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`UNIV. CHICAGO EX. 2026
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`

`

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`Cancer
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`

`

`Cancer Research
`
`A Journal of the American Association for Cancer Research
`
`_ F
`
`Volume 68 - Number 3
`
`ebruary 1, 2008 - Pages 627—956
`
`
`Reviews
`
`Human Leukocyte Antigen—G and Cancer Immunoediting.
`Mirjana Urosevic and Reinhard [)ulnnler............................................
`
`1103 Is Uverexpressed in Breast. Cancer and Represses
`p145“: liy Interacting with llistone Deaeelylases. Will Yarosh.
`'l‘omasa Ilarrienlos.'l‘araneh lismailpour. Limin Lin.
`Philip M. Carpenter. Kathryn Usarln. Ilntla Anton-Culver.
`and 'l'aosheng liu.1ng...693
`
`'l‘argeling the Hultaryotic Translation Initiation Factor 4E for
`Cancer 'l‘llcrapy. Jeremy R. (lralT. Bruce W. Konieek. Julia ll. Carter.
`
`
`and iirie (l. Mat'L‘lI.‘a'St)Il................................
`....631
`
`Mitochondrial Cytochrome B Gene Mutation Promotes Tumor
`Growth in Bladder Cancer. Santana Dasgnpta.
`Mohammad Uhaidul lltlvqltlf. Sunil llpadhyay, and David Sidransky ...........700
`
`Meeting Report
`
`Cell,Tumor. and Stem Cell Biology
`
`Meeting Report: Innovations in Prostate Cancer Research.
`Wadih Amp. Marl in 'I'repel. Bruce R. Keller. and Renata Pastplalini ..........635
`
`Priority Reports
`
`Alterations in Gemini? Expression Contribute to Alternative
`nIRNA Splicing Patterns and Tumor Cell Motility. Jung lleun l.ee.
`['hl'isline li. Ilorak. Chand Khanna. Zhnuiillg Meng. l.i Bong Y1].
`'l'ilaolhy I}. Veenstra. and Patricia 5. Steeg ...639
`
`A First-Generation Multiplex Iliomarker Analysis ol'llrinc for
`the Early Detection of Prostate Cancer. Bharallli taxman.
`David 5. Morris. Jianiun Ya. Javed SiddiquiJie Cao. liohil Mehra.
`llollerl J. Lonigro. Alex '[‘sodiknv. John T. Wei. Scott A. 'l'oinlins.
`and Anti M. Llllnntllyan.tvl5
`
`Molecular Biology. Pathobiology, and Genetics
`
`In vivo Switching of Human Melanoma Cells between
`Proliferative and Invasive States. Keith 5. Hook. Ussia M. IliehholT.
`Natalie (I. Schlegel. Lido Itiihheling. Nikita Robert. Leo .‘iehaerer.
`Silvio Ilctmni. and Reinhard hummer ....650
`
`Multiple Alternative Splicing Markers for Ovarian Cancer.
`Roscoe Klinek. Anne llramard. [.yna [like]. (icneviéve Iiiufresne-Marlin.
`Jlllien Uervais-ilirtl. Richard Madden, liric R. Paqnet. ChuShin Koh.
`Jillian l’. Venahles. Panagiolis l’rinos. Manuela JilaveaIm-I’elnnm.
`Raymund \-\-"el|inger. Claudine litltlcnurt. Bcnoil ('hnbol.
` ....65?
`
`and .‘iheril' Ahou iilela...........
`
`Modeling Genomic Diversity and Tumor Dependency in Malignant
`Melanoma. William M. Lin. Alissa C. Baker. Rameen Reroukhinl.
`
`Wendy Wineklcr. Wllei FengJL-nnifer M. Marmion. Elisabeth Laine.
`| leidi (ireulich. llsinyi 'i'seng. Casey Gales. l’. Stephen Hodi.
`Glenn liranoll‘. William R. Sellers. Roman K. ’l'homah'.
`
`Mal Ihew Meyers-on. 'l‘orld ll. (loluh. Reinhard Bummer.
