A
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`A LS of THE NEW YORK
`ACADEMY OF SCIENCES
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`VOLUME
`1284
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`Annals of the New York Academyof Scien
`v. 1284 (2013)
`General Collection
`W1 AN626YL
`2013-07-16 11:00:47
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`UNIV. CHICAGO EX. 2031
`
`The Renaissance
`of Cancer
`Immunotherapy
`
`The 7th International
`Cancer Vaccine Symposium
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`ISSUE EDITORS
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`edible
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`VOLUME
`ANNALS of Rocaeangers
`1284
`ACADEMY OF SCIENCES
` .ISBN-10: ISBN-13:
`
`
`
`
`
`ISSUE
`
`The Renaissance of CancerImmunotherapy
`C
`Ihe /th International Cancer Vaccine Symposium
`
`ISSUE EDITORS
`
`Olivera J. Finn* and Gerold Schuler?
`
`“Oniversily ol Pillsburah and "Whriversity Hospital
`
`
`of
`
`Enanger
`
`
`
`TABLE OF CONTENTS
`
`v
`
`1
`
`6
`
`12
`
`17
`
`24
`
`31
`
`46
`
`52
`
`57
`
`Introduction to The Renaissance of Cancer Immunotherapy
`Olivera J. Finn and Gerold Scluder
`Cancer immunoediting: antigens, mechanisms, andimplications to cancer
`immunotherapy
`MatthewD. Vesely and Robert D. Schreiber
`Cell-extrinsic effects of the tumor unfolded protein response on
`myeloidcells and T cells
`Maurizio Zanetti
`Immunotherapy in preneoplastic disease: targeting early procarcinogenic
`inflammatorychangesthat lead to immunesuppression and tumortolerance
`Bridget Keenan andElizabeth M. Jaffee
`Integrationof epidemiology, immunobiology, andtranslational research for
`brain tumors
`Hideho Okada, Michael E. Scheurer, Saumendra N. Sarkar, and Melissa L. Bondy
`Humandendritic cells subsets as targets and vectors for therapy
`EynavKlechevsky and Jacques Banchereau
`Dendritic cell immunotherapy
`Rachel Lubong Sabado and Nina Bhardwaj
`Molecular programmingofsteady-state dendritic cells: impact on
`autoimmunity andtumorimmunesurveillance
`Dylan J. Jolinson and Pamela $. Ohashi
`Preventing cancer bytargeting abnormally expressedself-antigens:
`MUCI vaccinesfor preventionof epithelial adenocarcinomas
`Pamela L. Beatty and Olivera J. Finn
`Immunological controlofcell cycle aberrationsfor the avoidanceof oncogenesis:
`the case of tetraploidy
`Laura Senovilla, Lorenzo Galluzzi, Maria Castedo, and Guido Kroemer
`
`

`

`62
`
`66
`
`71
`
`75
`
`80
`
`Ongoing adaptive immuneresponses in the microenvironment of
`melanoma metastases
`Nicolas van Baren and Pierre G. Cottle
`Mainfeatures of human T helper 17 cells
`Francesco Anmunziato, Lorenzo Cosini, Francesco Liotta, Enrico Maggi, and Sergio Romagnanti
`In silico modeling ofcancercell dissemination and metastasis
`Lic En Wai, Vipin Narang, Alexandre Gouaillard, Lai Guan Ng, and Jean-Pierre Abastado
`Commonpathways to tumorrejection
`Ena Wang, Davide Bedognetti, Sara ‘Tomei, and Francesco M. Marincola
`Cancer-induced immunosuppressive cascadesandtheir reversal
`by molecular-targeted therapy
`Yutaka Kawakami, Tomonori Yaguchi, Hidetoshi Sumimoto, Chie Kudo-Saito, Nobuo Tsukamoto,
`‘lomokoIwata-Kajilara, Shoko Nakamura, Hiroshi Nishio, Ryosuke Satomi, Asuka Kobayashi,
`Mayuri Tanaka, Jeong Hoon Park, Hajime Kamijuku, Takahiro ‘Tsujikawa, and Naoshi Kawamura
`
`‘The New York Academyof Sciencesbelieves it has a responsibility to provide an openlorum for discussionofscientific questions. ‘The
`positions taken bythe authors andissueeditors of Annals of the New York Academyof Sciences are their ownandnot necessarily those
`of the Academyunless specificallystated. The Academyhas nointent toinfluencelegislation by providing such forums.
