD40bp, LAP-1, CRAF-1, CAP-1, TRAFP)
4, FADD (MORTI), . ...,.. 5, TR4DD;"
..
,

_.

. .... ....-

.

. - . 3 " . -----" . . - . - .1..... .

6 , TRAP-I,
7, TRAP-2,
8, RIP

TI, Protein Tyrosine ~hos~hatas'es :

III, Protein Tyrosine Kinases:
I, TEZAK
3 -9

FAST

Case 1:07-cv-00780-SLR

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Page 47 of 84

. . ... .... ..-.. . - ..

Class ' ~ ' T N Ligand, Receptor and F

.-.... .-... _... "..-..- , .

--- ._." ...-.-- ._" ..-..* ... ..-."
.*

-1

.... . - ..-.-....
1 .

.

Receptor Associated. Factor Superfamily

Members in BGS Database

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 48 of 84

Ligands

Yes, Full length,
3,

LTa

Yes, Full Iength,

. .*.. ... ,... "

3,

w

,

...

..

4, FasL

. "... .... . .* ...,..*.*. ..... Yes, Futl length,
>

Yes, Full Iength,

7, CD37L

Yes, Full length,

Yes, Full length,

Case 1:07-cv-00780-SLR

Document 24-2

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Page 49 of 84

Rece-ptor Associated Factors

-

TRAFl(mouse)

Cell Aug. 26 1994

EB16 (human)
ZlATFD065 (HEMCL4 1 )

Nov. 28, 1994 (Submitted), CellFeb. 10 199$
Identified durinf S e ~ t .1994

...

-

TRAP3 (TRAF2) _,"._, . ..._____... .-.- .. ... --. -.--.--.....-... .. _ . 2, .___, .._. ... ... ,_ * ._. .__ ,.._._-"__
,

_

-,

_

..I ..

.----. .. ..-. -. ." ..
l . . t

l.l.

--.

TRAF2 (mouse)

Cell Aug. 26 1994

TR4P3 (human) H W M I

Mar 3 1995, deposited in GenBank, unpublished 9 9 4

3, TRAF3 (CD4Obp, LAPI, CRAF-1, CAP-I)

TRAF2 {mouse)
LAP1 (human) CRAF-1 (human)

Cell Aug. 26 1994

NOY.28,1994 (Submitted), Cell Feb. 10 1995
Science 10 1995

CAP-I (human) STXFI28

FEBS-Lett Jan 23 1995
Identified durina Sevt. I994

4, TRAP-1

Yes, Partial,

HMEGG76

5, TRAP3

Yes, Full Iength,

HSLCLl2

Case 1:07-cv-00780-SLR

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Page 50 of 84

Receptors
1, TWRI
3, TNFR2

Yes, Full length,
Yes, Full length,

3, TNFR-RP (LTPR) Yes, Full length, . . . . . . . . ...................... .-... ...................
-II

I

..

4, Fas CAPO)

Yes, Full length,

5, CD40

Yes, Full length,
Yes, ,-1280bp

6, CD30
7, CD27

Yes, Full length, Yes, Full length,
Yes, Full length,

8, 4-1BB
9, OX40

20, NGFR

Yes, -900bp

Case 1:07-cv-00780-SLR

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Page 51 of 84

Receptor Associated Factors
6 , FADD (MORTl)

Yes, Full length,
*

,FADD
MORT1

Feb. 23

1995 (Submitted) Cell May 19, 1995

Jan 30 1995 (Submitted) JBC April 7, 1995
,_
--..--....---.......I-.

13Zi'lrCS86 ldent ified bv death domain .Tan 20 I995 ,_... _ . __ . ._",_. _..^_ . .. ..._._ _ _ .-.-... -. ... . ...-- .... -.-.. ...7, RIP
8,
??

..f. .--.....--..-

-I.'

TRADD

Yes, FuII, Splicing
Yes, Partial,
??

9, FAP-I,
10, TRAK

11, FAST

Yes, Full length,
Aug. 22 1995 (Deposited i GenBadK, unpublished) n

12, MLN62

PTXA F08 IHRGBO64 lldcnt(ficd on Nov. 1994

Case 1:07-cv-00780-SLR

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Page 52 of 84

Novel TNF Ligand, Receptor and
..
I

... . .. .. ..
C

I .

..

I

-.

>-.

..... .- . . -.... .

. .
I . . .

-

.

. --*

_.-...** ..__...

