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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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2
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Kina E, Laverdure JP, Durette C, Lanoix J, Courcelles M, Zhao Q, Apavaloaei A, Larouche JD, Hardy MP, Vincent K, Gendron P, Hesnard L, Thériault C, Ruiz Cuevas MV, Ehx G, Thibault P, Perreault C. Breast cancer immunopeptidomes contain numerous shared tumor antigens. J Clin Invest 2024; 134:e166740. [PMID: 37906288 PMCID: PMC10760959 DOI: 10.1172/jci166740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
Hormone receptor-positive breast cancer (HR+) is immunologically cold and has not benefited from advances in immunotherapy. In contrast, subsets of triple-negative breast cancer (TNBC) display high leukocytic infiltration and respond to checkpoint blockade. CD8+ T cells, the main effectors of anticancer responses, recognize MHC I-associated peptides (MAPs). Our work aimed to characterize the repertoire of MAPs presented by HR+ and TNBC tumors. Using mass spectrometry, we identified 57,094 unique MAPs in 26 primary breast cancer samples. MAP source genes highly overlapped between both subtypes. We identified 25 tumor-specific antigens (TSAs) mainly deriving from aberrantly expressed regions. TSAs were most frequently identified in TNBC samples and were more shared among The Cancer Genome Atlas (TCGA) database TNBC than HR+ samples. In the TNBC cohort, the predicted number of TSAs positively correlated with leukocytic infiltration and overall survival, supporting their immunogenicity in vivo. We detected 49 tumor-associated antigens (TAAs), some of which derived from cancer-associated fibroblasts. Functional expansion of specific T cell assays confirmed the in vitro immunogenicity of several TSAs and TAAs. Our study identified attractive targets for cancer immunotherapy in both breast cancer subtypes. The higher prevalence of TSAs in TNBC tumors provides a rationale for their responsiveness to checkpoint blockade.
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Affiliation(s)
- Eralda Kina
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | | | | | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), and
| | | | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | | | | | | | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), and
| | | | - Maria Virginia Ruiz Cuevas
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Grégory Ehx
- Laboratory of Hematology, GIGA-I3, University of Liege and CHU of Liège, Liege, Belgium
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
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3
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Cuevas MVR, Hardy MP, Larouche JD, Apavaloaei A, Kina E, Vincent K, Gendron P, Laverdure JP, Durette C, Thibault P, Lemieux S, Perreault C, Ehx G. BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens. Genome Biol 2023; 24:188. [PMID: 37582761 PMCID: PMC10426134 DOI: 10.1186/s13059-023-03029-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens' RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
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Affiliation(s)
- Maria Virginia Ruiz Cuevas
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Eralda Kina
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada.
- Laboratory of Hematology, GIGA-I3, University of Liege, CHU of Liege, Liege, Belgium.
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Cuevas MVR, Hardy MP, Larouche JD, Apavaloaei A, Kina E, Vincent K, Gendron P, Laverdure JP, Durette C, Thibault P, Lemieux S, Perreault C, Ehx G. Abstract 2987: BamQuery: a new proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
MHC class I-associated peptides (MAPs), collectively referred to as the immunopeptidome, have a pivotal role in cancer immunosurveillance. While MAPs were long thought to be solely generated by the degradation of canonical proteins, recent advances in the field of proteogenomics (genomically-informed proteomics) evidenced that ∼10% of them originate from allegedly noncoding genomic sequences. Among these sequences, endogenous retroelements (EREs) are under intense scrutiny as a possible source of actionable tumor antigens (TAs). With the increasing number of cancer-oriented immunopeptidomic and proteogenomic studies comes the need to accurately attribute an RNA expression level to each MAP identified by mass-spectrometry. Here, we introduce BamQuery (BQ), a computational tool to attribute an exhaustive RNA expression to MAPs of any genomic origin (exon, intron, UTR, intergenic) from bulk and single-cell RNA-sequencing data. By using BQ on large datasets of published MAPs identified by mass spectrometry, we show that many of them can arise from more than one genomic region. Indeed, 27% of MAPs reported as deriving from protein-coding exons (canonical MAPs) could also arise from non-canonical genomic regions, sometimes with greater probability, and 61% of non-canonical MAPs could arise from more than a single genomic origin (334 possible regions on average per non-canonical MAP; up to 35,343 for EREs). The consideration of all these origins evidenced an unsuspected high RNA expression in normal human tissues of (i) published neoantigens/TAs (mutated or not); (ii) MAPs derived from proteasomal splicing, supposedly not genomically templated, and (iii) MAPs derived from viruses. In particular, the high expression of candidate immunotherapeutic targets such as TAs highlights the relevance of BamQuery and the necessity of using it to validate such antigens before translating their usage in clinical trials. We also demonstrate that BamQuery can be used to directly identify safe and actionable TAs as well as to predict their immunogenicity through our freely accessible web portal (https://bamquery.iric.ca/search). Therefore, BQ could become an essential tool in any TA prioritization pipeline in the near future.