`Meenhard llerlyn. Gad Gel z. and Levi A. Garraway ”(164
`
`‘l‘risletraprnlin Downnregulales Interleukinms and Vascular
`Endothelial Growth Factor in Malignant Glioma Cells.
`lislller .‘iuswam. Yanyan |.i. Xiaowen Zhang. G. Yancey Gillespie.
`Xuelin LLJoth. Shaeka. Liang |.I1. |.ei Zheng, and [’eler l-I. King..........674
`
`Spontaneous Squamous Cell Carcinoma Induced by the Somatic
`lnaclivation of Retinohiaslonm and ill-p.53 ‘I‘umor Suppressors.
`Ana Belen Marti nea-t‘ruz. Mirenlxu Santos. M. I-‘ernanda Lara.
`(‘arnien Segrelles. Sergio Ruiz. Marla Moral. Corina Lora.
`Ramon tiart‘ia-Iiseuclem. and Jesus M. Paramiu68$
`
`Enhanced Activation of Epidermal Growth Factor Receptor
`Caused by rI‘I"nor-Derived E-Cndherin Mutations. Anja Bremm.
`Axel Waleh. Margit Fuelinjiirg h‘lagesJustus Duyster. Gisela Keller.
`Christine llernulnnsliitllt'r. Ktll'l-l‘lrlt‘tlrlt‘li liecker. Sandra llauser.
`Rupert Longer. Claus | lann con Weyhern. ileinz lliiller.
`... a..."
`and Birgit [.uher ......................707
`
`CCNSINephmhlastoma tlvereapresaed Malricellular Protein
`Regulates lnlegriu Expression. Adhesion. and Dissemination
`in Melanoma. Viviana Vallacehi. Mario Itariiolti. I-‘ranccsca Ratli.
`
`llelia Iii Slasi. l‘aola lit-ho. Annamaria De Filippo. (iahrina 'l‘ragni.
`Andrea Ralsari. Antonino L‘arhone. Lit-la Rivoltini, Giorgio l‘armiani.
`Nuurctitline Lazar. Bernard Perhal. and Monica Rodolfo 715
`
`Modulation of OnCogenic Phenotype in Human Glioma Cells by
`Cytomegalovirus Nil—Mediated Milogenicily. Charles 3. Collins.
`Liliana Soroeeanu. Scull lienham, Weliyue Zliang.
`and Matthias [-l. Kraus7&4
`
`Tumor Cell-Secreted (Taveolin—I l-Ias l’roangiogenie Activities in
`Prostate Cancer. Salallahlin A. 'l'ahir. Huang Yang. Alexei A. tiohsov.
`Mattillni Wattlllahe. Kcrl-iehi rl'nl‘lala.Jo.-;epl‘lir1e Atltlai.
`F.| Moataz Abdel l-'al.l.ah. Itov Kadrnon. and Timothy C. 'I‘hompson .......73l
`
`The Tumor Suppressor LKBI Regulates Lung Cancer Cell Polarity
`by Mediating crlc42 Recruitment and Aclivity. .‘ilnnnin Zhang.
`Kallierine Sellaier-llules. liarlio R. Khuri. Wei Xhou. Paula M. Vertino.
`and Adam I.MarlllsNt]
`
`The Human 'I'rithorax Protein hASIIZ Funclions as an tlncoprotein.
`Juliane |.iiseher—l’ilv.lafl". Isabella Unwlisla. Jiirg Vermorts. Karslen Kapellc.
`'l'ill Rraunschweig. tit-so \A’alscnulnn. (.flnmtal Rodgerrkia—Sehamherger.
`Ilenning Selulchlautz. Stephan Uri-sellers. iilisahelh Kremmer.
`Richard |.i|isehkis. Christa t'erni. Axel Wellnlann.
`and Bernhard lnsther
`
`L055 of l.khl I’rovekea Highly Invasive lindomelrial
`Adenoearcinonlaa. Cristina M. Contreras. Sins-Inna Unrumnrllw.
