Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Marios Giannakis; Xinmeng Jasmine Mu; Sachet A. Shukla; Zhi Rong Qian; Ofir Cohen; Reiko Nishihara; Samira Bahl; Yin Cao; Ali Amin-Mansour; Mai Yamauchi; Yasutaka Sukawa; Chip Stewart; Mara Rosenberg; Kosuke Mima; Kentaro Inamura; Katsuhiko Nosho; Jonathan A. Nowak; Michael S. Lawrence; Edward L. Giovannucci; Andrew T. Chan; Kimmie Ng; Jeffrey A. Meyerhardt; Eliezer M. Van Allen; Gad Getz; Stacey B. Gabriel; Eric S. Lander; Catherine J. Wu; Charles S. Fuchs; Shuji Ogino; Levi A. Garraway

doi:https://doi.org/10.1016/j.celrep.2016.03.075

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Marios Giannakis, Xinmeng Jasmine Mu, Sachet A. Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A. Nowak, Michael S. Lawrence, Edward L. Giovannucci, Andrew T. ChanKimmie Ng, Jeffrey A. Meyerhardt, Eliezer M. Van Allen, Gad Getz, Stacey B. Gabriel, Eric S. Lander, Catherine J. Wu, Charles S. Fuchs, Shuji Ogino, Levi A. Garraway

Research output: Contribution to journal › Article › peer-review

Abstract

Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and integrated the results with tumor immunity, pathology, and survival data. We identified recurrently mutated genes in CRC, such as BCL9L, RBM10, CTCF, and KLF5, that were not previously appreciated in this disease. Furthermore, we investigated the genomic correlates of immune-cell infiltration and found that higher neoantigen load was positively associated with overall lymphocytic infiltration, tumor-infiltrating lymphocytes (TILs), memory T cells, and CRC-specific survival. The association with TILs was evident even within microsatellite-stable tumors. We also found positive selection of mutations in HLA genes and other components of the antigen-processing machinery in TIL-rich tumors. These results may inform immunotherapeutic approaches in CRC. More generally, this study demonstrates a framework for future integrative molecular epidemiology research in colorectal and other malignancies.

Original language	English
Pages (from-to)	857-865
Number of pages	9
Journal	Cell Reports
Volume	15
Issue number	4
DOIs	https://doi.org/10.1016/j.celrep.2016.03.075
State	Published - 26 Apr 2016
Externally published	Yes

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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https://doi.org/10.1016/j.celrep.2016.03.075

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Giannakis, M., Mu, X. J., Shukla, S. A., Qian, Z. R., Cohen, O., Nishihara, R., Bahl, S., Cao, Y., Amin-Mansour, A., Yamauchi, M., Sukawa, Y., Stewart, C., Rosenberg, M., Mima, K., Inamura, K., Nosho, K., Nowak, J. A., Lawrence, M. S., Giovannucci, E. L., ... Garraway, L. A. (2016). Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Reports, 15(4), 857-865. https://doi.org/10.1016/j.celrep.2016.03.075

@article{4b5735b711f6470f86fdd13795ff6a3f,

title = "Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma",

abstract = "Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and integrated the results with tumor immunity, pathology, and survival data. We identified recurrently mutated genes in CRC, such as BCL9L, RBM10, CTCF, and KLF5, that were not previously appreciated in this disease. Furthermore, we investigated the genomic correlates of immune-cell infiltration and found that higher neoantigen load was positively associated with overall lymphocytic infiltration, tumor-infiltrating lymphocytes (TILs), memory T cells, and CRC-specific survival. The association with TILs was evident even within microsatellite-stable tumors. We also found positive selection of mutations in HLA genes and other components of the antigen-processing machinery in TIL-rich tumors. These results may inform immunotherapeutic approaches in CRC. More generally, this study demonstrates a framework for future integrative molecular epidemiology research in colorectal and other malignancies.",

author = "Marios Giannakis and Mu, {Xinmeng Jasmine} and Shukla, {Sachet A.} and Qian, {Zhi Rong} and Ofir Cohen and Reiko Nishihara and Samira Bahl and Yin Cao and Ali Amin-Mansour and Mai Yamauchi and Yasutaka Sukawa and Chip Stewart and Mara Rosenberg and Kosuke Mima and Kentaro Inamura and Katsuhiko Nosho and Nowak, {Jonathan A.} and Lawrence, {Michael S.} and Giovannucci, {Edward L.} and Chan, {Andrew T.} and Kimmie Ng and Meyerhardt, {Jeffrey A.} and {Van Allen}, {Eliezer M.} and Gad Getz and Gabriel, {Stacey B.} and Lander, {Eric S.} and Wu, {Catherine J.} and Fuchs, {Charles S.} and Shuji Ogino and Garraway, {Levi A.}",

