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 journalArticle

183 Citations (Scopus)

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 languageEnglish
Pages (from-to)857-865
Number of pages9
JournalCell Reports
Volume15
Issue number4
DOIs
Publication statusPublished - 2016 Apr 26

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Tumors
Colorectal Neoplasms
Tumor-Infiltrating Lymphocytes
Lymphocytes
Neoplasms
Infiltration
Gene Components
Exome
Genes
Molecular Epidemiology
Antigen Presentation
T-cells
Microsatellite Repeats
Pathology
Immunity
Cohort Studies
Machinery
Prospective Studies
T-Lymphocytes
Mutation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Giannakis, M., Mu, X. J., Shukla, S. A., Qian, Z. R., Cohen, O., Nishihara, R., ... 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

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

In: Cell Reports, Vol. 15, No. 4, 26.04.2016, p. 857-865.

Research output: Contribution to journalArticle

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
Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R et al. Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Reports. 2016 Apr 26;15(4):857-865. https://doi.org/10.1016/j.celrep.2016.03.075
Giannakis, Marios ; Mu, Xinmeng Jasmine ; Shukla, Sachet A. ; Qian, Zhi Rong ; Cohen, Ofir ; Nishihara, Reiko ; Bahl, Samira ; Cao, Yin ; Amin-Mansour, Ali ; Yamauchi, Mai ; Sukawa, Yasutaka ; Stewart, Chip ; Rosenberg, Mara ; Mima, Kosuke ; Inamura, Kentaro ; Nosho, Katsuhiko ; Nowak, Jonathan A. ; Lawrence, Michael S. ; Giovannucci, Edward L. ; Chan, Andrew T. ; Ng, Kimmie ; Meyerhardt, Jeffrey A. ; Van Allen, Eliezer M. ; Getz, Gad ; Gabriel, Stacey B. ; Lander, Eric S. ; Wu, Catherine J. ; Fuchs, Charles S. ; Ogino, Shuji ; Garraway, Levi A. / Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. In: Cell Reports. 2016 ; Vol. 15, No. 4. pp. 857-865.
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