Citation Format: Maria-Virginia Ruiz Cuevas, Marie-Pierre Hardy, Jean-David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean-Philippe Laverdure, Chantal Durette, Pierre Thibault, Sebastien Lemieux, Claude Perreault, Gregory Ehx. BamQuery: a new proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2987.
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Affiliation(s)
| | | | | | | | - Eralda Kina
- 1University of Montreal, Montreal, Quebec, Canada
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5
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Apavaloaei A, Zhao Q, Hesnard L, Vincent K, Hardy MP, Durette C, Lanoix J, Laverdure JP, Larouche JD, Cuevas MVR, Ehx G, Lemieux S, Thibault P, Perreault C. Abstract 2993: Unmutated tumor antigens are abundant and contribute to tumor control in melanoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Recognition of MHC-I-associated tumor antigens (TAs) by CD8+ T cells is central to antitumor immunity. Owing to the elevated tumor mutational burden (TMB) in melanoma, the marked efficacy of immune checkpoint blockade (ICB) has been attributed to the recognition of mutated TAs. However, recent reports showed that response to ICB in melanomas with low TMB is associated with CD8+ T-cell reactivity against melanocyte lineage-associated antigens (LSAs). Here, we systematically evaluated the contribution of all TA classes, i.e., mutated and unmutated, canonical and non-canonical, to the antigenic landscape of melanoma. We characterized the TAs from melanoma biopsies and patient-derived cell lines using proteogenomics. Out of 79450 MHC-I-associated peptides (MAPs) identified from 19 samples, we found 557 unmutated TAs classified as tumor-specific (TSA), tumor-associated (TAA), or LSAs. These TAs most often derived from annotated open-reading frames, followed by ncRNAs and intergenic regions. By contrast, only 6 MAPs were mutated and tumor-specific, which could be partially explained by a decreased expression of mutations within MAP-generating genomic regions. While the number of unmutated TAs with predicted presentation (TApres) in melanoma patients was similar between responders and non-responders pre-ICB, non-responders showed marks of inefficient antigen presentation. In consequence, only responders lost TApres upon treatment, in tandem with an expansion in tumor-infiltrating lymphocytes. These results reveal a previously underappreciated contribution of unmutated TAs to tumor control in melanoma and suggest that enhancing their recognition could improve the ICB efficacy in non-responders.
Citation Format: Anca Apavaloaei, Qingchuan Zhao, Leslie Hesnard, Krystel Vincent, Marie-Pierre Hardy, Chantal Durette, Joël Lanoix, Jean-Philippe Laverdure, Jean-David Larouche, Maria Virginia Ruiz Cuevas, Grégory Ehx, Sébastien Lemieux, Pierre Thibault, Claude Perreault. Unmutated tumor antigens are abundant and contribute to tumor control in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2993.