`J. Marshall l'laynie. Lane]. Shirley. Esra A. Akhay. Shana N. Wingo.
`John 0. Schorge. Russell R. llroatldus. Kwok-Kia Wong. Nalieel Bardeesy.
`and Diego ll. (Tastrillon ....?59
`
`Sixteen-anase Gene Expression ldenlil‘ies [.uminal Breast
`Cancers with Poor Prognosis. Pascal l-'inetti. Nathalie ('ervera.
`limnlannclle Charafe—Jautlrel. (Christian t'hahannon. Colette (Sharpie.
`Max ('haffanel'.JocelyncJacquemier. Patrice Viens. Daniel ilirnhaum.
`
`and Francois llcrtucci ..
`.....767
`
`Genotoxic Stress—induced Expression ol‘p53 and Apoptosis in
`Leukemie Clam llemocytes with (.‘ytoplnsmically Sequestered p53.
`Slefimie iliiltger. lirnilyJerszyk. llen Low. and Charles W:Ilker................'i'?7
`
`

`

`
`
`Contents (Continued)
`
`RCIJ: Represses Smad Signaling in Transforming Growth Factor—I3
`Resistance. Degang Wang. Jianyin Long. Fangyan Dai. Min Liang.
`Kin-l Ina l-‘eng. and Xia Lin .........783
`
`Epitope Landscape in Breast and Colorectal Cancer. Neil l-l. Segal.
`1). Williams Parsons. Karl S. l’eggs. Victor Velculescu. Ken W. Kinzler.
`Bert Vogelstein. and James I’. AllisonSB‘J
`
`(1)43. but not P-Selectin (ilyeoprotein Ligand-l, Functions as an
`ti—Selectin Counter-Receptor in Human Pm-R—Cell Leukemia HALL-l.
`Chizu Nommmra.]iro Kikuchi. Nobutaka Kiyokawa. l'iidenori Ozaki.
`Kanae Milsunaga. Hidenohu Ando. Akiko Kanamori. Reiji Kannagi.
`Jnnichiro Fujimoto. Kazuo Muroi. Yusuke liurukawa. and
`Milsuru Nakamnra .....
`..........................79l)
`
`ARCGZ Expression and Side Population Abundance Regulated by a
`'I'ransforrning Growth Factor B‘Directed Epithelial-Mesenchpnal
`Transition. Liqun Yin. Paola Cast agnino. and Richard K. Assoian “am-300
`
`Repression of R-Cell Linker {RLNK} and B-Cell Adaptor for
`Phosphoinosilide 3-anasc [RCAPi Is Important for Lymphocyte
`‘I‘ransi'ormal ion by Rel Proteins. annr antaJefl‘rey Delrow.
`A mar lirawid. Anirvan M. Sengtipla. {iaol'eng lien. and Celine Gélinas
`
`'l'he RGFR-STATS Oncogenic Pathway Up-regulates the time]
`tindonuclease to Reduce DNA Damage after Topoisomerase [
`Inhibition. Arnanil Vigneron, Erick Gamelin, and Olivier Coqneret .....815
`
` Experimental Therapeutics, Molecular Targets.
`
`
`and Chemical Biology
`
`‘l‘anloxifen Resistance in Breast Tumors [5 Driven by Growth Factor
`Receptor Signaling with Repression of Classic Estrogen Receptor
`Gononlic Function. Suleiman Massarweh. C. Kent Osborne.
`Chad J. Creighton. Lanfang Qin. Anna 'l'simelaon, Shixia Huang.
`Heidi Weiss. Mol Iial‘l'ar Rimawi. and Rachel Schiff..................................326
`
`Inhibition of Endoplasmic Reticulum Stress-Induced Apoptosis
`of Melanoma Cells by the ARC Protein. |.i I'lua Chen. Chen Chen jiang.
`Ralph Watts. Rick F. ‘l‘llorne. Kelly A. Kieida. Kn Dong Zheng.
`and Peter Hersey....
