CNPN 2021 Virtual Annual Meeting (May 10 – 12, 2021)

Bioinformatics Solutions Inc. (BSI) is proud to support the Canadian proteomics community at this year’s Canadian National Proteomics Network (CNPN) 2021 Virtual Annual Meeting, which will take place from May 10 – 12, 2021.

On Monday, May 10th, we are excited to have Dr. Jonathan Krieger represent BSI as an invited speaker during the Bioinformatics session, with his talk entitled: “A facile immunopeptidomics workflow for capturing the HLA-I ligandome with PEAKS XPro”. Then on Wednesday, May 12th, we have the privilege of presenting Dr. Pouya Faridi, from Monash University, with his talk entitled: “PEAKS online: a high-throughput platform for discovery and quantitative immunopeptidomics”.

Throughout the week, attendees will be able to stop by the virtual booth to learn more about our products and services.

For more details, check out their website.

Presentation Abstracts

A facile immunopeptidomics workflow for capturing the HLA-I ligandome with PEAKS XPro
Presented by Jonathan R. Krieger, Ph.D., Bioinformatics Solutions Inc.

Identifying antigens displayed specifically on tumour cell surfaces by human leukocyte antigen (HLA) proteins is important for the development of immunotherapies and cancer vaccines. The difficulty in capturing an HLA ligandome stems from the fact that many HLA ligands are derived from splicing events or contain mutations. To address this challenge, we developed an immunopeptidomics workflow using PEAKS XPro that uses de novo sequencing to uncover such peptides and identifies missense mutations for neoantigen discovery, and that is applicable to any immunopeptidomic mass spectrometry dataset. Herein we demonstrate this workflow using an established public immunopeptidomic dataset.

PEAKS online: a high-throughput platform for discovery and quantitative immunopeptidomics
Presented by Pouya Faridi, Ph.D., Monash Biomedicine Discovery Institute, Monash University

The peptides presented by Human Leukocyte Antigens (immunopeptidome) play a critical role in adaptive immunity, allowing the surveillance of intra-and extracellular states by T cells. The most precise method for investigating immunopeptidomes is through immunoaffinity purification of pHLA and subsequent sequencing of the bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data acquired is interrogated using algorithms that rely upon a reference proteome for spectral matching. However, the absence of sequence information for non-canonical peptides in the predicted proteome precludes using this workflow for their identification.

We have developed a novel workflow to identify non-canonical spliced peptide antigens by incorporating the PEAKS software in the immunopeptidomics workflow. We have applied our approach to p-HLA derived from multiple cancer cell lines, including melanoma, triple-negative breast cancer, mesothelioma, DIPG, colon cancer, and mice models of breast cancer and melanoma. Surprisingly we found 20-30% of peptides present by HLA-I are generating through splicing post-translational modification. Of note, in each sample ~100-300 spliced peptides were derived from cancer-associated antigens, making them cancer-specific spliced peptides. We have confirmed the authenticity of a series of CAA spliced peptides by corresponding synthetic peptides. We also found a subset of the CAA shown that several of these peptides are immunogenic. Clinical studies for vaccination of melanoma patients with some of the discovered cancer-specific spliced peptides are ongoing.

These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that may be exploited therapeutically and suggest that spliced peptides may be a major class of tumour antigens. We found spliced peptides may yield more immunogenic epitopes than are available from the viral/cancer genome. Moreover, some antigens lack high-affinity HLA-ligands, and the peptide splicing mechanism can generate higher affinity neoepitopes for interaction with host HLA allomorphs. Understanding the nature and abundance of spliced peptides has high relevance for our understanding of potential novel targets of T cell immunity and will have significant implications for further immunotherapeutic approaches.