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Affiliation(s)
| | | | | | | | | | | | - Joël Lanoix
- 1University of Montreal, Montreal, Quebec, Canada
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Ehx G, Vincent K, Larouche JD, Durette C, Laverdure JP, Lanoix J, Bonneil E, Hardy MP, Coté C, Noronha N, Hesnard L, Zhao Q, Laumont CM, Lemieux S, Thibault P, Perreault C. The tumor-specific antigen landscape of acute myeloid leukemia. Mol Immunol 2022. [DOI: 10.1016/j.molimm.2022.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Apavaloaei A, Hesnard L, Hardy MP, Benabdallah B, Ehx G, Thériault C, Laverdure JP, Durette C, Lanoix J, Courcelles M, Noronha N, Chauhan KD, Lemieux S, Beauséjour C, Bhatia M, Thibault P, Perreault C. Induced pluripotent stem cells display a distinct set of MHC I-associated peptides shared by human cancers. Cell Rep 2022; 40:111241. [PMID: 35977509 DOI: 10.1016/j.celrep.2022.111241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022] Open
Abstract
Previous reports showed that mouse vaccination with pluripotent stem cells (PSCs) induces durable anti-tumor immune responses via T cell recognition of some elusive oncofetal epitopes. We characterize the MHC I-associated peptide (MAP) repertoire of human induced PSCs (iPSCs) using proteogenomics. Our analyses reveal a set of 46 pluripotency-associated MAPs (paMAPs) absent from the transcriptome of normal tissues and adult stem cells but expressed in PSCs and multiple adult cancers. These paMAPs derive from coding and allegedly non-coding (48%) transcripts involved in pluripotency maintenance, and their expression in The Cancer Genome Atlas samples correlates with source gene hypomethylation and genomic aberrations common across cancer types. We find that several of these paMAPs were immunogenic. However, paMAP expression in tumors coincides with activation of pathways instrumental in immune evasion (WNT, TGF-β, and CDK4/6). We propose that currently available inhibitors of these pathways could synergize with immune targeting of paMAPs for the treatment of poorly differentiated cancers.
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Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | | | - Gregory Ehx
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Kapil Dev Chauhan
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Christian Beauséjour
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pharmacology and Physiology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mick Bhatia
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Chemistry, University of Montreal, Montreal, QC H3T 1J4, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
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Trofimov A, Brouillard P, Larouche JD, Séguin J, Laverdure JP, Brasey A, Ehx G, Roy DC, Busque L, Lachance S, Lemieux S, Perreault C. Two types of human TCR differentially regulate reactivity to self and non-self antigens. iScience 2022; 25:104968. [PMID: 36111255 PMCID: PMC9468382 DOI: 10.1016/j.isci.2022.104968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/24/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are reported as disease-associated. Thus, 10%–30% of most frequent cord blood TCRs are associated with common pathogens and autoantigens. TDT-dependent TCRs present distinct structural features and are less shared among subjects. TDT-dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes. Over 108 TCR CDR3 sequences from ∼103 individuals and 7 cohorts were analyzed The TCR repertoire is composed of two layers: neonatal and TDT-dependent layer ∼70% of frequent cord blood TCRs are associated with common pathogens Acute graft-vs-host disease correlates with a high proportion of TDT-dependent TCRs
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Affiliation(s)
- Assya Trofimov
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Quebec Institute for Learning Algorithms (Mila), Montreal, Quebec H2S 3H1, Canada
- Currently Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Currently Department of Physics, University of Washington, Seattle, WA 98195-1560, USA
| | - Philippe Brouillard
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Quebec Institute for Learning Algorithms (Mila), Montreal, Quebec H2S 3H1, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Jonathan Séguin
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Ann Brasey
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Gregory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Currently Interdisciplinary Cluster for Applied Geno-Proteomics (GIGA-I3), University of Liege, Liege 4000, Belgium
| | | | - Lambert Busque
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Silvy Lachance
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Computer Science and Research Operations, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Biochemistry at University of Montreal, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Corresponding author
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
- Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
- Corresponding author
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Cleyle J, Hardy MP, Minati R, Courcelles M, Durette C, Lanoix J, Laverdure JP, Vincent K, Perreault C, Thibault P. Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability. Mol Cell Proteomics 2022; 21:100228. [PMID: 35367648 PMCID: PMC9134101 DOI: 10.1016/j.mcpro.2022.100228] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. Although the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30,000 unique MHC I-associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.
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Affiliation(s)
- Jenna Cleyle
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada; Molecular Biology Program, Université de Montréal, Montreal, Quebec, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Robin Minati
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada; Molecular Biology Program, Université de Montréal, Montreal, Quebec, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada; Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada; Department of Chemistry, Université de Montréal, Montreal, Quebec, Canada.
