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Article ; Online: Proteomics special issue: Precision immunology and oncology.

Ramarathinam, Sri H / Purcell, Anthony W

2021 Volume 21, Issue 17-18, Page(s) e2000159

MeSH term(s)	Humans ; Medical Oncology ; Neoplasms ; Precision Medicine ; Proteomics
Language	English
Publishing date	2021-09-12
Publishing country	Germany
Document type	Editorial
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202000159
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Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: New insights and approaches for analyses of immunopeptidomes.

Illing, Patricia T / Ramarathinam, Sri H / Purcell, Anthony W

Current opinion in immunology

2022 Volume 77, Page(s) 102216

Abstract: Human leucocyte antigen (HLA) molecules play a key role in health and disease by presenting antigen to T-lymphocytes for immunosurveillance. Immunopeptidomics involves the study of the collection of peptides presented within the antigen-binding groove of ...

Abstract	Human leucocyte antigen (HLA) molecules play a key role in health and disease by presenting antigen to T-lymphocytes for immunosurveillance. Immunopeptidomics involves the study of the collection of peptides presented within the antigen-binding groove of HLA molecules. Identifying their nature and diversity is crucial to understanding immunosurveillance especially during infection or for the recognition and potential eradication of tumours. This review discusses recent advances in the isolation, identification, and quantitation of these peptide antigens. New informatics approaches and databases have shed light on the extent of peptide antigens derived from unconventional sources including peptides derived from transcripts associated with frame shifts, long noncoding RNA, incorrectly annotated untranslated regions, post-translational modifications, and proteasomal splicing. Several challenges remain in successful analysis of immunopeptides, yet recent developments point to unexplored biology waiting to be unravelled.
MeSH term(s)	Antigens ; HLA Antigens ; Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II ; Humans ; Peptides ; T-Lymphocytes
Chemical Substances	Antigens ; HLA Antigens ; Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II ; Peptides
Language	English
Publishing date	2022-06-15
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2022.102216
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Article ; Online: Isolation of HLA Bound Peptides by Immunoaffinity Capture and Identification by Mass Spectrometry.

Pandey, Kirti / Ramarathinam, Sri H / Purcell, Anthony W

Current protocols

2021 Volume 1, Issue 3, Page(s) e92

Abstract: This article describes the purification of HLA-bound peptides and their subsequent sequencing by mass spectrometry. These methods can be used for both HLA class I and class II molecules and can be adapted to different species depending on the ... ...

Abstract	This article describes the purification of HLA-bound peptides and their subsequent sequencing by mass spectrometry. These methods can be used for both HLA class I and class II molecules and can be adapted to different species depending on the availability of specific antibodies. Peptides can be successfully isolated from a variety of sample types, including in vitro cultured cells and primary tissues. The method involves the affinity capture of HLA-peptide complexes and separation of peptides from HLA heavy chains, followed by tailored interrogation by mass spectrometry to take into account the non-tryptic nature of endogenously derived HLA-bound peptides. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of immunoaffinity column Alternate Protocol 1: Preparation of microscale immunoaffinity column Basic Protocol 2: Generation of cell lysate and HLA immunoaffinity purification Alternate Protocol 2: Microscale immunoaffinity purification Basic Protocol 3: Separation of HLA peptides by reverse-phase high-performance liquid chromatography (RP-HPLC) Alternate Protocol 3: Isolation of HLA peptides using molecular weight cutoff (MWCO) filter Basic Protocol 4: Mass spectrometry and data analysis.
MeSH term(s)	Antibodies ; Chromatography, High Pressure Liquid ; Histocompatibility Antigens ; Mass Spectrometry ; Peptides
Chemical Substances	Antibodies ; Histocompatibility Antigens ; Peptides
Language	English
Publishing date	2021-03-26
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.92
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Article ; Online: MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes.

Shahbazy, Mohammad / Ramarathinam, Sri H / Li, Chen / Illing, Patricia T / Faridi, Pouya / Croft, Nathan P / Purcell, Anthony W

Briefings in bioinformatics

2024 Volume 25, Issue 2

Abstract: The major histocompatibility complex (MHC) encodes a range of immune response genes, including the human leukocyte antigens (HLAs) in humans. These molecules bind peptide antigens and present them on the cell surface for T cell recognition. The ... ...