`
`Aggravated Endoplasmic Reticulum Stress as a Basis for Enhanced
`(ilioblastomo Cell Killing by Bortezomih in Combination with
`Celeeoxib or its Non-Coxib Analogue. 2,5-DimethyI-Celecoxih.
`Adel Kardosh. iineousc li. Golden. Peter Pyrko.]asim Uddin.
`Florence M. Holman. 'I‘llomas C. Chen. Stan G. Louie. Nicos A. Petasis.
` "- nun“ un-
`and Axel ll. Schiinthal.......
`..843
`
`‘I‘alnoxifen Stimulates the Growth of Cyclin Dl—Overexpressing
`Breast Cancer Cells by Promoting the Activation of Signal
`Transducer and Activator of Transcription 3. Yuki lshii.
`u..." no“...
`Samuel Waxman. and Doris Germain
`
`
`Prostate Stem Cell Antigen Vaccination Induces a Long-term
`Protective Immune Response against Prostate Cancer in the
`Absence of Autoimmunity. Maria dc Ia Lav. Garcia-Hernandez.
`Andrew Gray. llolyn Hubby. Otto]. Klinger. and W. Martin Kast............86l
`
`'l'nmor—Induced Senescenl T Cells with Suppressor Function:
`A Potential Form of Tumor Immune Evasion. Carolina L. Montes.
`
`Andrei l. ChapovaLJonas Nelson, Vhenosa Orhne. Xiaoyu leang.
`Dan ll. Scholar-e. Scotl E. Stromc. and Brian R. Uastman.........................87IJ
`
`Systematic High-Content Proleomic Analysis Reveals Substantial
`Immunologic Changes in Colorectal Cancer. Uta Hermit.
`Lars l’liilipsen. 5ehaslian liarlsch. Rerlrarn Wiedcnmann.
`Ilanil'l t'. Raumgart. Marcus lliimmerlc. and Andreas SturmSRfl
`
`Self-Tolerance Does Not Restrict the CD4+ T—Helper Response
`against the p53 Tumor Antigen. Marjolein M. Lauwen.
`Sander Zwaveling. Linda dc Quartel. S. Carmela t-‘erreira Mote.
`Janine A.C. Grashorn. Cornelia JM. Melief. Sjoerd H. van (ler Burg.
`and Rienk ()ffringa.......893
`
`Induction of EBV—Latent Membrane Protein l-Specific MHC
`Class II‘Restricted T—Cell Responses againsl Natural Killer
`Lymphoma Cells. Hiroya Kohayashi. Toshihiro Nagalo. Miki Takahara.
`Kcisuke Sato. Shoji Kjrnura. Naoko Aoki. Makoto Aznmi.
`Masatoshi 'l‘aleno. Yasuaki l'larabuchi. and Esteban Cells 901
`
`Endocrinology
`
`HRS Receptor Mediates Anoikis in Human Colt-rectal Carcinoma
`Cell Lines. Luciana M. Laguingc. Reed N. Samara. Wenge Wang.
`Wafik S. El-Deiry. Georgia Corner. Leonard Augenlieht. Lope Mishra.
`and J. Milburn Jessup..909
`
`Clinical Research
`
`Cancer-Associated Stromal Fibroblasts Promote Pancreatic Tumor
`
`Progression. Rosa F. Hwang. 'l‘odd Moore. 'l‘lliruvengadaln Arumugam.
`Vijaya Ramachandran. Keith D. Amos. Armando Rivera. Baoan Ii.
`Douglas B. Evans. and Craig D. Logsdon .....................................................9 18
`
`Epidemiology
`
`Tumor lmmunobiological Differences in Prostate Cancer between
`African-American and European~AnIerican Men. Tiffany A. Wallace.
`Robyn L. l’rueitt. Ming Yi. Tiffany M. lioweJohn W. Gillespie.
`Harris G. Yfanlis, Robert M. Stephens. Neil E. Cnporaso,
`
`Christopher A. |.olTredo. and Stefan Ambs ..92?