`This material was copied
`at the NLM and may be
`Subject USCopyright Laws
`
`

`

`This material may be protected by Copyright law (Title 17 U.S. Code)
`
`
`
`
`Ann. N.Y. Acad. Sci. ISSN 0077-8923
`
`ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
`Issue; The Renaissance of Cancer immunotherapy
`
`Cancer immunoediting: antigens, mechanisms,
`and implications to cancer immunotherapy
`
`Matthew D. Vesely and Robert D. Schreiber
`Department of Pathology and Immunology, Washington University School of Medicine, St, Louis, Missourt
`
`Address for correspondence: Robert D. Schreiber, Department of Pathology and Immunology, Washington Universily School
`of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, schreiber@immunology.wustledu
`
`Accumulated data from animal models and humancancer patients strongly support the concept that the immune
`systemcanidentify and control nascent tumorcells in a process called cancer immunosurveillance. In addition, the
`immunesystem canalso promote tumorprogression through chronic inflammation, immunoselectionofpoorly im-
`munogenic variants, and suppressing antitumorimmunity, Together, the dual host-protective and tumor-promoting
`actions of immunityare referred to as cancer immunoediting. The current framework of cancer immunoediting is
`a dynamic process comprised of three distinct phases: elimination, equilibrium, and escape. Recently, we demon-
`strated that immunoselection by CD8* 'T cells of tumorvariants lacking strong tumor-specific antigens represents
`one mechanism by whichcancercells escape tumor immunityand points towardthe future of personalized cancer
`therapy.
`
`Keywords: cancer immunoediling;
`genome
`
`immunosurveillance;
`
`tumor antigens;
`
`immunotherapy;
`
`tumor escape; cancer
`
`the escapephase, during which edited tumors ofre-
`Introduction
`duced immunogenicity begin to growprogressively
`.
`a
`
`
`Cancer immunoediting SEEOreUL ores he
`
`in. an immunologically unrestrained manner, estab-
`A plethora of evidence now provides strong.
`‘
`oe
`:
`ne
`;
`lish an immunosuppressive tumor microenyiron-
`support
`for cancer
`immunoediting,
`a process
`ment, and eventually becomeclinically apparent.
`wherein immunity functions not only as an ex-
`Importantly, escape from immune control is now
`:
`-
`trinsic tumor suppressor but also to shape tumor
`acknowledgedto beoneof the hallmarksof cancer. !
`i
`+t i .
`ere
`immunogenicity.’
`In its most complex form, cancer
`The antigens of unedited tumors
`immunoediting occurs in three sequential phases:
`A central tenet of tumor immunologyin general,
`elimination, equilibrium, and escape. Elimination
`and the cancer immunoediting process in- par:
`is a modern view of the older notion of cancer
`ticular,
`is
`that
`tumorcells express antigens that
`immunosurveillance,
`in which innate and adap-
`distinguish them fromtheir nontransformed coun-
`tive immunity work togetherto detect and destroy
`terparts, thus permitting their recognition by T cells
`transformedcells long before they become clinically
`andtheir eventual destruction by immunological
`apparent. However, sometimes tumor cell variants
`mechanisms. Althougha deep understanding of hu-
`may not be completely eliminated but instead en-
`man and mouse tumorantigens currently exists, it
`ter into an equilibrium phase in which the immune
`comes nearlyentirely from analyses of tumorcells
`system controls net tumor cell outgrowth; in this
`derived from immunocompetent hosts, which were
`phase, adaptive immunityconstrains the growthof
`likely subjected to the sculpting forces of cancer
`clinically undetectable occult tumorcells and ed-
`immunoediting during their development. Littlets
`its tumorcell immunogenicity.” Finally, the func-
`known about the antigens expressed in nascent tu-
`tional dormancyof the tumorcell population may
`morcells, for example, whether theyare sufficient
`be broken, leading to progression of the cells into
`
`JO1}bi/inyas 124105
`dor
`ences
`1
`Ano NY Aead Sei, 124412013) 1 502015 New York Academy of St
`This material was copied
`at the NLM and may be
`Subject US Copyright Laws
`
`

`

`Tumor antigens and cancer immunoediting
`
`Vesely & Schreiber
`
`to induce host-protective, antitumor immune re-
`sponses, or whether their expression is modulated
`by the immunesystem.