Abstract	The major histocompatibility complex (MHC) encodes a range of immune response genes, including the human leukocyte antigens (HLAs) in humans. These molecules bind peptide antigens and present them on the cell surface for T cell recognition. The repertoires of peptides presented by HLA molecules are termed immunopeptidomes. The highly polymorphic nature of the genres that encode the HLA molecules confers allotype-specific differences in the sequences of bound ligands. Allotype-specific ligand preferences are often defined by peptide-binding motifs. Individuals express up to six classical class I HLA allotypes, which likely present peptides displaying different binding motifs. Such complex datasets make the deconvolution of immunopeptidomic data into allotype-specific contributions and further dissection of binding-specificities challenging. Herein, we developed MHCpLogics as an interactive machine learning-based tool for mining peptide-binding sequence motifs and visualization of immunopeptidome data across complex datasets. We showcase the functionalities of MHCpLogics by analyzing both in-house and published mono- and multi-allelic immunopeptidomics data. The visualization modalities of MHCpLogics allow users to inspect clustered sequences down to individual peptide components and to examine broader sequence patterns within multiple immunopeptidome datasets. MHCpLogics can deconvolute large immunopeptidome datasets enabling the interrogation of clusters for the segregation of allotype-specific peptide sequence motifs, identification of sub-peptidome motifs, and the exportation of clustered peptide sequence lists. The tool facilitates rapid inspection of immunopeptidomes as a resource for the immunology and vaccine communities. MHCpLogics is a standalone application available via an executable installation at: https://github.com/PurcellLab/MHCpLogics.
MeSH term(s)	Humans ; Data Visualization ; Peptides/chemistry ; HLA Antigens/genetics ; Histocompatibility Antigens ; Machine Learning ; Cluster Analysis
Chemical Substances	Peptides ; HLA Antigens ; Histocompatibility Antigens
Language	English
Publishing date	2024-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae087
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Article ; Online: Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.

Scull, Katherine E / Pandey, Kirti / Ramarathinam, Sri H / Purcell, Anthony W

Molecular & cellular proteomics : MCP

2021 Volume 20, Page(s) 100143

Abstract: Human leukocyte antigen (HLA) molecules are cell-surface glycoproteins that present peptide antigens on the cell surface for surveillance by T lymphocytes, which contemporaneously seek signs of disease. Mass spectrometric analysis allows us to identify ... ...

Abstract	Human leukocyte antigen (HLA) molecules are cell-surface glycoproteins that present peptide antigens on the cell surface for surveillance by T lymphocytes, which contemporaneously seek signs of disease. Mass spectrometric analysis allows us to identify large numbers of these peptides (the immunopeptidome) following affinity purification of solubilized HLA-peptide complexes. However, in recent years, there has been a growing awareness of the "dark side" of the immunopeptidome: unconventional peptide epitopes, including neoepitopes, which elude detection by conventional search methods because their sequences are not present in reference protein databases (DBs). Here, we establish a bioinformatics workflow to aid identification of peptides generated by noncanonical translation of mRNA or by genome variants. The workflow incorporates both standard transcriptomics software and novel computer programs to produce cell line-specific protein DBs based on three-frame translation of the transcriptome. The final protein DB also includes sequences resulting from variants determined by variant calling on the same RNA-Seq data. We then searched our experimental data against both transcriptome-based and standard DBs using PEAKS Studio (Bioinformatics Solutions, Inc). Finally, further novel software helps to compare the various result sets arising for each sample, pinpoint putative genomic origins for unconventional sequences, and highlight potential neoepitopes. We applied the workflow to study the immunopeptidome of the acute myeloid leukemia cell line THP-1, using RNA-Seq and immunopeptidome data. We confidently identified over 14,000 peptides from three replicates of purified HLA peptides derived from THP-1 cells using the conventional UniProt human proteome. Using the transcriptome-based DB generated using our workflow, we recapitulated >85% of these and also identified 1029 unconventional peptides not explained by UniProt, including 16 sequences caused by nonsynonymous variants. Our workflow, which we term "immunopeptidogenomics," can provide DBs, which include pertinent unconventional sequences and allow neoepitope discovery, without becoming too large to search. Immunopeptidogenomics is a step toward unbiased search approaches that are needed to illuminate the dark side of the immunopeptidome.
MeSH term(s)	Databases, Protein ; Epitopes ; Genomics ; HLA Antigens/genetics ; HLA Antigens/metabolism ; Humans ; Peptides/genetics ; Peptides/metabolism ; Proteome ; RNA-Seq ; Software ; THP-1 Cells ; Transcriptome ; Workflow
Chemical Substances	Epitopes ; HLA Antigens ; Peptides ; Proteome
Language	English
Publishing date	2021-09-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2021.100143
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Zs.A 5599: Show issues

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Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: HLA class II immunopeptidomics reveals that co-inherited HLA-allotypes within an extended haplotype can improve proteome coverage for immunosurveillance.