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10
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Apavaloaei A, Laverdure JP, Perreault C. PSMB11 regulates gene expression in cortical thymic epithelial cells. Cell Rep 2021; 36:109546. [PMID: 34496243 DOI: 10.1016/j.celrep.2021.109546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/30/2020] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The PSMB11 proteasomal subunit, expressed only in cortical thymic epithelial cells (cTECs), is essential for the development of functional CD8+ T cells. An attractive yet unproven theory holds that PSMB11 generates unique major histocompatibility complex class I (MHC I)-associated peptides required for positive selection. We recently reported that PSMB11 regulates the expression of hundreds of genes in cTECs, mainly by differential proteolysis of transcription factors. Thereby, PSMB11 maintains the distinctness of cTECs relative to medullary TECs (mTECs) and promotes cortex-to-medulla migration of developing thymocytes. These conclusions have been challenged by Ohigashi and colleagues, who suggest that their data show that PSMB11 uniquely controls antigen presentation without affecting cTEC biology. Here, we perform a comprehensive reanalysis of transcriptomic and proteomic data from the Ohigashi lab and confirm our original conclusions. This Matters Arising paper is in response to Ohigashi et al. (2019), published in Cell Reports. See also the response by Ohigashi and Takahama (2021), published in this issue of Cell Reports.
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Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer, Montreal, QC H3C 3J7, Canada; Department of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | | | - Claude Perreault
- Institute for Research in Immunology and Cancer, Montreal, QC H3C 3J7, Canada; Department of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada.
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11
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Ehx G, Larouche JD, Durette C, Laverdure JP, Hesnard L, Vincent K, Hardy MP, Thériault C, Rulleau C, Lanoix J, Bonneil E, Feghaly A, Apavaloaei A, Noronha N, Laumont CM, Delisle JS, Vago L, Hébert J, Sauvageau G, Lemieux S, Thibault P, Perreault C. Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes. Immunity 2021; 54:737-752.e10. [PMID: 33740418 DOI: 10.1016/j.immuni.2021.03.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/24/2020] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) has not benefited from innovative immunotherapies, mainly because of the lack of actionable immune targets. Using an original proteogenomic approach, we analyzed the major histocompatibility complex class I (MHC class I)-associated immunopeptidome of 19 primary AML samples and identified 58 tumor-specific antigens (TSAs). These TSAs bore no mutations and derived mainly (86%) from supposedly non-coding genomic regions. Two AML-specific aberrations were instrumental in the biogenesis of TSAs, intron retention, and epigenetic changes. Indeed, 48% of TSAs resulted from intron retention and translation, and their RNA expression correlated with mutations of epigenetic modifiers (e.g., DNMT3A). AML TSA-coding transcripts were highly shared among patients and were expressed in both blasts and leukemic stem cells. In AML patients, the predicted number of TSAs correlated with spontaneous expansion of cognate T cell receptor clonotypes, accumulation of activated cytotoxic T cells, immunoediting, and improved survival. These TSAs represent attractive targets for AML immunotherapy.
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Affiliation(s)
- Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Caroline Rulleau
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Sébastien Delisle
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Josée Hébert
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montreal, QC H3C 3J7, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
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12
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Larouche JD, Trofimov A, Hesnard L, Ehx G, Zhao Q, Vincent K, Durette C, Gendron P, Laverdure JP, Bonneil É, Côté C, Lemieux S, Thibault P, Perreault C. Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues. Genome Med 2020; 12:40. [PMID: 32345368 PMCID: PMC7189544 DOI: 10.1186/s13073-020-00740-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed in embryonic stem cells (ESCs) and germline cells but are repressed in differentiated somatic cells. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a system-level evaluation of their expression in human tissues is lacking. METHODS Using RNA sequencing data, we analyzed ERE expression in 32 human tissues and cell types, including medullary thymic epithelial cells (mTECs). A tissue specificity index was computed to identify tissue-restricted ERE families. We also analyzed the transcriptome of mTECs in wild-type and autoimmune regulator (AIRE)-deficient mice. Finally, we developed a proteogenomic workflow combining RNA sequencing and mass spectrometry (MS) in order to evaluate whether EREs might be translated and generate MHC I-associated peptides (MAP) in B-lymphoblastoid cell lines (B-LCL) from 16 individuals. RESULTS We report that all human tissues express EREs, but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. ERE expression was particularly high in two MHC I-deficient tissues (ESCs and testis) and one MHC I-expressing tissue, mTECs. In mutant mice, we report that the exceptional expression of EREs in mTECs was AIRE-independent. MS analyses identified 103 non-redundant ERE-derived MAPs (ereMAPs) in B-LCLs. These ereMAPs preferentially derived from sense translation of intronic EREs. Notably, detailed analyses of their amino acid composition revealed that ERE-derived MAPs presented homology to viral MAPs. CONCLUSIONS This study shows that ERE expression in somatic tissues is more pervasive and heterogeneous than anticipated. The high and diversified expression of EREs in mTECs and their ability to generate MAPs suggest that EREs may play an important role in the establishment of self-tolerance. The viral-like properties of ERE-derived MAPs suggest that those not expressed in mTECs can be highly immunogenic.