_,,-

_ ...

. -....-.-... .
+ .

Receptor Associated Factor Superfamily

Members in HGS Database

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 53 of 84

ugands
I. Full l e n ~ t hthenes:
1,
F ~ S iigand-like

BTPAN08 BUVE091

2, TNF-like

(Th'F gamma) (TNF delta)

3, TNF-like
4, TNF-like

HLTBT71
RPDD012
. , ...-..-- -- b

(TNF epsiIon)

- .. . - . II...G enes are not full lenwh--.-. ...--.......... - ...,. ..-.. -- .- - - 1, Lpmphotoxin-beta-like
2, Fas ligand-like

HTGAKlO
HSBAG72

3, Fas ligand-like
4, Fas ligand-Iike

HEMBK77 HBNAZ12 HATAF70
'

5, Lyrnphotoxin-Iike
6, Lymphotoxin-like

KlESCLl9
HKPABS4
xrIEIpFK35

7, CDSOL-like
8, CD30L-like

Case 1:07-cv-00780-SLR

Document 24-2

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Page 54 of 84

I. Full length genes
1 ,

TNFR p73-like

2,

TNFR p75-like
TNFR p75-like

3,

4, TNFR p75-Iike . . . . . . . . . . . . . . . . . . --........... ""._ -....*. ..- .. -.-._.-

11. Genes are not full length
1,

TYFR p55-like

2,

TXFR p75-like

3, TXFR p55-like
4, OXJO-like 5, OX4O-like

6, Fas-like
7, CD40-like

8, CD40-Iike

WCEFL28
HDSAPSO
BOFMB09

Case 1:07-cv-00780-SLR

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Page 55 of 84

Receotor Associated Factors
I.
7

FUII

length genes:

1, T R A F ~ (TRAP-3)
-9

TRAF2-like (MLN62)

3, TRADD splicing variant

6, FADD

11. Genes are not full leneh:
1, F.4DD-like

Case 1:07-cv-00780-SLR

Document 24-2

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Page 56 of 84
Page 2

Alignment Repon d T N n HGS Far an, using C l u d method w i PAM250 residuew i h die. eg Monday, bdqber 16.1595 1&4T AM
- V A H - V Z I - - p - - 0 - - - L L - - - - - - W Z 4
I

- L K R G R A L L A S C Y Majority

Case 1:07-cv-00780-SLR

Document 24-2

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Page 57 of 84
3,

ATignmcrU Report olM R HGS Fas arb I 1 Clushl memod wilh PAM2!50 residuewighI Monday, 0:lober 16.1995 l41 Ah4 . a4 - P A S S C G T Y P O A Y K - V - L
I

Paoe 3 wHajoriey

Case 1:07-cv-00780-SLR

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Page 58 of 84
r.
Page 1

Phylogenetk tree oIMn HOS Fas a#. Mond~y, W'Wr16,1995 10:40 AM

1Clustal methodwilh P A W 0 residue wg ' tM

Case 1:07-cv-00780-SLR

Document 24-2

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Page 59 of 84

PhyIqmetk h a of TNFL H GS al& usin Mondey, 03o5er 16,1935 5:49 PM

JWmhed with P M S Omidue mi# bbl

Page 1

Case 1:07-cv-00780-SLR

Document 24-2

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Page 60 of 84

1

I

1

-

AQnment Report of DeathDomain Alig, ush Cluttal mehodwith PAM250we rdDb. weight

i
I

Tuesday,Ocfober 17, 7995 124 PM
- - - - - - V I D E - - - - - - - G - - W X E P A R E t - - I - - G L s B s ~ x mjarity
I

Page I
I

aecoradm 'Dlcozation # l aShade Ivirh s o l i d bright ~.llowlrccihas chat rnatch the : C O a S M ' 2 ? r -1y.