`such questions might be
`We
`realized that
`answered by defining the
`antigens
`expressed
`sarcoma cell
`lines
`in unedited
`derived from
`3'-methylcholanthrene (MCA)-treated,
` immun-
`odeficient Rag2 ’
`mice because such induced
`tumor cells phenotypically resemble highly im-
`munogenic, nascent, primary tumorcells.” How-
`ever, current methodsto identify tumor antigens
`using expression-cloning approaches are time and
`effort intensive, andare not well suited to establish-
`ing a tumor’s antigenic landscape. Recent advances
`in genomesequencing have madepossible rapid and
`cost effective methods to define cancer genomes,
`andhaveestablished that, while they acquire some
`mutations involved in the transformation process
`(driver mutations), cancercells also develop many
`passenger mutations, in part, asa consequenceofthe
`genomic instability that is a characteristic oftrans-
`formedcells. It has been proposedthat someofthese
`mutations result in the expression of tumor-specific
`proteins that are,
`in turn, tumor-specific antigens
`for I’ cells." However, until recently, this had not
`been experimentally demonstrated.
`Recent work from our laboratory’ used a novel
`form of exomesequencing (CONA capture sequene-
`ing or CNA CapSeq) to define the mutational pro-
`file of two independent, unedited MCA sarcomas
`(d42m1 and H4im1). By pipelining the sequencing
`data for one of these tumors (d42m1) into major
`histocompatibility complex (MHC) class | epitope
`prediction alporithims, we identified a potential mu-
`labional antipen of the unedited d42mtecells, vali
`dated its identity as the major rejection anlipen us-
`ing expression Cloning techniques, and showed that
`antigen loss via al cell-dependent immunoselec
`lion process represents the mechanism underlying
`cancer Immunoediting of this tumor, ‘his study’
`thus provides mechanistic insights into the pro
`cess of cancer immunoediting and ports to the
`future potential that cancer genomeanalysis may
`haveonthefields of tumor immunology and cancer
`immunotherapy.
`Cancer genome sequencingand antigen
`discovery
`Using cDNA CapSeq, weidentified 3,737 nonsyn-
`onyMous mutations in d42m1 cells and 2,677 non-
`
`synonymous mutations in FH3lm1 cells. However,
`only 5% of the mutations were shared between
`d42m1 and H31m1, which explains the unique im-
`munogenicity that each cell line displays. Interest-
`ingly, both d42m1 and H3imt hadactivating mu-
`tations in codon 12 of the Kras proto-oncogene
`andinactivating mutations in the tumorsuppres-
`sor gene Trp53, When comparing the sequencedata
`of d42m1 and H3lm1 sarcomacells to those of hu-
`man cancer genomes, we found that the former most
`closely resemble genomes of carcinogen-induced
`lung cancers from smokers in both the number and
`type of mutations (e.g., C/A or G/T transversions).
`Thus, cancer exome sequencing of d42m1 and
`H3}m1 cells demonstrated a carcinogen signature
`similarto that foundin ling cancer cells fram smok-
`ers, but distinct from other human cancers. ‘This
`raises the possibility that a similar discovery ap-
`proach may beusedto find tumor-specific antigens
`in humanlung cancer.
