Identification of T Cell Antigens for Precision-Targeted Immune Therapy of Cancer

Sofie Ramskov

Research output: Book/ReportPh.D. thesis

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Abstract

With unprecedented successes in recent years, cancer immune therapy has entered mainstream oncology and has, next to surgery, radiation and chemotherapy, been established as a fourth pillar of cancer treatment. However, despite its success, only a subgroup of patients benefit from treatment and a general problem with most immune therapies is that they are not specifically targeted to the patient’s tumors, but rather provide a general boost of immune activity. This translates into two issues. Firstly, the general activation of virtually all effector T cells of the immune system leads to substantial side effects from autoreactive T cells. Secondly, in patients with a lack of pre-existing T cell recognition of the tumor, efficacy is compromised. Precisiontargeted immune therapy aims to solve these issues by steering the T cells towards specific targets on the tumor. The presented thesis comprises four research papers with the common theme of identification and characterization of such T cell targets. In a first paper we identify four novel shared, overexpressed T cell antigens in breast cancer. We demonstrate an enrichment of T cell responses in patients compared to healthy donors and find that the peptides giving rise to T cell responses cluster in “immunological hotspots”. Breast cancer is one of the leading causes of cancer related deaths in women, but in terms of immune therapy much less explored than other types of cancer, partly due to a minimally described landscape of T cell targets. The study therefore provides an important contribution to the characterization of novel T cell targets for precision-targeted immune therapy and immunomonitoring of breast cancer. In a second paper, we describe the first identification of T cell targets derived from mutational products, so-called neoepitopes, in renal cell carcinoma patients. Tumors of renal cell carcinoma patients have the highest number of insertions and deletions of all cancers, mutation types expected to be highly immunogenic due to their low similarity to the original wildtype sequence. We therefore evaluate the immunogenicity of neopeptides originating from insertions and deletions compared to neopeptides originating from single nucleotide variations. Furthermore we compare tumor fragments and tumor cell lines as sources for whole exome sequencing and mutational mapping. In a third paper, we investigate the impact of neoantigen intratumor heterogeneity on T cell tumor immunity. Heterogeneity of tumors poses a big challenge for cancer treatment in general, not least for cancer immune therapy, where the outgrowth of tumor escape variants lead to failure of response. We observe a correlation between the burden of clonal neoantigens and overall survival in primary lung adenocarcinomas and we demonstrate that advanced non-small cell lung cancer and melanoma patients with tumors enriched for clonal neoantigens respond better to treatment with PD-1 and CTLA-4 checkpoint inhibitors. In line with these findings we further identify T cell responses against clonal neoepitopes in two non-small cell lung cancer patients, represented by a homogenous and a heterogeneous tumor. Lastly, in a fourth paper, we report a finding across three different cancer cohorts, that T cell recognition of neopeptides bound by the human leukocyte antigen (HLA)-C subtype compares to or even exceeds T cell recognition of neopeptides bound by HLA-A and -B subtypes. HLA-C has previously posed less attention in terms of cancer immunogenicity studies, partly explained by a previous lack of reagents and suitable prediction algorithms and partly explained by a lower expression, which has fostered an anticipation of lower immunogenicity. Based on our findings we argue that HLA-C might indeed play a substantial role in tumor cell recognition and advocate for the inclusion of HLA-C restricted (neo)peptides in future antigen-defined studies and therapy. Together these four studies contribute to the identification and characterization of novel targets for immune therapy of cancer and facilitate the development of precision-targeted strategies. With identification of new targets and the associated novel insights to what makes a good immune target, it is anticipated that precision-targeted immune therapy will raise the already successful bar of immune therapy.
Original languageEnglish
PublisherDTU Health Technology
Number of pages58
Publication statusPublished - 2019