note = "Funding Information: We thank N. Gupta, E. Nickerson, and S. Seepo for additional project management and the Broad Sequencing platform, as well as Xin Jin, Julian Hess, Diana Miao, Yohei Masugi, and Pavan Bachireddy for helpful discussions. We thank the participants and staff of the NHS and the HPFS for their valuable contributions, as well as the following state cancer registries for their help: AL, AZ, AR, CA, CO, CT, DE, FL, GA, ID, IL, IN, IA, KY, LA, ME, MD, MA, MI, NE, NH, NJ, NY, NC, ND, OH, OK, OR, PA, RI, SC, TN, TX, VA, WA, and WY. The authors assume full responsibility for analyses and interpretation of these data. This work was conducted with the support of a KL2/Catalyst Medical Research Investigator Training award from Harvard Catalyst/The Harvard Clinical and Translational Science Center (National Center for Research Resources and the National Center for Advancing Translational Sciences, NIH, Award KL2 TR001100; M.G.). This work was also supported by the Dana-Farber Cancer Institute Leadership Council (M.G.), the 2014 Colon Cancer Alliance-AACR Fellowship for Biomarker Research Grant Number 14-40-40-GIAN (M.G.), the Perry S. Levy Endowed Fellowship (M.G.), the BroadNext10 (E.M.V.A.) and BroadIgnite (E.M.V.A.) grants, the Project P Fund (C.S.F.), the Blavatnik Family Foundation (C.J.W.), and the Friends of the Dana-Farber Cancer Institute (S.O.), as well as NIH grants U54 HG003067 (E.S.L., S.B.G.), K07 CA190673 (R.N.), K07 CA148894 (Ki.N.), K24 DK098311 (A.T.C.), R01 CA137178 (A.T.C.), R01 CA155010 (C.J.W.), P01 CA87969, UM1 CA186107, P01 CA55075, UM1 CA167552, R01 CA151993 (S.O.), R35 CA197735 (S.O.), R01 CA118553 (C.S.F.), R01 CA168141 (C.S.F.), and P50 CA127003 (M.G., L.A.G., C.S.F.). Funding Information: We thank N. Gupta, E. Nickerson, and S. Seepo for additional project management and the Broad Sequencing platform, as well as Xin Jin, Julian Hess, Diana Miao, Yohei Masugi, and Pavan Bachireddy for helpful discussions. We thank the participants and staff of the NHS and the HPFS for their valuable contributions, as well as the following state cancer registries for their help: AL, AZ, AR, CA, CO, CT, DE, FL, GA, ID, IL, IN, IA, KY, LA, ME, MD, MA, MI, NE, NH, NJ, NY, NC, ND, OH, OK, OR, PA, RI, SC, TN, TX, VA, WA, and WY. The authors assume full responsibility for analyses and interpretation of these data. This work was conducted with the support of a KL2/Catalyst Medical Research Investigator Training award from Harvard Catalyst/The Harvard Clinical and Translational Science Center (National Center for Research Resources and the National Center for Advancing Translational Sciences, NIH, Award KL2 TR001100; M.G.). This work was also supported by the Dana-Farber Cancer Institute Leadership Council (M.G.), the 2014 Colon Cancer Alliance-AACR Fellowship for Biomarker Research Grant Number 14-40-40-GIAN (M.G.), the Perry S. Levy Endowed Fellowship (M.G.), the BroadNext10 (E.M.V.A.) and BroadIgnite (E.M.V.A.) grants, the Project P Fund (C.S.F.), the Blavatnik Family Foundation (C.J.W.), and the Friends of the Dana-Farber Cancer Institute (S.O.), as well as NIH grants U54 HG003067 (E.S.L., S.B.G.), K07 CA190673 (R.N.), K07 CA148894 (Ki.N.), K24 DK098311 (A.T.C.), R01 CA137178 (A.T.C.), R01 CA155010 (C.J.W.), P01 CA87969, UM1 CA186107, P01 CA55075, UM1 CA167552, R01 CA151993 (S.O.), R35 CA197735 (S.O.), R01 CA118553 (C.S.F.), R01 CA168141 (C.S.F.), and P50 CA127003 (M.G., L.A.G., C.S.F.). Publisher Copyright: {\textcopyright} 2016 The Authors.",