Ramarathinam, Sri H / Ho, Bosco K / Dudek, Nadine L / Purcell, Anthony W

Proteomics

2021 Volume 21, Issue 17-18, Page(s) e2000160

Abstract: Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA-DR, -DQ, and -DP. These molecules share approximately 70% sequence similarity and all present peptide ligands to circulating T cells. While the peptide ... ...

Abstract	Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA-DR, -DQ, and -DP. These molecules share approximately 70% sequence similarity and all present peptide ligands to circulating T cells. While the peptide repertoires of numerous HLA-DR, -DQ, and -DP allotypes have been examined, there have been few reports on the combined repertoire of these co-inherited molecules expressed in a single cell as an extended HLA haplotype. Here we describe the endogenous peptide repertoire of a human B lymphoblastoid cell line (C1R) expressing the class II haplotype HLA-DR12/DQ7/DP4. We have identified 71350 unique naturally processed peptides presented collectively by HLA-DR12, HLA-DQ7, or HLA-DP4. The resulting "haplodome" is complemented by the cellular proteome defined by standard LC-MS/MS approaches. This large dataset has shed light on properties of these class II ligands especially the preference for membrane and extracellular source proteins. Our data also provides insights into the co-evolution of these conserved haplotypes of closely linked and co-inherited HLA molecules; which together increase sequence coverage of cellular proteins for immune surveillance with minimal overlap between each co-inherited HLA-class II allomorph.
MeSH term(s)	Chromatography, Liquid ; HLA-DQ Antigens/genetics ; Haplotypes ; Histocompatibility Antigens Class II ; Humans ; Monitoring, Immunologic ; Proteome ; Tandem Mass Spectrometry
Chemical Substances	HLA-DQ Antigens ; Histocompatibility Antigens Class II ; Proteome
Language	English
Publishing date	2021-08-17
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202000160
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics.

Shahbazy, Mohammad / Ramarathinam, Sri H / Illing, Patricia T / Jappe, Emma C / Faridi, Pouya / Croft, Nathan P / Purcell, Anthony W

Molecular & cellular proteomics : MCP

2023 Volume 22, Issue 4, Page(s) 100515

Abstract: Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex [human leukocyte antigen (HLA) in humans]. These HLA-peptide complexes are presented on the cell surface for immune T-cell recognition. ... ...

Abstract	Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex [human leukocyte antigen (HLA) in humans]. These HLA-peptide complexes are presented on the cell surface for immune T-cell recognition. Immunopeptidomics denotes the utilization of tandem mass spectrometry to identify and quantify peptides bound to HLA molecules. Data-independent acquisition (DIA) has emerged as a powerful strategy for quantitative proteomics and deep proteome-wide identification; however, DIA application to immunopeptidomics analyses has so far seen limited use. Further, of the many DIA data processing tools currently available, there is no consensus in the immunopeptidomics community on the most appropriate pipeline(s) for in-depth and accurate HLA peptide identification. Herein, we benchmarked four commonly used spectral library-based DIA pipelines developed for proteomics applications (Skyline, Spectronaut, DIA-NN, and PEAKS) for their ability to perform immunopeptidome quantification. We validated and assessed the capability of each tool to identify and quantify HLA-bound peptides. Generally, DIA-NN and PEAKS provided higher immunopeptidome coverage with more reproducible results. Skyline and Spectronaut conferred more accurate peptide identification with lower experimental false-positive rates. All tools demonstrated reasonable correlations in quantifying precursors of HLA-bound peptides. Our benchmarking study suggests a combined strategy of applying at least two complementary DIA software tools to achieve the greatest degree of confidence and in-depth coverage of immunopeptidome data.
MeSH term(s)	Humans ; Benchmarking ; Peptides/analysis ; Histocompatibility Antigens Class I/metabolism ; Proteomics/methods ; Tandem Mass Spectrometry ; Histocompatibility Antigens Class II
Chemical Substances	Peptides ; Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II
Language	English
Publishing date	2023-02-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2023.100515
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Article ; Online: Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics.

Purcell, Anthony W / Ramarathinam, Sri H / Ternette, Nicola

Nature protocols

2019 Volume 14, Issue 6, Page(s) 1687–1707

Abstract: Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm of the adaptive immune system facilitates the eradication of pathogen- ... ...

