Research Topic

Immunopeptidomic Approaches for the Identification of Tumor (neo)Antigens

About this Research Topic

Significant improvements in next generation sequencing (NGS), mass spectrometry technologies and proteo-genomics bioinformatics pipelines have facilitated major breakthroughs in the discovery of tumor-associated antigens (TAAS), mutated neoantigens, as well as non-mutated neoantigens that are derived from unconventional coding sequences in the genome. These antigens arise during the process of tumorigenesis, and are typically not expressed or presented on the surface of normal healthy cells, and hence, they could play a key role in tumor immune recognition and be key targets of immunotherapeutic approaches. Nevertheless, a large portion of biogenesis and the (neo)antigenic landscape in cancer remains unexplored, and our ability to identify antigens that are capable of inducing tumor rejection in-vivo is limited. It is further unclear how best to prioritize such clinically relevant antigens for development of anti-cancer vaccines and T cell based therapies, especially in patients who have not responded to conventional therapeutic approaches.

Mass spectrometry based immunopeptidomics is the only methodology enabling comprehensive interrogation of the MHC ligandome presented naturally in vivo. Cancer cell lines, tumors, healthy tissues and body fluids have been subjected to immunopeptidomics approaches aimed at identifying cancer-associated antigens among the endogenously presented peptides. This Research Topic will focus on the various aspects related to the development of experimental and computational methodologies enabling the comprehensive characterization of the cancer immunopeptidome and the identification of clinically relevant tumor-specific antigens.

We welcome the submission of Original Research articles, Reviews and Methods from leaders in the field, with the aim of giving a comprehensive picture on the cancer immunopeptidome, under the following key points:

1. Methodologies and protocols for the identification and characterization of the tumor MHC class I and class II immunopeptidomes, including post-translational modified peptides, mutated neoantigens, and other tumor-specific antigens, in pre-clinical models and humans.

2. Development and application of proteo-genomics pipelines for identification of cancer-specific MHC binding peptides through MS based immunopeptidomics.

3. Immunopeptidomics as a tool to study response to cancer therapy.

We are confident that this Research Topic will help to better define the antigenic landscape of tumors, and will provide improvements related to existing technological and computational challenges affecting the yield, throughput, and accuracy of antigens discovered through MS-based immunopeptidomics. Based on this background, we also expect our collection to open the way to the development of new ideas and strategies to study responses to cancer therapy by characterizing dynamic changes in the repertoire of presented antigens.

Topic Editor Dr. Lill is employed by Genetech, a member of the Roche Group. Topic Editor Dr. Bassani-Sternberg declares no competing interests with regards to the Research Topic theme


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Significant improvements in next generation sequencing (NGS), mass spectrometry technologies and proteo-genomics bioinformatics pipelines have facilitated major breakthroughs in the discovery of tumor-associated antigens (TAAS), mutated neoantigens, as well as non-mutated neoantigens that are derived from unconventional coding sequences in the genome. These antigens arise during the process of tumorigenesis, and are typically not expressed or presented on the surface of normal healthy cells, and hence, they could play a key role in tumor immune recognition and be key targets of immunotherapeutic approaches. Nevertheless, a large portion of biogenesis and the (neo)antigenic landscape in cancer remains unexplored, and our ability to identify antigens that are capable of inducing tumor rejection in-vivo is limited. It is further unclear how best to prioritize such clinically relevant antigens for development of anti-cancer vaccines and T cell based therapies, especially in patients who have not responded to conventional therapeutic approaches.

Mass spectrometry based immunopeptidomics is the only methodology enabling comprehensive interrogation of the MHC ligandome presented naturally in vivo. Cancer cell lines, tumors, healthy tissues and body fluids have been subjected to immunopeptidomics approaches aimed at identifying cancer-associated antigens among the endogenously presented peptides. This Research Topic will focus on the various aspects related to the development of experimental and computational methodologies enabling the comprehensive characterization of the cancer immunopeptidome and the identification of clinically relevant tumor-specific antigens.

We welcome the submission of Original Research articles, Reviews and Methods from leaders in the field, with the aim of giving a comprehensive picture on the cancer immunopeptidome, under the following key points:

1. Methodologies and protocols for the identification and characterization of the tumor MHC class I and class II immunopeptidomes, including post-translational modified peptides, mutated neoantigens, and other tumor-specific antigens, in pre-clinical models and humans.

2. Development and application of proteo-genomics pipelines for identification of cancer-specific MHC binding peptides through MS based immunopeptidomics.

3. Immunopeptidomics as a tool to study response to cancer therapy.

We are confident that this Research Topic will help to better define the antigenic landscape of tumors, and will provide improvements related to existing technological and computational challenges affecting the yield, throughput, and accuracy of antigens discovered through MS-based immunopeptidomics. Based on this background, we also expect our collection to open the way to the development of new ideas and strategies to study responses to cancer therapy by characterizing dynamic changes in the repertoire of presented antigens.

Topic Editor Dr. Lill is employed by Genetech, a member of the Roche Group. Topic Editor Dr. Bassani-Sternberg declares no competing interests with regards to the Research Topic theme


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

10 July 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

10 July 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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