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Affiliation(s)
- Jean-David Larouche
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Assya Trofimov
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
| | - Leslie Hesnard
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Gregory Ehx
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Qingchuan Zhao
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Krystel Vincent
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Chantal Durette
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
| | - Patrick Gendron
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
| | - Éric Bonneil
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
| | - Caroline Côté
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
| | - Sébastien Lemieux
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada.
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada.
| | - Claude Perreault
- Institute of Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC, H3C 3J7, Canada.
- Department of Medicine, Université de Montréal, Montréal, QC, Canada.
- Division of Hematology-Oncology, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada.
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13
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Courcelles M, Durette C, Daouda T, Laverdure JP, Vincent K, Lemieux S, Perreault C, Thibault P. MAPDP: A Cloud-Based Computational Platform for Immunopeptidomics Analyses. J Proteome Res 2020; 19:1873-1881. [PMID: 32108478 DOI: 10.1021/acs.jproteome.9b00859] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The immunopeptidome corresponds to the repertoire of peptides presented at the cell surface by the major histocompatibility complex (MHC) molecules. Cytotoxic T cells scan this repertoire to identify nonself antigens that can arise from tumors or infected cells. The identification of actionable antigenic targets is key to the development of therapeutic cancer vaccines, T-cell therapy, and other T-cell receptor-based biologics. The growing clinical interest for immunopeptidomics has accelerated the development of high throughput proteogenomic platforms that provide a system-level analysis of MHC-associated peptides. Improvement in sensitivity and throughput of mass spectrometers now allows the detection of a few thousands of peptides from less than 100 million cells. To manage the amount of data generated by these instruments, we have developed the MHC-associated peptide discovery platform (MAPDP), a novel open-source cloud-based computational platform for immunopeptidomic analyses. It provides convenient access from a web portal to immunopeptidomes stored in the database, filtering tools, various visualizations, annotations (e.g., IEDB, dbSNP, gnomAD), peptide-binding affinity prediction (mhcflurry, NetMHC), HLA genotyping, and the generation of personalized proteome databases. MAPDP functionalities are demonstrated here by the discovery of MHC peptides featuring new genetic variants identified in two previously published ovarian carcinoma data sets.
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Affiliation(s)
- Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Tariq Daouda
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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14
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Apavaloaei A, Hardy MP, Larouche JD, Zhao Q, Vincent K, Laverdure JP, Durette C, Lanoix J, Thibault P, Perreault C. Abstract B16: Identification of tumor-specific antigens shared by induced pluripotent stem cells. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-b16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The development of cancer immunotherapeutics is limited by the tumor-specific antigen (TSA) discovery. Cancer cells and pluripotent stem cells, i.e., embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), show a significant transcriptomic overlap. Indeed, when used as prophylactic vaccines in another study, iPSCs prevented tumor growth in mouse models of lung, breast, and skin cancer, suggesting that we could mine iPSCs for the discovery of TSAs. We use a recently developed proteogenomic approach combining RNA-sequencing and mass spectrometry to characterize the immunopeptidome (MHC class I-associated peptides) of iPSCs. Analyses of hitherto one human iPS cell line allowed us to identify 9 MHC class I-associated antigens that were not expressed by normal somatic tissues and thus are likely immunogenic. 50% of these antigens were highly expressed in different cancer types from The Cancer Genome Atlas, highlighting their potential for cancer immunotherapy. Expression of these TSAs resulted from aberrant expression of noncoding genomic regions and not from mutations, making them ideal candidates for antigen-based cancer vaccines. Our study indicates which stem cell features present in cancer cells might be harnessed for cancer immunotherapy. Moreover, we show for the first time that the immunopeptidome of iPSCs reflects the state of pluripotency. Cancer stem cells are known to drive disease relapse after treatment, while cancer circulating cells possessing pluripotent stem cell features are more efficient at producing metastases. These factors indicate that treatments targeted at stemness could improve clinical outcome, and that iPSC-informed TSAs hold promise for prophylactic and therapeutic cancer vaccines.