Case 1:07-cv-00780-SLR

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Page 61 of 84

Fhylogenetiotree of Death DwmlnN g Tuesday, Oelober 17,lQ95127 PM

using J. Heh method wllh PAMZSO w

e wt wife. , r

paw'

1

1

TRADD
Reaper

Case 1:07-cv-00780-SLR

Document 24-2

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Page 62 of 84

' Alignment Reponof TNR h HGS Ali, wir

Yusld method wfth PAM250 residue wight W Monday, OabSer 16,1995 7354 PM H L G - - - - - - - - - L L W - P L - L G L - L - L A A S - - - P Q - - P - - - -5oyity
I
I I I

page1

10

20

30

h a 2 7 ?roteta h L % t U Pzacmin h NCFR Llal 2 0 e n ~:L h OX41 Prorcin h. lWPR I Qrotdn h TW~R Rotoi~ IZ h t W O ProtrL b C W O Pmteia h 4-18s Protein b Fas protein
Itl'lsBSa
uEET79Y;X =5z5 9XX

-

B m lY C S uI 1

h ' ' e 2 7 pze-,e$a" ' h L'htaA Prcreia h tlrl ?:oteh h DXCO I o c : zsi:
h
Z Pora : ::

-

"

'h t:.ZR =I ?cm: r:?: b C 3 3 P=o;+i3 h c x s p:o:tr+ b 4 - 1 s P=oreia h fss ~c;ei= %7:s=5lm
-9XX

Case 1:07-cv-00780-SLR

Document 24-2

Filed 02/29/2008

Page 63 of 84
Paw 2
mj~zLcy
I

Alignment &epob olTWFR NOS A usi ;latal methad w ~ ~ ~ ~ 2 5 0 - la^ t~ h Monday. Odober 16,1985 7i Phi E4 ao----xQACTETOBTVCE CRPG-YCA-- s - - - - c I

-

--

EPS A P

- 7 . -

--* - -

R QvE
S E

W S EDLFQ
* - -

T - VIE-

RVF R T P V L

------- ---- h - - - - h TWFR Protsin --- - - - - t - - - - h Pas &-rein Protein --h
0x40 P:oecla

X

H

4-1BI

C

_

-

-

C

-

-

-

LSD
LNG W D P O G X S A P D Q W!259XX E HSISlil3KK

----

------

-----

V A P C T L

Case 1:07-cv-00780-SLR
..

Document 24-2

Filed 02/29/2008
wg t W ih

Page 64 of 84
Pass'

'

. Phylogenektree d TNFR h753SS All. uskn C W l methodHilhPAb4250 H C Monday. October 16,1995 PM

-

h NOFR (la) Protein
h OXQOP W i n kCDnPrmein hMFR I P o e n ll' h Fas p t e i n h4-158Protein
HMSBZ59XX h L-taR Protein h CD40 Pmtsin h TNFR II Protein HSABH13XX

.

Case 1:07-cv-00780-SLR

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Page 65 of 84

~1?153132i?irTT".1?3,1 rmo: nt==osfr fector rcct$=or cl 507 a.01-20 5 mIX55i38 !.W55:~l 355 z u w r ntcrosis Eac'ccrr cecrp.. t L 106 %.Be-17 c s ~ 1??6jl2i l v m 1 tumor r.ecsos~s s i i R factor receptor I~httusn ~ m e p S ~ ~ s ] SIGgRTT1 tt~cl10: r.eczosis f accar receptor type : prt%-scr set kzgth r 4 6 1

...

.

-

S C ~ E S= 70 (22.2 b i t s ) , W c S

Ilr:i:ias

= 8.Dc-20. S w P l S l = B .Oa-20 = 13/32 14051, 2osi;lver = 1 3 / 3 2 (55%). ? : a = + :
**-----

- Q ~ r r - .-..ss ,9.G-Q?cz0 :-

9 2= :

:

+GZ'S-C 54 KGZLVSX?S~5YEZJ~X4E;SQKn' 95

CatsmvC 3 -CtT+TPL+K<

m2221-C- -".'""-" "'
'---" ' '

-

'-'--'-

- -

,.-

&it=:

C i f L ~ ~ ~ P ~ ~ ~ ~ A 47s Q S A V P V *? P L ' W v 4s ? 133b?ilT?A?ivXIQ?355

Query:

Sbjet:

2 L 5 C S X V ~ T R ~ 2 6 5 C +T C C G+F+ 358 ~ X S K ~ Q O C H A G P Z ' Z 174

Case 1:07-cv-00780-SLR

Document 24-2

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Page 66 of 84

TNFR pS5-like HTTBN61
Qe? u,

%Cn--l 0 (1Sl letters1

-

C~ !Y$D!?~ 1 ~L3TPiPXL Muzinc tmoz a c o S e:ss fector XI rtecp.. g 5 ! ~ 6 0 4 6 I&KiiiSMTN?F.l Mwse Pmbz neerosi~ f ~ c r o r 8 receptor . 55.j!~59236 4 5 . E155 Yu:irre = i i i A far p55 t w r nacrosia fa.. c5!L263C9 IKiSTMFX Mcr museuius hrmoz ~ecrosis?actor Ice..

