T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes

Daniele Mennonna, Cristina Maccalli, Michele C. Romano, Claudio Garavaglia, Filippo Capocefalo, Roberta Bordoni, Marco Severgnini, Gianluca De Bellis, John Sidney, Alessandro Sette, Alessandro Gori, Renato Longhi, Marco Braga, Luca Ghirardelli, Ludovica Baldari, Elena Orsenigo, Luca Albarello, Elisabetta Zino, Katharina Fleischhauer, Gina MazzolaNorma Ferrero, Antonio Amoroso, Giulia Casorati, Giorgio Parmiani, Paolo Dellabona

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Objective Patient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies. Design We undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions. Results Several unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8+ and CD4+ T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8+ T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo. Conclusions These results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component.

Original languageEnglish
Pages (from-to)454-463
Number of pages10
JournalGut
Volume66
Issue number3
DOIs
Publication statusPublished - 1 Mar 2017
Externally publishedYes

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Colorectal Neoplasms
T-Lymphocytes
Mutation
Neoplastic Stem Cells
Genes
Cell Culture Techniques
Neoplasms
HLA Antigens
Tissue Donors
T-Lymphocyte Epitopes
Neoplasm Genes
Neoplasm Antigens
Cellular Structures
Allergy and Immunology
DNA Sequence Analysis
Epitopes
Stem Cells
Complementary DNA
Alleles
Antigens

Keywords

  • antigens
  • Cancer immunobiology
  • colorectal cancer
  • gene mutation
  • immune response

ASJC Scopus subject areas

  • Gastroenterology

Cite this

Mennonna, D., Maccalli, C., Romano, M. C., Garavaglia, C., Capocefalo, F., Bordoni, R., ... Dellabona, P. (2017). T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. Gut, 66(3), 454-463. https://doi.org/10.1136/gutjnl-2015-309453

T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. / Mennonna, Daniele; Maccalli, Cristina; Romano, Michele C.; Garavaglia, Claudio; Capocefalo, Filippo; Bordoni, Roberta; Severgnini, Marco; De Bellis, Gianluca; Sidney, John; Sette, Alessandro; Gori, Alessandro; Longhi, Renato; Braga, Marco; Ghirardelli, Luca; Baldari, Ludovica; Orsenigo, Elena; Albarello, Luca; Zino, Elisabetta; Fleischhauer, Katharina; Mazzola, Gina; Ferrero, Norma; Amoroso, Antonio; Casorati, Giulia; Parmiani, Giorgio; Dellabona, Paolo.

In: Gut, Vol. 66, No. 3, 01.03.2017, p. 454-463.

Research output: Contribution to journalArticle

Mennonna, D, Maccalli, C, Romano, MC, Garavaglia, C, Capocefalo, F, Bordoni, R, Severgnini, M, De Bellis, G, Sidney, J, Sette, A, Gori, A, Longhi, R, Braga, M, Ghirardelli, L, Baldari, L, Orsenigo, E, Albarello, L, Zino, E, Fleischhauer, K, Mazzola, G, Ferrero, N, Amoroso, A, Casorati, G, Parmiani, G & Dellabona, P 2017, 'T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes', Gut, vol. 66, no. 3, pp. 454-463. https://doi.org/10.1136/gutjnl-2015-309453
Mennonna, Daniele ; Maccalli, Cristina ; Romano, Michele C. ; Garavaglia, Claudio ; Capocefalo, Filippo ; Bordoni, Roberta ; Severgnini, Marco ; De Bellis, Gianluca ; Sidney, John ; Sette, Alessandro ; Gori, Alessandro ; Longhi, Renato ; Braga, Marco ; Ghirardelli, Luca ; Baldari, Ludovica ; Orsenigo, Elena ; Albarello, Luca ; Zino, Elisabetta ; Fleischhauer, Katharina ; Mazzola, Gina ; Ferrero, Norma ; Amoroso, Antonio ; Casorati, Giulia ; Parmiani, Giorgio ; Dellabona, Paolo. / T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. In: Gut. 2017 ; Vol. 66, No. 3. pp. 454-463.
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T1 - T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes

AU - Mennonna, Daniele

AU - Maccalli, Cristina

AU - Romano, Michele C.

AU - Garavaglia, Claudio

AU - Capocefalo, Filippo

AU - Bordoni, Roberta

AU - Severgnini, Marco

AU - De Bellis, Gianluca

AU - Sidney, John

AU - Sette, Alessandro

AU - Gori, Alessandro

AU - Longhi, Renato

AU - Braga, Marco

AU - Ghirardelli, Luca

AU - Baldari, Ludovica

AU - Orsenigo, Elena

AU - Albarello, Luca

AU - Zino, Elisabetta

AU - Fleischhauer, Katharina

AU - Mazzola, Gina

AU - Ferrero, Norma

AU - Amoroso, Antonio

AU - Casorati, Giulia

AU - Parmiani, Giorgio

AU - Dellabona, Paolo

PY - 2017/3/1

Y1 - 2017/3/1

N2 - Objective Patient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies. Design We undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions. Results Several unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8+ and CD4+ T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8+ T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo. Conclusions These results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component.

AB - Objective Patient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies. Design We undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions. Results Several unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8+ and CD4+ T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8+ T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo. Conclusions These results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component.

KW - antigens

KW - Cancer immunobiology

KW - colorectal cancer

KW - gene mutation

KW - immune response

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