Dataset Information

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

ABSTRACT: Immunopeptidome analysis of colorectal adenocarcinoma tissues as well as adjacent benign tissues was performed to characterize the natural HLA class I and class II presented ligandome represented in the context of malignancy as well as in benign tissue of the colon.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Michael Ghosh

LAB HEAD: Hans-Georg Rammensee

PROVIDER: PXD009602 | Pride | 2019-03-12

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	UPN_10_HLA-class_II_CRC_malignant_Rep1.msf	Msf
	UPN_10_HLA-class_II_CRC_malignant_Rep1.raw	Raw
	UPN_10_HLA-class_II_CRC_malignant_Rep2.msf	Msf
	UPN_10_HLA-class_II_CRC_malignant_Rep2.raw	Raw
	UPN_10_HLA-class_II_NMT_benign_Rep1.msf	Msf

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Publications

Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation.

Löffler Markus W MW Kowalewski Daniel J DJ Backert Linus L Bernhardt Jörg J Adam Patrick P Schuster Heiko H Dengler Florian F Backes Daniel D Kopp Hans-Georg HG Beckert Stefan S Wagner Silvia S Königsrainer Ingmar I Kohlbacher Oliver O Kanz Lothar L Königsrainer Alfred A Rammensee Hans-Georg HG Stevanović Stefan S Haen Sebastian P SP

Cancer research 20180522 16

Immune cell infiltrates have proven highly relevant for colorectal carcinoma prognosis, making colorectal cancer a promising candidate for immunotherapy. Because tumors interact with the immune system via HLA-presented peptide ligands, exact knowledge of the peptidome constitution is fundamental for understanding this relationship. Here, we comprehensively describe the naturally presented HLA ligandome of colorectal carcinoma and corresponding nonmalignant colon (NMC) tissue. Mass spectrometry i ...[more]

PMID: 29789417

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Project description:Various cancer immunotherapies rely on the T cell recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remains challenging. Here, we introduce the open-access Peptides for Cancer Immunotherapy Database (PCI-DB, https://pci-db.org/), a comprehensive resource of immunopeptidome data originating from various malignant and benign primary tissues that provides the research community with a convenient tool to facilitate the identification of peptide targets for immunotherapy development. The PCI-DB includes > 6.6 million HLA class I and > 3.4 million HLA class II peptides from over 40 tissue types and cancer entities analyzed uniformly using high-sensitive nf-core bioinformatics pipelines and applying a global peptide false discovery rate (FDR) approach. First application of the database provided insights into the representation of cancer-testis antigens (CTA) across malignant and benign tissues and enabled the identification and characterization of the cross-tumor entity and entity-specific tumor-associated antigens as well as naturally presented neoepitopes from frequent cancer mutations. Further, we used the PCI-DB to design personalized peptide vaccines for two patients suffering from metastatic cancer. PCI-DB enabled the composition of both a multi-peptide vaccine comprising non-mutated, highly frequent tumor-associated antigens matching the immunopeptidome of the individual patient´s tumor and a neoepitope-based vaccine matching the mutational profile of the cancer patient. Both vaccine approaches induced potent and long-lasting T-cell responses, accompanied by long-term survival of these advanced cancer patients. In conclusion, the PCI-DB provides a highly versatile tool to broaden the understanding of cancer-related antigen presentation and, ultimately, supports the development of novel immunotherapies.