Citation Format: Anca Apavaloaei, Marie-Pierre Hardy, Jean-David Larouche, Qingchuan Zhao, Krystel Vincent, Jean-Philippe Laverdure, Chantal Durette, Joel Lanoix, Pierre Thibault, Claude Perreault. Identification of tumor-specific antigens shared by induced pluripotent stem cells [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr B16.
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Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
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15
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Zhao Q, Laverdure JP, Lanoix J, Durette C, Côté C, Bonneil É, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C. Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer. Cancer Immunol Res 2020; 8:544-555. [PMID: 32047025 DOI: 10.1158/2326-6066.cir-19-0541] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/03/2019] [Accepted: 02/07/2020] [Indexed: 11/16/2022]
Abstract
High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecologic malignancies in the world, has not significantly benefited from advances in cancer immunotherapy. Although HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSA) using a mass spectrometry pipeline that interrogated all reading frames of all genomic regions. In 23 HGSC tumors, we identified 103 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only three of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation (n = 2) or from noncoding sequences (n = 7). One group of TSAs (n = 91) derived from aberrantly expressed unmutated genomic sequences, which were not expressed in normal tissues. These aberrantly expressed TSAs (aeTSA) originated primarily from nonexonic sequences, in particular intronic (29%) and intergenic (22%) sequences. Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. Although mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. Taking into account the frequency of aeTSA expression and HLA allele frequencies, we calculated that, in Caucasians, the median number of aeTSAs per tumor would be five. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.
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Affiliation(s)
- Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada.,Department of Computer Science and Operations Research, Université de Montréal, Montreal, Quebec, Canada
| | - Douglas G Millar
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Pamela S Ohashi
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada. .,Department of Chemistry, Université de Montréal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada. .,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
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16
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Laumont CM, Vincent K, Hesnard L, Audemard É, Bonneil É, Laverdure JP, Gendron P, Courcelles M, Hardy MP, Côté C, Durette C, St-Pierre C, Benhammadi M, Lanoix J, Vobecky S, Haddad E, Lemieux S, Thibault P, Perreault C. Noncoding regions are the main source of targetable tumor-specific antigens. Sci Transl Med 2018; 10:10/470/eaau5516. [DOI: 10.1126/scitranslmed.aau5516] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/15/2018] [Indexed: 12/15/2022]
Abstract
Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but few have been identified thus far. We therefore developed a proteogenomic approach to enable the high-throughput discovery of TSAs coded by potentially all genomic regions. In two murine cancer cell lines and seven human primary tumors, we identified a total of 40 TSAs, about 90% of which derived from allegedly noncoding regions and would have been missed by standard exome-based approaches. Moreover, most of these TSAs derived from nonmutated yet aberrantly expressed transcripts (such as endogenous retroelements) that could be shared by multiple tumor types. Last, we demonstrated that, in mice, the strength of antitumor responses after TSA vaccination was influenced by two parameters that can be estimated in humans and could serve for TSA prioritization in clinical studies: TSA expression and the frequency of TSA-responsive T cells in the preimmune repertoire. In conclusion, the strategy reported herein could considerably facilitate the identification and prioritization of actionable human TSAs.