. 256 5.6e-12 156 5.9e-12 . 256 6.Oe-12 . 256 6.3e-12 I ti5iXS7745 ~~~ Sowe aWA for 55-PDa t q s o r necrosis ... 256 5.h-12 ~5 j15027.5 1 F:ui4TNm Ewan tunor necrosis faczor zscepr,?r( . . . 254 T. O e - 1 1 g 5 ~ ~ l j t 2 1 f r 1 ' 5 2 2 TEi? alpha gene. 264 l.Qe-11 ghlH33294 1 izXTNF3 E ~ f ~ t i t haor necrosis factor receptor ... .! 254 I.Oe-11 G i i ~ S 8 2 B tli k k ? m H o w sapiens turnor necrosis factor re.. . 260 1.0e-ll gbixE:1211 t: ; ~i EL^'^ t m z necrosis facror recaptar ... . ~ m ic uo 264 1. ~e-:I . ~ 5 ! ~ 5 9 3 7 j7 : P T cumclr nec=osis Zsctor 53 rareptsr (TE'X-2) ~ L . Z .
..
complete c t s . Lesgtiq = L556

2 2 2
2

2

1
1 1 1 '

-i

Case 1:07-cv-00780-SLR

Document 24-2

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Page 67 of 84

>gpl~6046B (ENSW~WPL-1 rmrrinr tumor necrosis

factor receptor 1 lMus msculus]

>
score

= 60

[27.2 hits], Expect = 0.00066.
6

Sum P ( 2 ) = 0.00066
4

Identities = 14135 ( 4 0 9 ) . Positives

19/35 ( 5 4 % ) . Fruaa

+3

Score = 37 t i 7 . O bits). Expect

-

0.00066,

Sum P ( 2 )

= 0.00066
,

(585 . sflsf . ..IZentities,_~~~?/~2., po,q&.titi~ss la-t 79tjT- .?r-..--...-.*.

=.+2 ..--.-

a-

.---.. .- -- ---......-.

Query:
Sbjct:

LO4 tLY*~?Cav?x? 139
Z Y

+ c+vP

0

325 LLrsSiCSv?A? 336

> ~ / K ~ ~ ~ S ~ ] U S % T R Z O Stumor necrosis fcctor receptor [Mus =scl?lus] ~,L
Length = 454
Seore = 60 (27.2 blta). W e c t

=

0.00066. Sum Pf21 = 0.00066

Zdentitirs = 1 4 / 3 5 ( 4 0 i ) . Positives = 19135 (54k). Braze = +J
Query:

15 V T X P K T P N H S P S S P A S ~ ~ S ~ r V X S T E L 119

+T
Sbj ct :

+P S?+S + T

GFS P

F

v ST +

264 X , T P A P ~ A F S P T S ~ F S T P O F S S ~298 P S~

Seore = 3 7 [17,0 b i t s ] , m e e k = 0.00066, Sua P(2) = 0.00066

Identities = 7/12 (58k1, Positives r 4/32 ( f S O ) , Prama = +2

Case 1:07-cv-00780-SLR

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Page 68 of 84

Plus Strmd FSPs:
Score

= 467 l129.0 bits), Expect 1.5e-34, Sum P(2) = 1.5e-34 ~ d a r i t i t i e s= 1291174 (7411, ?ositives = 129/17C (7481, Stranb
Query:
87 ~ G A C ~ ~ T G T W A N ~ A C

-

-

Plco / Plus
C ~

C

1 4 6T ~

A

~

~

A

Shjc t :

47 n ; A G A C C 9 G C T M ~ I T ~ T T C T ~ T C P . G ~ l r O T I I T C A 106 C m TA

11 111 1

I Ill

I 1 I 1 1 1 1 1 1 1 1 1 IIIII t 1 1 1 1 It 11 1

Beora = L32 ( 2 5 . 5 b i t s ) , Z q e e t = l.5~-24, S m P l i ; = 1.5e-31 Itez:lti+s = 30/35 (85%1, Positives = 5 9 / 3 5 (85%). Stzt=b = Plus /

?lus

Score

s 138 (63.2 b i t s ) , "wect t 5.0%-20, Suta P(21 = f.0e-20 Ideiitities = 25/36 (6901. Positives = 39136 (80%). ? = m e = +1