Cite this

@phdthesis{8a17a36a70314f0bbd0ff5d18289d169,
title = "Identification of T Cell Antigens for Precision-Targeted Immune Therapy of Cancer",
abstract = "With unprecedented successes in recent years, cancer immune therapy has entered mainstream oncology and has, next to surgery, radiation and chemotherapy, been established as a fourth pillar of cancer treatment. However, despite its success, only a subgroup of patients benefit from treatment and a general problem with most immune therapies is that they are not specifically targeted to the patient’s tumors, but rather provide a general boost of immune activity. This translates into two issues. Firstly, the general activation of virtually all effector T cells of the immune system leads to substantial side effects from autoreactive T cells. Secondly, in patients with a lack of pre-existing T cell recognition of the tumor, efficacy is compromised. Precisiontargeted immune therapy aims to solve these issues by steering the T cells towards specific targets on the tumor. The presented thesis comprises four research papers with the common theme of identification and characterization of such T cell targets. In a first paper we identify four novel shared, overexpressed T cell antigens in breast cancer. We demonstrate an enrichment of T cell responses in patients compared to healthy donors and find that the peptides giving rise to T cell responses cluster in “immunological hotspots”. Breast cancer is one of the leading causes of cancer related deaths in women, but in terms of immune therapy much less explored than other types of cancer, partly due to a minimally described landscape of T cell targets. The study therefore provides an important contribution to the characterization of novel T cell targets for precision-targeted immune therapy and immunomonitoring of breast cancer. In a second paper, we describe the first identification of T cell targets derived from mutational products, so-called neoepitopes, in renal cell carcinoma patients. Tumors of renal cell carcinoma patients have the highest number of insertions and deletions of all cancers, mutation types expected to be highly immunogenic due to their low similarity to the original wildtype sequence. We therefore evaluate the immunogenicity of neopeptides originating from insertions and deletions compared to neopeptides originating from single nucleotide variations. Furthermore we compare tumor fragments and tumor cell lines as sources for whole exome sequencing and mutational mapping. In a third paper, we investigate the impact of neoantigen intratumor heterogeneity on T cell tumor immunity. Heterogeneity of tumors poses a big challenge for cancer treatment in general, not least for cancer immune therapy, where the outgrowth of tumor escape variants lead to failure of response. We observe a correlation between the burden of clonal neoantigens and overall survival in primary lung adenocarcinomas and we demonstrate that advanced non-small cell lung cancer and melanoma patients with tumors enriched for clonal neoantigens respond better to treatment with PD-1 and CTLA-4 checkpoint inhibitors. In line with these findings we further identify T cell responses against clonal neoepitopes in two non-small cell lung cancer patients, represented by a homogenous and a heterogeneous tumor. Lastly, in a fourth paper, we report a finding across three different cancer cohorts, that T cell recognition of neopeptides bound by the human leukocyte antigen (HLA)-C subtype compares to or even exceeds T cell recognition of neopeptides bound by HLA-A and -B subtypes. HLA-C has previously posed less attention in terms of cancer immunogenicity studies, partly explained by a previous lack of reagents and suitable prediction algorithms and partly explained by a lower expression, which has fostered an anticipation of lower immunogenicity. Based on our findings we argue that HLA-C might indeed play a substantial role in tumor cell recognition and advocate for the inclusion of HLA-C restricted (neo)peptides in future antigen-defined studies and therapy. Together these four studies contribute to the identification and characterization of novel targets for immune therapy of cancer and facilitate the development of precision-targeted strategies. With identification of new targets and the associated novel insights to what makes a good immune target, it is anticipated that precision-targeted immune therapy will raise the already successful bar of immune therapy.",
author = "Sofie Ramskov",
year = "2019",
language = "English",
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Identification of T Cell Antigens for Precision-Targeted Immune Therapy of Cancer. / Ramskov, Sofie.

DTU Health Technology, 2019. 58 p.

Research output: Book/ReportPh.D. thesis

TY - BOOK

T1 - Identification of T Cell Antigens for Precision-Targeted Immune Therapy of Cancer

AU - Ramskov, Sofie

PY - 2019

Y1 - 2019

N2 - With unprecedented successes in recent years, cancer immune therapy has entered mainstream oncology and has, next to surgery, radiation and chemotherapy, been established as a fourth pillar of cancer treatment. However, despite its success, only a subgroup of patients benefit from treatment and a general problem with most immune therapies is that they are not specifically targeted to the patient’s tumors, but rather provide a general boost of immune activity. This translates into two issues. Firstly, the general activation of virtually all effector T cells of the immune system leads to substantial side effects from autoreactive T cells. Secondly, in patients with a lack of pre-existing T cell recognition of the tumor, efficacy is compromised. Precisiontargeted immune therapy aims to solve these issues by steering the T cells towards specific targets on the tumor. The presented thesis comprises four research papers with the common theme of identification and characterization of such T cell targets. In a first paper we identify four novel shared, overexpressed T cell antigens in breast cancer. We demonstrate an enrichment of T cell responses in patients compared to healthy donors and find that the peptides giving rise to T cell responses cluster in “immunological hotspots”. Breast cancer is one of the leading causes of cancer related deaths in women, but in terms of immune therapy much less explored than other types of cancer, partly due to a minimally described landscape of T cell targets. The study therefore provides an important contribution to the characterization of novel T cell targets for precision-targeted immune therapy and immunomonitoring of breast cancer. In a second paper, we describe the first identification of T cell targets derived from mutational products, so-called neoepitopes, in renal cell carcinoma patients. Tumors of renal cell carcinoma patients have the highest number of insertions and deletions of all cancers, mutation types expected to be highly immunogenic due to their low similarity to the original wildtype sequence. We therefore evaluate the immunogenicity of neopeptides originating from insertions and deletions compared to neopeptides originating from single nucleotide variations. Furthermore we compare tumor fragments and tumor cell lines as sources for whole exome sequencing and mutational mapping. In a third paper, we investigate the impact of neoantigen intratumor heterogeneity on T cell tumor immunity. Heterogeneity of tumors poses a big challenge for cancer treatment in general, not least for cancer immune therapy, where the outgrowth of tumor escape variants lead to failure of response. We observe a correlation between the burden of clonal neoantigens and overall survival in primary lung adenocarcinomas and we demonstrate that advanced non-small cell lung cancer and melanoma patients with tumors enriched for clonal neoantigens respond better to treatment with PD-1 and CTLA-4 checkpoint inhibitors. In line with these findings we further identify T cell responses against clonal neoepitopes in two non-small cell lung cancer patients, represented by a homogenous and a heterogeneous tumor. Lastly, in a fourth paper, we report a finding across three different cancer cohorts, that T cell recognition of neopeptides bound by the human leukocyte antigen (HLA)-C subtype compares to or even exceeds T cell recognition of neopeptides bound by HLA-A and -B subtypes. HLA-C has previously posed less attention in terms of cancer immunogenicity studies, partly explained by a previous lack of reagents and suitable prediction algorithms and partly explained by a lower expression, which has fostered an anticipation of lower immunogenicity. Based on our findings we argue that HLA-C might indeed play a substantial role in tumor cell recognition and advocate for the inclusion of HLA-C restricted (neo)peptides in future antigen-defined studies and therapy. Together these four studies contribute to the identification and characterization of novel targets for immune therapy of cancer and facilitate the development of precision-targeted strategies. With identification of new targets and the associated novel insights to what makes a good immune target, it is anticipated that precision-targeted immune therapy will raise the already successful bar of immune therapy.