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17
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Dumont-Lagacé M, Gerbe H, Daouda T, Laverdure JP, Brochu S, Lemieux S, Gagnon É, Perreault C. Detection of Quiescent Radioresistant Epithelial Progenitors in the Adult Thymus. Front Immunol 2017; 8:1717. [PMID: 29259606 PMCID: PMC5723310 DOI: 10.3389/fimmu.2017.01717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/21/2017] [Indexed: 11/13/2022] Open
Abstract
Thymic aging precedes that of other organs and is initiated by the gradual loss of thymic epithelial cells (TECs). Based on in vitro culture and transplantation assays, recent studies have reported on the presence of thymic epithelial progenitor cells (TEPCs) in young adult mice. However, the physiological role and properties of TEPC populations reported to date remain unclear. Using an in vivo label-retention assay, we previously identified a population of quiescent but non-senescent TECs. The goals of this study were therefore (i) to evaluate the contribution of these quiescent TECs to thymic regeneration following irradiation-induced acute thymic injury and (ii) to characterize their phenotypic and molecular profiles using flow cytometry, immunohistology, and transcriptome sequencing. We report that while UEA1+ cells cycle the most in steady state, they are greatly affected by irradiation, leading to cell loss and proliferative arrest following acute thymic involution. On the opposite, the UEA1– subset of quiescent TECs is radioresistant and proliferate in situ following acute thymic involution, thereby contributing to thymic regeneration in 28- to 30-week-old mice. UEA1– quiescent TECs display an undifferentiated phenotype (co-expression of K8 and K5 cytokeratins) and express high levels of genes that regulate stem cell activity in different tissues (e.g., Podxl and Ptprz1). In addition, two features suggest that UEA1– quiescent TECs occupy discrete stromal niches: (i) their preferential location in clusters adjacent to the cortico-medullary junction and (ii) their high expression of genes involved in cross talk with mesenchymal cells. The ability of UEA1– quiescent TECs to participate to TEC regeneration qualifies them as in vivo progenitor cells particularly relevant in the context of regeneration following acute thymic injury.
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Affiliation(s)
- Maude Dumont-Lagacé
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hervé Gerbe
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Tariq Daouda
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.,Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
| | | | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.,Department of Informatics and Operational Research, Université de Montréal, Montréal, QC, Canada
| | - Étienne Gagnon
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montréal, QC, Canada
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18
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Pearson H, Daouda T, Granados DP, Durette C, Bonneil E, Courcelles M, Rodenbrock A, Laverdure JP, Côté C, Mader S, Lemieux S, Thibault P, Perreault C. MHC class I-associated peptides derive from selective regions of the human genome. J Clin Invest 2016; 126:4690-4701. [PMID: 27841757 DOI: 10.1172/jci88590] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/30/2016] [Indexed: 12/24/2022] Open
Abstract
MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.
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19
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Khan SM, Sleno R, Gora S, Zylbergold P, Laverdure JP, Labbé JC, Miller GJ, Hébert TE. The expanding roles of Gβγ subunits in G protein-coupled receptor signaling and drug action. Pharmacol Rev 2013; 65:545-77. [PMID: 23406670 DOI: 10.1124/pr.111.005603] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gβγ subunits from heterotrimeric G proteins perform a vast array of functions in cells with respect to signaling, often independently as well as in concert with Gα subunits. However, the eponymous term "Gβγ" does not do justice to the fact that 5 Gβ and 12 Gγ isoforms have evolved in mammals to serve much broader roles beyond their canonical roles in cellular signaling. We explore the phylogenetic diversity of Gβγ subunits with a view toward understanding these expanded roles in different cellular organelles. We suggest that the particular content of distinct Gβγ subunits regulates cellular activity, and that the granularity of individual Gβ and Gγ action is only beginning to be understood. Given the therapeutic potential of targeting Gβγ action, this larger view serves as a prelude to more specific development of drugs aimed at individual isoforms.
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Affiliation(s)
- Shahriar M Khan
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Room 1303, Montréal, Québec H3G 1Y6, Canada
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20
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Caron E, Vincent K, Fortier MH, Laverdure JP, Bramoullé A, Hardy MP, Voisin G, Roux PP, Lemieux S, Thibault P, Perreault C. The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation. Mol Syst Biol 2011; 7:533. [PMID: 21952136 PMCID: PMC3202804 DOI: 10.1038/msb.2011.68] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/23/2011] [Indexed: 01/13/2023] Open
Abstract
Self/non-self discrimination is a fundamental requirement of life. Endogenous peptides presented by major histocompatibility complex class I (MHC I) molecules represent the essence of self for CD8 T lymphocytes. These MHC I peptides (MIPs) are collectively referred to as the immunopeptidome. From a systems-level perspective, very little is known about the origin, composition and plasticity of the immunopeptidome. Here, we show that the immunopeptidome, and therefore the nature of the immune self, is plastic and moulded by cellular metabolic activity. By using a quantitative high-throughput mass spectrometry-based approach, we found that altering cellular metabolism via the inhibition of the mammalian target of rapamycin results in dynamic changes in the cell surface MIPs landscape. Moreover, we provide systems-level evidence that the immunopeptidome projects at the cell surface a representation of biochemical networks and metabolic events regulated at multiple levels inside the cell. Our findings open up new perspectives in systems immunology and predictive biology. Indeed, predicting variations in the immunopeptidome in response to cell-intrinsic and -extrinsic factors could be relevant to the rational design of immunotherapeutic interventions.