`
`d42m1 tumorvariants
`The d42m1 sarcomacell line displays a sporadicten-
`dency to produce escape tumors following trans-
`plantation into naive, syngeneic wild-type mice.
`Furthermore, cell
`lines derived from escape tu-
`mors of parental d42m1 (d42imt-esl, d42m1-es2,
`and d42m1-es3) consistently formed progressively
`growing tumors when transplanted into naive syn
`geneicrecipients. Thus, unedited d42m1 tumorcells
`can undergo immunoediting when transplanted
`into wild-type mice. The heterogeneous behavior
`of d42m1 tumorcells in naive immunocompetent
`miceis due to the parental d42m1 cell line consisting
`ofa disproportionate (80:20) mixture of regressor
`and progressor tumorcell clones.
`
`Identifying potential d42m1 tumor antigens
`from genomic data
`‘To identify tumor-specificantigens for D8! ‘T cells,
`we used the data from the cancer exome mutational
`analysis to identify the antigenic targets of d42m1
`specific CD8'
`cytotoxic “TV
`lymphocytes (CTLs).
`First, weassessed the thearetical capacity of peptides
`containing cach missense mutation to bind to MHC
`class | proteins (Le., to function as neoantigens) by
`it silico analysis. Second, we used a d42m1-specific
`CD8! CEL clone derived from a wild-type mouse
`that had rejected parental d42m1 tumorcells to as
`sess Lumorreactivity i vitro; the readoutol Clk ac
`livity against the tumorcells was IEN-y production
`
`Ann Noy Acad, Sei
`This material wes copied
`at the NLM and may be
`Subject US Copyright Laws
`
`12H4 (2013) 15
`
`SUS New York Acodernyool Senne os
`
`

`

`Vesely & Schreiber
`
`Tumor antigens and cancer immungeding
`
`by the CD8! 'T cells. The d42m1-specific C3 CTL
`clone was stimulated by parental d42m1 tumorcells
`and with all regressor d42m1 tumorcell variants,
`but it was not stimulated by progressor d42m1 tu-
`morcell variants or unrelated MCA sarcomacells.
`‘These results revealed that regressor d42m1 tumor
`cells share a commonrejection antigen. Wetherefore
`focused on thelimited number of epitopes common
`to all d42m1 regressor variants. And, together with
`the fact that recognition of all d42m1 regressor vari-
`ants by the CTL clone wasrestricted by H-21 > we
`predicted that an ROI3L mutation in spectrin-B2
`representedthe most likely rejection antigen candi-
`date becauseof its high affinity for H-2D".
`Next, we established that C3 CTL cells could
`discriminate between the mutant and wild-type
`spectrin-B2 peptide sequence 905-913 when pre-
`sented on H-2D", ‘To document that the anti-R913L
`spectrin-B2 response occurred under physiologic
`conditions, we used labeled H-2D" tetramers car-
`rying the mutant spectrin-B2 905-913 peptide to
`identify tumor antigen-specific CD8* ‘T cells in
`d42m1 tumors. Mutant spectrin-B2—specific CD8*
`T cells were detected in parental d42m1 tumors
`and draining lymph nodes, and increased in num-
`bers to peak values just prior to tumor rejection.
`In contrast, no mutant spectrin-B2-specifie CD8!
`T cells were detected in d42m1-es3 tumors, These
`data demonstrate that a mutated gene expressed se-
`lectively in unedited d42m1 tumorcells givesrise to
`a mutant protein that evokes a naturally occurring
`'T cell response in naive wild-type mice, Thus, mu-
`tant spectrin-B2 is a genuine tumor-specific antigen
`of d42m1 sarcomacells.
`
`Mutant spectrin-p2 is the major rejection
`antigen of d42m1 tumorcells
`‘To explore whether mutant spectrin-B2 represented
`the major rejection antigen of parental d42m1 tu-
`morcells, we enforced expressionofeither the mu-
`tant or wild-type forms of spectrin-B2 into cells
`of one of the d42m1 escape variants, d42m1-es3.