year = "2016",

month = apr,

day = "26",

doi = "https://doi.org/10.1016/j.celrep.2016.03.075",

language = "English",

volume = "15",

pages = "857--865",

journal = "Cell Reports",

issn = "2211-1247",

publisher = "Cell Press",

number = "4",

}

Giannakis, M, Mu, XJ, Shukla, SA, Qian, ZR, Cohen, O, Nishihara, R, Bahl, S, Cao, Y, Amin-Mansour, A, Yamauchi, M, Sukawa, Y, Stewart, C, Rosenberg, M, Mima, K, Inamura, K, Nosho, K, Nowak, JA, Lawrence, MS, Giovannucci, EL, Chan, AT, Ng, K, Meyerhardt, JA, Van Allen, EM, Getz, G, Gabriel, SB, Lander, ES, Wu, CJ, Fuchs, CS, Ogino, S & Garraway, LA 2016, 'Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma', Cell Reports, vol. 15, no. 4, pp. 857-865. https://doi.org/10.1016/j.celrep.2016.03.075

TY - JOUR

T1 - Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

AU - Giannakis, Marios

AU - Mu, Xinmeng Jasmine

AU - Shukla, Sachet A.

AU - Qian, Zhi Rong

AU - Cohen, Ofir

AU - Nishihara, Reiko

AU - Bahl, Samira

AU - Cao, Yin

AU - Amin-Mansour, Ali

AU - Yamauchi, Mai

AU - Sukawa, Yasutaka

AU - Stewart, Chip

AU - Rosenberg, Mara

AU - Mima, Kosuke

AU - Inamura, Kentaro

AU - Nosho, Katsuhiko

AU - Nowak, Jonathan A.

AU - Lawrence, Michael S.

AU - Giovannucci, Edward L.

AU - Chan, Andrew T.

AU - Ng, Kimmie

AU - Meyerhardt, Jeffrey A.

AU - Van Allen, Eliezer M.

AU - Getz, Gad

AU - Gabriel, Stacey B.

AU - Lander, Eric S.

AU - Wu, Catherine J.

AU - Fuchs, Charles S.

AU - Ogino, Shuji

AU - Garraway, Levi A.