Abstract	Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm of the adaptive immune system facilitates the eradication of pathogen-infected and cancerous cells, as well as the production of antibodies. Methods to identify these peptide antigens are critical to the development of new vaccines, for which the goal is the generation of effective adaptive immune responses and long-lasting immune memory. Here, we describe a robust protocol for the identification of MHC-bound peptides from cell lines and tissues, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUPLC-MS/MS) and recent improvements in methods for isolation and characterization of these peptides. The protocol starts with the immunoaffinity capture of naturally processed MHC-peptide complexes. The peptides dissociate from the class I human leukocyte antigens (HLAs) upon acid denaturation. This peptide cargo is then extracted and separated into fractions by HPLC, and the peptides in these fractions are identified using nUPLC-MS/MS. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2-3 d.
MeSH term(s)	Amino Acid Sequence ; Animals ; Cell Line ; Cells, Cultured ; Chemical Precipitation ; Chromatography, Affinity/methods ; Chromatography, High Pressure Liquid/methods ; Histocompatibility Antigens/immunology ; Histocompatibility Antigens Class I/immunology ; Humans ; Major Histocompatibility Complex ; Mice ; Peptides/analysis ; Peptides/immunology ; Tandem Mass Spectrometry/methods
Chemical Substances	Histocompatibility Antigens ; Histocompatibility Antigens Class I ; Peptides
Language	English
Publishing date	2019-05-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-019-0133-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Immunolyser: A web-based computational pipeline for analysing and mining immunopeptidomic data.

Munday, Prithvi Raj / Fehring, Joshua / Revote, Jerico / Pandey, Kirti / Shahbazy, Mohammad / Scull, Katherine E / Ramarathinam, Sri H / Faridi, Pouya / Croft, Nathan P / Braun, Asolina / Li, Chen / Purcell, Anthony W

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 1678–1687

Abstract: Immunopeptidomics has made tremendous contributions to our understanding of antigen processing and presentation, by identifying and quantifying antigenic peptides presented on the cell surface by Major Histocompatibility Complex (MHC) molecules. Large ... ...

Abstract	Immunopeptidomics has made tremendous contributions to our understanding of antigen processing and presentation, by identifying and quantifying antigenic peptides presented on the cell surface by Major Histocompatibility Complex (MHC) molecules. Large and complex immunopeptidomics datasets can now be routinely generated using Liquid Chromatography-Mass Spectrometry techniques. The analysis of this data - often consisting of multiple replicates/conditions - rarely follows a standard data processing pipeline, hindering the reproducibility and depth of analysis of immunopeptidomic data. Here, we present Immunolyser, an automated pipeline designed to facilitate computational analysis of immunopeptidomic data with a minimal initial setup. Immunolyser brings together routine analyses, including peptide length distribution, peptide motif analysis, sequence clustering, peptide-MHC binding affinity prediction, and source protein analysis. Immunolyser provides a user-friendly and interactive interface via its webserver and is freely available for academic purposes at https://immunolyser.erc.monash.edu/. The open-access source code can be downloaded at our GitHub repository: https://github.com/prmunday/Immunolyser. We anticipate that Immunolyser will serve as a prominent computational pipeline to facilitate effortless and reproducible analysis of immunopeptidomic data.
Language	English
Publishing date	2023-02-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.02.033
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Article: Endogenous H3.3K27M derived peptide restricted to HLA-A∗02:01 is insufficient for immune-targeting in diffuse midline glioma.

Wang, Stacie S / Pandey, Kirti / Watson, Katherine A / Abbott, Rebecca C / Mifsud, Nicole A / Gracey, Fiona M / Ramarathinam, Sri H / Cross, Ryan S / Purcell, Anthony W / Jenkins, Misty R

Molecular therapy oncolytics

2023 Volume 30, Page(s) 167–180

Abstract: Diffuse midline glioma (DMG) is a childhood brain tumor with an extremely poor prognosis. Chimeric antigen receptor (CAR) T cell therapy has recently demonstrated some success in DMG, but there may a need to target multiple tumor-specific targets to ... ...

Abstract	Diffuse midline glioma (DMG) is a childhood brain tumor with an extremely poor prognosis. Chimeric antigen receptor (CAR) T cell therapy has recently demonstrated some success in DMG, but there may a need to target multiple tumor-specific targets to avoid antigen escape. We developed a second-generation CAR targeting an HLA-A∗02:01 restricted histone 3K27M epitope in DMG, the target of previous peptide vaccination and T cell receptor-mimics. These CAR T cells demonstrated specific, titratable, binding to cells pulsed with the H3.3K27M peptide. However, we were unable to observe scFv binding, CAR T cell activation, or cytotoxic function against H3.3K27M
Language	English
Publishing date	2023-08-15
Publishing country	United States
Document type	Journal Article
ISSN	2372-7705
ISSN	2372-7705
DOI	10.1016/j.omto.2023.08.005
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