`
`Direct Evidence for EpithelialvMesenchymal Transitions in Breast
`Cancer. Anthony]. 'l‘rimholi. Koichi Fukino. Alain do Bruin. Gun Wei.
`Lei Sheri. Stephan M. Tanner. Nicholas Creasap. Thomas J. Rosol.
`Michael L. Robinson. Charis ling. Michael C. ()strowski.
`and Gustavo Leone ...................................................................................937
`
`Raf and MER Protein Kinases Are Direct Molecular Targets
`for the Chemopreventive Effect of Quercetin. a Major Flavonol
`in Red Wine. Ki Won [.ee. Nam joo Kong. YongASeok l-leo.
`Evgeny A. liogozin. Angelo Pugliese. Mun Kynng Hwang.
`G. ‘l'im Bowden. Ann M. Bode. l'lynngjoo Lee. and Zigang Dong...........946
`
`Correction: SNAII Silencing and Inhibition of Breast
`Tumor Growth...956
`
`Correction: ll-‘N Signaling in Aggressive l-‘ibmmatosis 9‘36
`
`Correction: RPSZ7L Modulates DNA Damage Response...................956
`
`

`

`
`Thls material may be protected by Copyright law [one 17 u.5. Cadet
`
`
`
`
`t
`
`Epitope Landscape in Breast and Colorectal Cancer
`
`Neil l-l. Segal,” 1). Williams Parsons," Karl S. l’cggsf'j Victor ‘t’eleutescu;l
`Ken w. Kinner,‘ Bert Vogetstein." and James P. Allison“
`
`and 'tnuullnology I'rogrnrn. Memorial .‘iloall hellel'ing t'ullccr
`'Iicpnrlmcul of Medicine. "I.ud\\'tg ('I'nlcr I'or (iancer llittiittttotlu'rnl
`ulnl 'I'lu'rupclltics at
`t'cuter. New York. New ‘i'ork'. und '|.u(l\\'ig (‘enlel'
`i'oI' ('anl‘cr ticnclit.
`'I'lle Inluts Hopkins Kilnrncl ['alu'ct' Center. littllilnort‘. Maryland
`
`Abstract
`
`individual cancers contain many mutant.
`The finding that
`genes not present in normal tissues has prompted consider—
`able.
`interest
`in the cancer epitope landscape. To further
`understand such effects, we applied in silica—based epilope
`prediction algorithms and high throughput post hoc analysis
`to identify candidate tumor antigens. Analysis of 1,152
`peptides containing misseuse mutations previously identified
`in breast and coloreetal cancer
`revealed that
`individual
`
`cancers accumulate on average ,_ I0 and -—7 novel and
`unique Ill.A-l't*02til cpitopes,
`respectively,
`including genes
`implicated in the neoplastic process. These data suggest
`that, with appropriate manipulation ol‘ the immune system.
`tumor cell destruction in site may provide a polyvalent lmnor
`vaccine without a requirement for knowledge of the targeted
`antigens. |(Ianccr Itc.‘ 2t)ttit:68{3]:889-—92|
`
`Introduction
`
`Several clas.
`:s of tumor antigens have been described and
`named according to their distribution in normal and neoplastic
`tissues. These. include the shared differentiation antigens. such as
`Inclan-MMMt'l'l
`[1. 2} in melanoma:
`fitncer testes or germ cell
`antigens. such as Mntitt—l (3) and NY—tiHL)-l
`[-1] in adult testes and
`diverse tumor types: and unique tumor antigens, which generally
`carry mutations. such as t'liKJ in {melanoma [5} and CASP-B in
`head and neck cancer to].
`the unique tumor antigens was
`The.
`ilnntunogenicity of
`recognized in several seminal studies including animal transplant
`models {7] amt chemically or UV tiglll‘--imtuccd tumors (8. 9].
`'l'hey are of particular interest because they result from somatic
`mutations in individual tumors and are absent from normal tissues
`
`ll). providing antitumor specilicity without anticipated
`(It).
`deleterious uutoinnntmity. Somatic mutations
`tan he classified
`as either "drivers" or “passengers". Passenger mutations provide
`no positive or negative selective advantage to the ttunor but are
`retained by chance during cell division and clonal expansion.