`Wheninjected into wild-type mice, d42m1-es3 tu-
`mor cell clones expressing wild-type spectrin-B2
`grewprogressivelyanddisplayedsimilar growth ki-
`netics to the parental d42m1-es3cell line. In con-
`trast, dd2m1-es3 tumorcell clones expressing mu-
`lant spectrin-B2 were rejected in wild-type but not
`mice. Furthermore, CD8* T cells specific
`Rag?
`for mutant spectrin-B2 were detected bytetramer
`
`staining of d42mi-es3 tumors that had been re-
`constituted with mutant spectrin-(32. These results
`demonstratethat expression of mutant spectrin-B2
`is both necessary andsufficient forthe rejection of
`d42m1 tumors, and thus validate it as a major re-
`jection antigen of d42m1 sarcomacells.
`
`Immunoselection is the immunoediting
`mechanism for d42m1 tumorcells
`‘T’ cell-
`Next, we formulated the hypothesis that
`dependent
`immunoselection was a likely mecha-
`nismfavoring outgrowthof tumorvariants that lack
`strong rejection antigens. This possibility ts consis-
`tent with our finding that every d42m1 clonethat
`expresses mutant spectrin-B2 was rejected, whereas
`every clone orvariant that lacks mutant spectrin-B2
`formed progressively growing tumors. ‘lo formally
`test this hypothesis, weassessedthe in vivo behavior
`ofa disproportionate mixtureofcells consisting of
`a majority of highly immunogenic d42m1 tumor
`cells expressing mutant spectrin-B2 (Le., d42m1-
`T2) and a minority of a d42m1 tumorcell clone
`lacking mutant spectrin-B2 (i.e, d42m1-T3). When
`this mixture was transplantedinto wild-type mice,
`5 of 20 (25%) developedescapetumors, a result that
`closely resembles what was observed with parental
`d42m1 tumor cells in wild-typerecipients. Further-
`more, tumors that grewout in wild-type mice con-
`sisted of 98%d42m1-T3 tumorcells and lacked mu-
`tant spectrin-B2. Thus, escape variants of parental
`d42m1 tumorcells develop as a consequence ofa
`‘T cell-dependent immunoselection process that fa-
`vors the outgrowth of tumorcell clones lacking the
`major rejection antigen,
`For d42m1 tumorcells, we show that an im-
`munoselection process acting on an oligoclonal
`parental
`tumorcell population leads to the out-
`growth oftumorcell variants that lack the major
`tumor
`rejection antigen,
`in this case, mutant
`spectrin-B2. The immunoselection that occurs
`upon exposureto anintact immunesystem is depen-
`dent on adaptive immunity since neither parental
`d42ml1 tumorcells nor the mixture of regressor
`and progressor d42mt
`tumorcell clones under-
`goes editing whenpassedthrough Rag2
`mice; yet
`theyare edited following transplantation into im-
`munocompetent wild-type mice. Thus, in the case
`of d42m1, thetarget ofthe immunoselection pro-
`cess has beenclearly identified as a major rejection
`antigen. However,this finding does not rule out the
`
`P0195 NewYork Academy of Sciences
`This material was copied
`atthe NLM and may be
`Subject US Copyright Laws
`
`3
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`

`Turnor antigens and cancer immunoediting
`
`Vesely & Schreiber
`
`possibility that similar immunoediting mechanisms
`might select for mutations in critical components of
`the MHC class | antigen processing and presenta-
`tion pathway, such as the class | heavy chain,* (52
`microglobulin, or components of IFN-y receptor
`signaling,' all of which are knownto regulate tumor
`cell recognition by tumor-specific CD8* 'T cells,
`
`Personalized immunotherapy and
`genomics: the antigen landscape
`
`Recent advances in genome sequencing have re-
`sulted in unprecedented Opportunities to assess ge-
`netic influences ondisease development. For can-
`cer, Most genomesequencing studies have focused
`onidentifying newdriver mutationsthat promote
`neoplastic development andmetastasis, in the hope
`of obtaining insights that
`lead to novel cancer-
`targeted therapeutics or that provide prognostic
`value.” However, we have shown that
`this same
`technology, when combined with aninsilico epi-
`tope prediction algorithm, can be used to identify
`expressed mutations in cancer cells that result
`in
`expression of tumor-specific antigens that can be
`targets for immune-mediated elimination, We pre-
`dict that this approach maynot only provide new
`insights into basic mechanisms underlying cancer
`immunoediting but also new opportunities for in-
`dividualized cancer immunotherapy.