N1 - Funding Information: We thank N. Gupta, E. Nickerson, and S. Seepo for additional project management and the Broad Sequencing platform, as well as Xin Jin, Julian Hess, Diana Miao, Yohei Masugi, and Pavan Bachireddy for helpful discussions. We thank the participants and staff of the NHS and the HPFS for their valuable contributions, as well as the following state cancer registries for their help: AL, AZ, AR, CA, CO, CT, DE, FL, GA, ID, IL, IN, IA, KY, LA, ME, MD, MA, MI, NE, NH, NJ, NY, NC, ND, OH, OK, OR, PA, RI, SC, TN, TX, VA, WA, and WY. The authors assume full responsibility for analyses and interpretation of these data. This work was conducted with the support of a KL2/Catalyst Medical Research Investigator Training award from Harvard Catalyst/The Harvard Clinical and Translational Science Center (National Center for Research Resources and the National Center for Advancing Translational Sciences, NIH, Award KL2 TR001100; M.G.). This work was also supported by the Dana-Farber Cancer Institute Leadership Council (M.G.), the 2014 Colon Cancer Alliance-AACR Fellowship for Biomarker Research Grant Number 14-40-40-GIAN (M.G.), the Perry S. Levy Endowed Fellowship (M.G.), the BroadNext10 (E.M.V.A.) and BroadIgnite (E.M.V.A.) grants, the Project P Fund (C.S.F.), the Blavatnik Family Foundation (C.J.W.), and the Friends of the Dana-Farber Cancer Institute (S.O.), as well as NIH grants U54 HG003067 (E.S.L., S.B.G.), K07 CA190673 (R.N.), K07 CA148894 (Ki.N.), K24 DK098311 (A.T.C.), R01 CA137178 (A.T.C.), R01 CA155010 (C.J.W.), P01 CA87969, UM1 CA186107, P01 CA55075, UM1 CA167552, R01 CA151993 (S.O.), R35 CA197735 (S.O.), R01 CA118553 (C.S.F.), R01 CA168141 (C.S.F.), and P50 CA127003 (M.G., L.A.G., C.S.F.). Funding Information: We thank N. Gupta, E. Nickerson, and S. Seepo for additional project management and the Broad Sequencing platform, as well as Xin Jin, Julian Hess, Diana Miao, Yohei Masugi, and Pavan Bachireddy for helpful discussions. We thank the participants and staff of the NHS and the HPFS for their valuable contributions, as well as the following state cancer registries for their help: AL, AZ, AR, CA, CO, CT, DE, FL, GA, ID, IL, IN, IA, KY, LA, ME, MD, MA, MI, NE, NH, NJ, NY, NC, ND, OH, OK, OR, PA, RI, SC, TN, TX, VA, WA, and WY. The authors assume full responsibility for analyses and interpretation of these data. This work was conducted with the support of a KL2/Catalyst Medical Research Investigator Training award from Harvard Catalyst/The Harvard Clinical and Translational Science Center (National Center for Research Resources and the National Center for Advancing Translational Sciences, NIH, Award KL2 TR001100; M.G.). This work was also supported by the Dana-Farber Cancer Institute Leadership Council (M.G.), the 2014 Colon Cancer Alliance-AACR Fellowship for Biomarker Research Grant Number 14-40-40-GIAN (M.G.), the Perry S. Levy Endowed Fellowship (M.G.), the BroadNext10 (E.M.V.A.) and BroadIgnite (E.M.V.A.) grants, the Project P Fund (C.S.F.), the Blavatnik Family Foundation (C.J.W.), and the Friends of the Dana-Farber Cancer Institute (S.O.), as well as NIH grants U54 HG003067 (E.S.L., S.B.G.), K07 CA190673 (R.N.), K07 CA148894 (Ki.N.), K24 DK098311 (A.T.C.), R01 CA137178 (A.T.C.), R01 CA155010 (C.J.W.), P01 CA87969, UM1 CA186107, P01 CA55075, UM1 CA167552, R01 CA151993 (S.O.), R35 CA197735 (S.O.), R01 CA118553 (C.S.F.), R01 CA168141 (C.S.F.), and P50 CA127003 (M.G., L.A.G., C.S.F.). Publisher Copyright: © 2016 The Authors.

PY - 2016/4/26

Y1 - 2016/4/26

N2 - Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and integrated the results with tumor immunity, pathology, and survival data. We identified recurrently mutated genes in CRC, such as BCL9L, RBM10, CTCF, and KLF5, that were not previously appreciated in this disease. Furthermore, we investigated the genomic correlates of immune-cell infiltration and found that higher neoantigen load was positively associated with overall lymphocytic infiltration, tumor-infiltrating lymphocytes (TILs), memory T cells, and CRC-specific survival. The association with TILs was evident even within microsatellite-stable tumors. We also found positive selection of mutations in HLA genes and other components of the antigen-processing machinery in TIL-rich tumors. These results may inform immunotherapeutic approaches in CRC. More generally, this study demonstrates a framework for future integrative molecular epidemiology research in colorectal and other malignancies.

AB - Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and integrated the results with tumor immunity, pathology, and survival data. We identified recurrently mutated genes in CRC, such as BCL9L, RBM10, CTCF, and KLF5, that were not previously appreciated in this disease. Furthermore, we investigated the genomic correlates of immune-cell infiltration and found that higher neoantigen load was positively associated with overall lymphocytic infiltration, tumor-infiltrating lymphocytes (TILs), memory T cells, and CRC-specific survival. The association with TILs was evident even within microsatellite-stable tumors. We also found positive selection of mutations in HLA genes and other components of the antigen-processing machinery in TIL-rich tumors. These results may inform immunotherapeutic approaches in CRC. More generally, this study demonstrates a framework for future integrative molecular epidemiology research in colorectal and other malignancies.

UR - http://www.scopus.com/inward/record.url?scp=84963553379&partnerID=8YFLogxK

U2 - https://doi.org/10.1016/j.celrep.2016.03.075

DO - https://doi.org/10.1016/j.celrep.2016.03.075

M3 - Article

SN - 2211-1247

VL - 15

SP - 857

EP - 865

JO - Cell Reports

JF - Cell Reports

IS - 4

ER -

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

Abstract

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UN SDGs

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