Score r 73 (33.4 b i t s ) , Expect = S.Oe-20, Sum P(2) = 5.De-20 Zdentities = 13/13 t4701, PosOtives = 15123 t65%), Fzame +3

-

Case 1:07-cv-00780-SLR

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>mIX75962 1HSIiOX40M51 OX40 h m l o g u e :i m sapiene] !o o Length = 277 score = 52 (23.9 b i t s ) , Expect = 0.026, s m P(31 n 0.026 u 16entitias = 9/17 (52%). Positives = 9/17 I S Z I ) , Fr= +2

Score

= 52 (23.9 bits), Expect -*r 0.036, Sun P ( 3 ) = 0.035 1denri:ies = 10/38 (2611, Posit3ves 16/33 (42P), Frame = +3
786 L ' ~ J G S S C T S C P ~ 1 0 ~ B S C ~ T I W . 899 L++ G C CP C++ bc C T+ 3

.r

Query:

Sbjc t :

116 ~ S ~ ~ ? @ C P ? G H F S P G D N Q A C X P t j T N C T ? ? ~ 153

IdeaticSes =.9/22 140P1, Positives = 1-1 / 2 2 , . ..- , - -...- ---.- . --. . .*.- - -.- ..,- ,.. ,. , .. . a. . . . -

Score = 5 1 (23.5 bits), m e e t = 0.025, S m P ( 3 1 = 0.026

-(5011 -

-..i-..

? x m e .--.*.-.2.---.,,..._,.. .. = +

-..-

.

,

_... .,... ..

.

Score e 4 5 (20.7Sits1, %pact=

Ideatiries

P

9.22, S m ? ( ? ) r0.20 1/14 (55%). Positives = 5/14 I6C%), lrvne

-

+Z

Score = 4 4 (20.2 bits), w e c f = 1 9 Swm ~ ( 3 = 0 6 .. ) .4 xdt3tities = 6/17 (35%). Pasitives = 12117 (7011. Prme = +2
Query:

Sbjct:

170 K?NNSTCQPCPYGSYSN 22 0 ++ N+ C+PC G Y++ SB RSQNTVmCG?G?YND 74

Seorc -- 4 1 (10.9 bits], Expeer = 0.026, Sum P13). = 0.026 X d k ~ t i t i e s 9 / 2 2 ( 4 0 9 ) , Positives 10122 f45%1, Fr?spo = +3
Query:

-

-

Sbjct :

615 ?ZPTsLl?FtTL?RA5PGPSRGK 680 Pf PR S GPS P* 186 PITvQPT~wPRTSQGPSTRW 207

score = 40 (18.4 bits), Expect = 0.035. Sum PO). * 0.095 Identities r 7/30 (23%], ~ositlver= 16/30 [53%), Frame = +2
Query:

Sbjc t :

176 ~ ~ Q P C P Y G ~ S M O S ~ C P A G T E 265 V ?A ++ C+PC 4 + +GS+ * T* V
77 SSAPC~~PCTWQJLRSGSE~LKQLCTITQ~ 106

Score = 3 6 (16.6 b i b ) , *%pact = 0.12. P ( 3 ) = 0.12 Identities = 6 1 8 ( 7 5 % ) ) Positives = 7 1 8 ( 8 7 % ) . Frame
Query:

-

+2

236 XcPiujT~? 259

RC
Sbjct:

Am+?

108 WUAGTpP 125

Case 1:07-cv-00780-SLR

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Page 70 of 84

Cloning. Expression and Purification in Progress:
1, TNF-like

(TNF d e b )

BLTBT71

hlultiple tissue RNA blot analysis using EIPDDO12 Insert as probe
. . __

showed that - . gene is expressed ...n .almost -.. the tissues.I--.".r ...-. ... . this .. . . "._.. ..* - ._..--- i - --. .-......all tested. _. _ _ .. -. . . ,.. However, the expression in the heart was the highest folIowed by
,
. % . . . I . I .

.--

placenta and kidney.

7' - : TNF-like

(TNF epsilon)

HfDD012

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I, Protein Jqas purified from bacuIovirus expression system.
If, Poiyclonal antibody was made.

IIT, Functional

study is in progress.

Case 1:07-cv-00780-SLR

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K.B. Tan
Alem Truneh
10.18.95

RNA Expression: TNF and TNFR Like Genes

..

.