`in contrast. driver mutations provide a selective advantage that
`promotes the tumorigcnic process. The generation of mutations is
`continuous due to the itnpcrtcet nature of DNA replication and
`repair. 'l'hus, the generation] ol‘ additional antigens during tumor
`progression. whether driver or passenger
`([2). provides a
`continuously renewable source ot‘ antigen.
`itccenl analyses of breast and colorccta] cancers showed a
`remarkable number ol' somatic mutations in human cancer (13].
`
`Iteqln Is for reprints: James I}. Allison. Ludwig t's-ntei' ol' l'aliccr ImmunolIlerapr.
` n
`Memorial .‘ilrntIriii-lli-
`' ('i-nler. -tl.-'i
`i-'..'tsl with .‘itrvel. 1’.- ifit’itl. New York. NY
`'(‘t
`
`ttitlhfi. I'.-m.'|il: ullisonjtrr'nl.‘
`I'g.
`
`'Iitllllt'l .\meri.cuu .'\
`Iciuliun tor ('unct'r Itcsein'cll.
`
`tit!i:|ll.l litt'lftllltlH-fi-l iJl‘AN-lli-lttltll')
`
`Among >lll.tttltl genes analyzed. a total oi‘ Lilli? somatic mutations
`were identified in II breast and II colorct‘lal cancers. Approxi—
`onltely 83% were Inisscnse mutations.
`(illi- nonsense. and the
`remainder were insertions. dclclions. duplications. and changes
`in noncoding regions. When extrapolated to the whole genome.
`it was calculated that
`individual
`tulllors harbored an average ol'
`~91! amino acid—altering [i.c..
`Iitmsynonymous'l mutations. The
`kind ol‘ internmtion available l'rom such large-scale sequencing
`studies of individual tumors has not heretofore hccn available but
`
`clearly has implications for tumor immunity.
`to the current
`study. we designed an in since approach to
`examine whether llIc mutations identified in Sjoltlom ct at. {til}
`have the potential to gl‘llm‘alc novel cpitopes that might serve as
`targets l'or an immune response. Using cpitope prediction
`algorithms and high throughput post hoc analysis. we found
`evidence to support
`the notion that
`the human tuluorigenic
`process results ill
`the generation ol‘ multiple immune targets.
`Individual breast and colorectut cancers accumulated tlll average of
`w it} and - Tr' novel and unique ltt.A—:‘\”‘[l2llt epitopcs. respectively:
`several within genes that may be drivers. These results provide
`insights into the unique innntlllc prolilcs ol‘ individual tumors with
`potential clinical relevance.
`
`Materials and Methods
`
`l’cplidc sequences corresponded to missensc
`Iipitope prediction.
`mutations identified during the discovery phase hy Siohlom el at. {lit}.
` c. {'olicatomers ol' thcsc
`llankcd by up to It] amino acids on either
`I
`peptides New analyzed with several t'pilopt‘ prediction algorithms tor |t|..-\-
`:\"t|2tll hindcls. Muior htslocolnpnlitiilily complex [Mlit'l-l antigenic
`pcplidc processing prediction tMM’I’I': not H}. developed at the Max-Flam}.
`institute. titcililutes the prediction ol'epilopi-s that can hind lo Mltt' class I
`molecules huscd on it score calculated tor each suhsquu-uce. [inch amino
`acid at n specilic position within :1 suhseqtlcncc is given a value that has
`been prt-t‘illcnlated and stored in static matrices. The precnlclllnliou was
`done either tiy BIL-1i“ I IE] or Si'lii’lil'i'l II
`I Hi]. lit-pending on the algorithm
`selected. the values were then multiplied lliIM.-\H} or added [Nil-'I‘l‘l'l‘llli In
`dctct'minc the score tor the suhsequcncc. I’cplidcs qltatilicd as positive it
`they scored
`ltitiand nit-”t. respectively { I?. lit}. ltnNKI’l-Zl’ [ It); uses specific
`scoring Inatl'iccs from st‘ls til-peptides known to bind to Milt‘ Itlolccutes as
`1|“. Ian-diplm of MIIC-peplidc hindiilg. I’cptidt's qtlalilicd as positive it the
`percentage optimum was
`-'-:'iti“t. or higher. NelMl It‘
`tit).