`Thelarge datasets of information from the many
`cancer genome initiatives could be of value te tumor
`IMMUNO’ mints for definingthe antigen landscape
`as Opposed to the mutational landscape—of human
`cancers.” One application of this approach is that
`it could be used to identify the subset of cancer
`paticnts whose tumors express antigens that may
`he better targeted by Immunotherapy. For example,
`only about 25%of patients treated with anti-C'l LA
`J respond positively, and the reasons for this limited
`response remain unknown. We suggest that patients
`who respondto checkpoint blockade immunother
`apy may have more ImmMunNovenic, tumor specie
`mutations, and that
`these antigens can be iden
`tified using cancer exome sequencing and high
`throughput: bioinformatics;
`in other words,
`the
`genomics approach may provide a mechanism to
`stratify those patients who would benefit most from
`this type of therapy. A second application of this
`approach mayprovide a mechanismto longitudi-
`nally evaluate changes in a tumor’s antigenic pro-
`file as a consequence of ongoing immunotherapy,
`
`A third applicationis the rapididentificationol the
`Most immunogenic epitopes within a tumor, with
`the goal of developing personalized cancer vaccines
`lor patients.
`Itis difficult to predict whetherthis type of analy-
`sis will yield prognostic valuein theclinic, as genome
`analysis can becostly andrequires streamlined com-
`putational analysis. Nevertheless, third-generation
`sequencing technologies are already commercially
`available, and costs for cancer genome sequencing
`have already started to fall sha rply andarelikely to
`continue dropping over the next decade, It should
`thus befeasible to routinely perform this type of
`genomic analysis on individual patient’s cancercells
`in the not-too-distant future,
`
`Remaining questions
`Our recent study’ demonstrates that immunoedit-
`ing of a tumorresults from ‘T cell-dependent im-
`munoselection for tumorcell variants that
`fail
`to
`express highly antigenic mutations. These results
`not only provide definitive evidence for at
`least
`one mechanismunderlying the cancer immunoedit-
`ing process, but also demonstrate the key role that
`tumor-specific mutations play in the development
`of a tumor’s immunogenic phenotype and subse-
`quent fate,
`a single mutant protein
`It
`is
`interesting that
`manifests such immunodominance as d42m1 tu-
`morcells, an immunodominancethatin some ways
`resembles the immunodominance of certain viral
`antigens, Manyfactors may contribute to the im-
`munodominanceof mutant spectrin-f2. Ontheba-
`sis ofsilico analysis, the mutant 905-91 3 sequence
`is predicted to interact with H-2D” with very high
`allinity in contrast to the corresponding wild-type
`sequence, which is predicted to bind only weakly.
`However, several other factors mayalso contribute
`lo the Immunodominance of mutant spectrin B2,
`including antigen abundance, antigen cross pre
`sentiabilily, T cell repertoire, or presence of epitopes
`recognized by regulatory T cells. Clearly, more work
`is needed to refinethe capacity to accurately predict
`the antigenicity of a mutated protein.
`His unclear from our work whether the mecha
`nism of cellular transformation influences the types
`of antigens that are eventually expressed by can
`cer cells.