AB - With unprecedented successes in recent years, cancer immune therapy has entered mainstream oncology and has, next to surgery, radiation and chemotherapy, been established as a fourth pillar of cancer treatment. However, despite its success, only a subgroup of patients benefit from treatment and a general problem with most immune therapies is that they are not specifically targeted to the patient’s tumors, but rather provide a general boost of immune activity. This translates into two issues. Firstly, the general activation of virtually all effector T cells of the immune system leads to substantial side effects from autoreactive T cells. Secondly, in patients with a lack of pre-existing T cell recognition of the tumor, efficacy is compromised. Precisiontargeted immune therapy aims to solve these issues by steering the T cells towards specific targets on the tumor. The presented thesis comprises four research papers with the common theme of identification and characterization of such T cell targets. In a first paper we identify four novel shared, overexpressed T cell antigens in breast cancer. We demonstrate an enrichment of T cell responses in patients compared to healthy donors and find that the peptides giving rise to T cell responses cluster in “immunological hotspots”. Breast cancer is one of the leading causes of cancer related deaths in women, but in terms of immune therapy much less explored than other types of cancer, partly due to a minimally described landscape of T cell targets. The study therefore provides an important contribution to the characterization of novel T cell targets for precision-targeted immune therapy and immunomonitoring of breast cancer. In a second paper, we describe the first identification of T cell targets derived from mutational products, so-called neoepitopes, in renal cell carcinoma patients. Tumors of renal cell carcinoma patients have the highest number of insertions and deletions of all cancers, mutation types expected to be highly immunogenic due to their low similarity to the original wildtype sequence. We therefore evaluate the immunogenicity of neopeptides originating from insertions and deletions compared to neopeptides originating from single nucleotide variations. Furthermore we compare tumor fragments and tumor cell lines as sources for whole exome sequencing and mutational mapping. In a third paper, we investigate the impact of neoantigen intratumor heterogeneity on T cell tumor immunity. Heterogeneity of tumors poses a big challenge for cancer treatment in general, not least for cancer immune therapy, where the outgrowth of tumor escape variants lead to failure of response. We observe a correlation between the burden of clonal neoantigens and overall survival in primary lung adenocarcinomas and we demonstrate that advanced non-small cell lung cancer and melanoma patients with tumors enriched for clonal neoantigens respond better to treatment with PD-1 and CTLA-4 checkpoint inhibitors. In line with these findings we further identify T cell responses against clonal neoepitopes in two non-small cell lung cancer patients, represented by a homogenous and a heterogeneous tumor. Lastly, in a fourth paper, we report a finding across three different cancer cohorts, that T cell recognition of neopeptides bound by the human leukocyte antigen (HLA)-C subtype compares to or even exceeds T cell recognition of neopeptides bound by HLA-A and -B subtypes. HLA-C has previously posed less attention in terms of cancer immunogenicity studies, partly explained by a previous lack of reagents and suitable prediction algorithms and partly explained by a lower expression, which has fostered an anticipation of lower immunogenicity. Based on our findings we argue that HLA-C might indeed play a substantial role in tumor cell recognition and advocate for the inclusion of HLA-C restricted (neo)peptides in future antigen-defined studies and therapy. Together these four studies contribute to the identification and characterization of novel targets for immune therapy of cancer and facilitate the development of precision-targeted strategies. With identification of new targets and the associated novel insights to what makes a good immune target, it is anticipated that precision-targeted immune therapy will raise the already successful bar of immune therapy.

M3 - Ph.D. thesis

BT - Identification of T Cell Antigens for Precision-Targeted Immune Therapy of Cancer

PB - DTU Health Technology

ER -