`'31] predicts
`pcptide-Mllt‘ binding using nrliliciat neural networks {ANN} and Weight
`Iliztlriccs. For ANN. used for
`|ii.i\-t\‘*tt‘_’tll prediction. pcplidcs scored
`positive it 1Cyl is "53500.
`list, we searched for ultiquc cpilopcs within
`Post hoc analysis.
`eoncatamers ol'wiId-type and mutant peptides. iipilopes i(i(r1|[ili[tll in It“.
`"wild-type concotamer" included both [me wild-typi- cpitopes and artifacts
`across the concatemttion sites and were removed trout
`l'nrlhcr analysis.
`The “nnitnnl concalaincr“ was then used to search for remaining cpilopcs.
`To ensure that potential In Iaul epitopt-s did not spun concatenation sites.
`the "mutant concillanu'ru used in this colllirnlnlory phase included
`additional
`redundant characters spaced hclu'ccn peptidcs.
`lIu-rt'hy
`permitting contiruntlion ol' epilopcs contained entirely within a mutant
`
`www.aacrtournals.org
`
`889
`This materialwascnnied
`
`Cancer Res 2008; 58: (3}. February 1. 2003
`
`

`

`Cancer Research
`
`
`
`Table 1. HLA-A‘0201 epitopes (SYFPEITHI)
`
`
`
`'l‘olal epitopes
`(THC:
`'-:| epiliipe
`I‘lt‘:
`--_-'i epitope.
`
`l-‘er sample: tiltt'
`: ltt‘
`:(‘H('
`
`liL'
`
`t
`
`it'll
`||
`||
`
`Ave
`it!
`I311
`Ill}!
`
`5]}
`1.7
`[m7
`hit
`
`M in
`2
`8
`'J
`
`Mars
`I?
`3t}
`3t}
`
`2
`ti
`ll..'tti
`ill I
`I’I.'.I' peptide: tiltt‘
`3
`ti
`Il,-I2
`[Llfi
`: ltt'
`3
`i:
`am
`[Llit
`: circuit
`
`
`Abbreviations: BC. breast cancers: ('Itt'. t'oloreclel cancers.
`
`
`peplide only. 'I‘hese were then aunoluled l'or specimen and tumor type as
`described in supplementary inlorinatiou in Siiililoin et al. [l3].
`listimales ol' epilope frequency. The Iolal numhcr nl‘ epilopes
`corresponding to each peptide. original specimen. and tumor type were
`calculated i'or the ||.?'.£| genes that were successfully sequential of IIIe
`H.023 t't'llfi genes. As per Sjohloni el
`ill. ( lit). we extraamlaled this number
`to the total number of genes in the human genome [conservatively
`estimated at H.203! by dividing the munher ol' idl'ltlil‘led epitopes by (tot.
`
`Results and Discussion
`
`A total of LISZ peptides containing missense mutations.
`previous];r
`identilied in breast and coloreetal cancer ([3] were
`concatenated into a single string of 21t.92rl amino acids and
`analyzed for potential MIIC class
`[ hinders.
`tipitopes we”.
`predicted using several algorithms
`then applied to post hoe
`analysis. This analysis entailed a series ol' manual steps. predefined
`calculations. and inacro-lnised algorithms to identity epilopes thgu
`are absent
`from corresponding wild-type sequences Inil prescnl
`within the mutant peptide. We restricted our analysis to “LA-
`i\"{12ti] ‘J—mer epitopes because this haplolype has been extensively
`
`studied and is repnasented in up to 27% ol‘ the population (2'3). All
`epitopes were confirmed to be unique tJ-mei's alter BLAS'I'analysis.
`searching for "short. nearly exact matches" in the "nr" database.