5

T ~ J- -F. TN.FL1.- . TNFRLI TNFRL2 Th'FRIi3.-.-OI40". . ~
113412 ~ANJS i\TG343
tumor

195197

HSABHIJX
AX;

103902 HTXBElO
ATG363

231556

117992

~>i~caik

38 lung

T cell

mN6I ATG 338 Itslis tumor

,

W4SW ATGi42 aEliva(U1

fibrobtart line

T cells

Case 1:07-cv-00780-SLR

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SUMMARY OF RNA EXPRESSION STUDIES ... .
Gene

MyeIoid cells
)FL60

cell RER I B) m

cell

sarcoma

Tissues

Primary Multiple cells forms
CD4'

TNFa
TNFLl
panmatic -cumor

Hmn
Jurkat

KGla

Heaff ax Bonemarrow Q31P
l~G6-3
m e y

Yes

'

TNml
fetal lung fibroblasr

j

TNFRU
Tell

.m

testis tumor

m -- ...KGla .

1I

I
KGla

I
.. .
'r

,acri\%tcdT cell .

OX40

I 1 KG1a

Iurkat -.- . - - .. .. -.-....-.. -

-

Jurht

I

Lung,Thymus CD4* Spleen CD8' Bonemamw a119 Tliymur1.~~4'
'

I

Ya

I '

C W

Case 1:07-cv-00780-SLR

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RNA Expression: TNF and TNFR Like

Genes

Df73

I

TNFLl TNFRLI TNFRL2

no entry = not tested,

-=

not dewcted,

+ to ++ = increasing amounts of RNA Setected.

Case 1:07-cv-00780-SLR

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RNA Expression: TNF and TNFR Like Genes

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Case 1:07-cv-00780-SLR

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.

.

.

. . ., 'I.." .
r . . .
I
. . . s t

.. ... .

:.:

.: . . .

Case 1:07-cv-00780-SLR

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..,r *

J...

*.

? 2 -.- +d

p 3

I RAT-

*

i

i.

1

ox-

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m - I g Binding to CdIs

Case 1:07-cv-00780-SLR

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Appelbaum/Dul 10115/95

EXPRESSION OF TNF-LXE(E PROTEIN

HGS clone 413412 = HTPANO8

Objectives:
Express as furion protein in E. coli--to be used for raising antibodies
Express in soluble form in E coli or other systems-to be used for receptor . binding and activity assays

Accomplishments:
. ... .9

.Plasmid DNA.fmm HGS strain (purified by.K B , Tan)

sequenced,.. .. .. ... ..-.

The DNA sequence in the open reading frame aeped with that reported by EGS.

There was a 1 bp difference upstream of the h t of 3 dosely spactd in-frame

AT0 codons, which makes it more likely that the first ATG is the hcdation initiator codon ( T T C m in HGS sequence is ATC,4TGG in SB sequence; the
latter is in good agreement with Kozak consensus upstrcain scqutnce)
coli expression: both expressed wkll as insoluble pmths; both have the potential for release of untagged protein following mterokinasc dfgestioa Protein purificatiodrabbit injection is planned

Two fusion constructs were made for

E

E

P,-DETI-DET2441-3aO

DETl DET2

DETl DET2

HPchydrophobic DET13epit g l 0 p2
D E ~ = ~ L S

PL= promoter * = 3 ATG codom

elwnwokinase site
(codons numbed from 1st ATG)

Case 1:07-cv-00780-SLR

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. I -

. . . . . .- I

*C..

-_.-

-

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PR1 R 1 R2 I1 R3 I3 R4 !HLHAB49 1 X X X X X X X X X X
I
\i

X

X

R5 12 R6 X X X X X X X X

I4 R7 PR7 . X X ( f u l l length) X X CfuZl .'length)
X X

X ( f u l l length) X (full length)

!HLHTJ50 1

X

X (discontinuous ESTs)

I

PRI R 1 R2 11 R3 I3 R4 R5 22 R6 -JHHEF37B-- 1 X X X X X IHBNAT51 1HT4SI80
i
---I
P R I R1 it2 I1 R3 13 R4 HMSBZ59-- .- . X X X X X !HFNDE43
.

14 R7 PR7

r

X
I

X cfujl length) X Cdiqcontinuous ESTs)

I

X

X ~ f u l ! length) l
f

Case 1:07-cv-00780-SLR

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EXHIBIT B

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EXHIBIT C

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EXHIBIT D

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EXHIBIT E

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