`In our model, sarcomas generated from
`chemical carcinogens are most similar, in the num
`ber and type of mutations, to carcinogen-induced
`
`Ann ALY, Acad
`This material was copied
`at the NLM and may be
`Cece PEete Pe
`
`Sel, THd (POS) Vet
`
`AOS Mow York Acoienrvy eal
`
`Sie
`
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`

`

`Vesely & Schreiber
`
`Tumor antigens and cancer immunoediling
`
`humancancers, such as lung cancers from smokers.
`For the past six decades, the MCA sarcomasystem
`has been an experimental workhorse for tumorim-
`munologists. This may be due to the carcinogen’s
`ability to generate a large numberof passenger mu
`tations, which allows for a greater number of po-
`tential neoantigens to formthat may be recognized
`by the immunesystem, Wespeculate that oncogene:
`driven models ofcancer, which harbor fewer passen-
`ger mutations than spontaneous cancers, may not
`be as readily eradicated or controlled by antitumor
`immunity. However, ina companionstudy to ours,
`Michel DuPageand ‘TylerJacks et al. demonstrateda
`key role of dominant antigens in the cancer immu-
`noediting process by using a sarcoma model driven
`by Kras activation and 7rp53inactivation,"
`
`Summary and conclusions
`
`Therecent revolution in genomics represents a sig-
`nificant
`transition in the evolution of the cancer
`immunoediting concept.
`In the past, efforts were
`mostly centered on demonstrating that
`the pro-
`cess occurs, identifying the key players in it, and
`attempting to define the positions that
`they play.
`Workin this area nowenters a newphase in which
`researchers can begin to elucidate the molecular
`mechanisms that drive the process, and determine
`the quality and quantity of tumorantigens expressed
`in nascently transformedcells that drive immune-
`mediated elimination and/or sculpting.
`The approach of exomesequencing,insilico anal-
`ysis, and CD8* T cell cloning are beneficial to both
`basic andclinical scientists. By defining the specific
`antigenic targets in cancer cells, newlevels of under-
`standing of host responses to tumors during ongo-
`ing therapy can be obtained. This, in turn, should
`facilitate the development of newtherapeutic op-
`portunities that direct
`the power and specificity
`of the immunesystem to control, and/or destroy,
`cancer.
`It may also be useful for identifying sub-
`sets of cancer patients whose tumors express anti-
`vens that can be mosteffectively targeted by check-
`
`point blockade immunotherapy, and may provide
`a mechanism to longitudinally evaluate changes
`in a tumor’s antigenic profile as a consequence
`of ongoing immunotherapy. Therefore, we pre-
`dict
`that a genomic approach to tumor antigen
`identification may, in the future, facilitate the de-
`velopment of individualized cancer immunothera-
`
`rather than simply
`pies directed at tumor-specific
`
`cancer-associated
`antigens.
`
`Acknowledgments
`
`This work was supported by grants to R.D.S. from
`the National CancerInstitute, the Ludwig Institute
`for Cancer Research, the Cancer Research Institute,
`and theWWWWFoundation. M.D.V.is supported
`by a predoctoral fellowship from the Cancer Re-
`search Institute.
`
`Conflicts of interest
`
`Theauthors declare no conflicts of interest.
`
`References
`
`1. Vesely, M.D. eral, 2001, Natural innate and adaptive immu
`nity to cancer. Anau, Rev. Immunol, 29: 235-271,
`Koebel, C.M. ef al. 2007. Adaptive inimunity maintains
`occull cancer in an equilibrium state, Nattire 450: 903-907.
`3. Khong, HLT. & NLP. Restifo, 2002. Natural selection of tumer
`yariants in the generation of “tumor escape” phenotypes.
`Nat. Hamitinol. 3: 999-1005,
`4. Hanahan, D. & RA. Weinberg, 2011, Hallmarks of cancer:
`the next generation, Coll 144: 646-674.
`5. Shankaran, Vo et al. 2001,
`IPNey and lymphoeytes prevent
`primary tumour development and shape tamour immun