`'l'wo hundred and forty-one epilopes were identified using Ml'tl’l'dl
`(lslifSYl’lil'l‘lll {lo}.
`()1) average. 8.2 and [3.6 epitopes were
`found per specimen in eolorectid and hreasl cancers. respectively-
`l'l'ahle. I). Each tumor contained a minimum of two and as man)r as
`Jill epitopes in a case of breast. cancer (Fig.
`I}.
`Next. we lot-.llsccl our attention on the I‘JI candidate cancer
`
`[til-1N] genes. (IAN genes were identified as containing imitations in
`at
`least
`two independent
`tmnors and were mutated al greater
`li‘equenev than non—(TAN genes when adjusted for size. nucleotide
`composition. and mutational spectra {t3}. We.
`identified
`‘17 potential epitopes in (MN genes l’l’ahle 2}. 111058 Upilflltt‘fi WW“
`identified in 6 of ll coloret‘tal cancers and T of ti lireast cancers.
`
`Additional algorithms including NetMilL.‘ (20. 2|). MM’I’P (I‘ll:f
`”WAS {15). and RANKPl-ZI’
`([9]. were then used.
`identifying
`an average of ӣ2 epitopes. The. maturity of epitopes predicted hy
`each of the different. algorithms were identified by at
`least
`two
`algorithms. Epitopes predicted by SYFPEI'I‘III. BIMAS.
`Ili‘tNKl‘liI’.
`and NetMllC overlapped by 59%. 'r': ‘56. 64%. and 75%. respectively.
`In sum. we found that. individual colorectal and breast cancers
`
`accumulated an average of —~ 7 and — [0 novel and unique ll].i'\-
`A’tl2[)] epitopes. respectively. Approximately one new epitope was
`generated for every It] mutations, and 45% of predicted epitopes
`were shown to be cleaved at their (700” terminal according to the
`I’M’roC proteasome prediction algorithm (refs. 23. 24; Table Iii;
`Note that these numbers are underestimates because other MIIL‘
`
`studied here. can presenl additional mutant
`molecules. not
`peptides depending on the hapiotvpe of individual patients.
`Because individual tumors potentially contain Six distinct MIIC
`class 1 molecules,
`including two loci each for ”LA-A.
`[ILA-ti.
`and [ILA—(.7.
`the estimated frequency of novel epitopes may he
`multiplied up to 6-fold. Thereby estimating that
`individual
`colorectal and breast cancers potentially accumulate up to ~ 40
`and ~ {it} novel Milt.‘ class [ restricted epitopes, respectively.
`[In a more. cautionary note. we have not yet shown that these
`‘é‘l’II-Upes are actually expressed in tumor cells; we have studied only
`
`
`Epitopes per sample
`
`epitopes by sample. Solid black
`bars, colorectal cancer samples;
`lined bars. breast cancer samples.
`
`rm /-
`r/é
`r
`fix
`/
`ieééé;
`Z11!
`:Nsanssszeeeaassousoo
`afiggsssssééwwmmmtfiimtig
`
`
`
`Cancer—Res 2003; 68: {'3'}: February 1. 2008
`
`{3&0
`This material was cooled.
`
`www.aacr]ournals.org
`
`
`
` Figure 1. Distribution of HLA'A'02Dt
`:W‘W
`
`%/
`3
`fig?
`
`7
`
`7
`
`

`

`Breast and Coiorectal Cancer Epitopes
`
`for drivers aiming those studied. Mutations in drivers may be
`advantageous in that
`the tuluor might not be able.
`to udown-
`rcgulate" expression of the epitope it it
`is required for continued
`neoplastic growth {addicted}. However. the exploitation of muta—
`tions in cancer
`immunotherupeutics is not dependent on the
`mutation being a driver. As long as the epilope is presented to the
`immune system appropriately.
`it can.
`in theory. stimulate an
`antitumor response. All of the. multiple. nousynonymous mutations
`in cancers therelore potentially contribute to multiple targets
`for
`immune attack. providi