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Affiliation(s)
- Etienne Caron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec, Canada
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21
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Bilodeau M, MacRae T, Gaboury L, Laverdure JP, Hardy MP, Mayotte N, Paradis V, Harton S, Perreault C, Sauvageau G. Analysis of blood stem cell activity and cystatin gene expression in a mouse model presenting a chromosomal deletion encompassing Csta and Stfa2l1. PLoS One 2009; 4:e7500. [PMID: 19838297 PMCID: PMC2759285 DOI: 10.1371/journal.pone.0007500] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/29/2009] [Indexed: 11/26/2022] Open
Abstract
The cystatin protein superfamily is characterized by the presence of conserved sequences that display cysteine protease inhibitory activity (e.g., towards cathepsins). Type 1 and 2 cystatins are encoded by 25 genes of which 23 are grouped in 2 clusters localized on mouse chromosomes 16 and 2. The expression and essential roles of most of these genes in mouse development and hematopoiesis remain poorly characterized. In this study, we describe a set of quantitative real-time PCR assays and a global expression profile of cystatin genes in normal mouse tissues. Benefiting from our collection of DelES embryonic stem cell clones harboring large chromosomal deletions (to be reported elsewhere), we selected a clone in which a 95-kb region of chromosome 16 is missing (Del16qB3Δ/+). In this particular clone, 2 cystatin genes, namely Csta and Stfa2l1 are absent along with 2 other genes (Fam162a, Ccdc58) and associated intergenic regions. From this line, we established a new homozygous mutant mouse model (Del16qB3Δ/16qB3Δ) to assess the in vivo biological functions of the 2 deleted cystatins. Stfa2l1 gene expression is high in wild-type fetal liver, bone marrow, and spleen, while Csta is ubiquitously expressed. Homozygous Del16qB3Δ/16qB3Δ animals are phenotypically normal, fertile, and not overtly susceptible to spontaneous or irradiation-induced tumor formation. The hematopoietic stem and progenitor cell activity in these mutant mice are also normal. Interestingly, quantitative real-time PCR expression profiling reveals a marked increase in the expression levels of Stfa2l1/Csta phylogenetically-related genes (Stfa1, Stfa2, and Stfa3) in Del16qB3Δ/16qB3Δ hematopoietic tissues, suggesting that these candidate genes might be contributing to compensatory mechanisms. Overall, this study presents an optimized approach to globally monitor cystatin gene expression as well as a new mouse model deficient in Stfa2l1/Csta genes, expanding the available tools to dissect cystatin roles under normal and pathological conditions.
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Affiliation(s)
- Mélanie Bilodeau
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Tara MacRae
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Louis Gaboury
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Nadine Mayotte
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Véronique Paradis
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Sébastien Harton
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
- Leukemia Cell Bank of Quebec and Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
- Leukemia Cell Bank of Quebec and Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- * E-mail:
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22
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Deneault E, Cellot S, Faubert A, Laverdure JP, Fréchette M, Chagraoui J, Mayotte N, Sauvageau M, Ting SB, Sauvageau G. A functional screen to identify novel effectors of hematopoietic stem cell activity. Cell 2009; 137:369-79. [PMID: 19379700 PMCID: PMC5770201 DOI: 10.1016/j.cell.2009.03.026] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 01/19/2009] [Accepted: 03/16/2009] [Indexed: 12/22/2022]
Abstract
Despite tremendous progress made toward the identification of the molecular circuitry that governs cell fate in embryonic stem cells, genes controlling this process in the adult hematopoietic stem cell have proven to be more difficult to unmask. We now report the results of a novel gain-of-function screening approach, which identified a series of 18 nuclear factors that affect hematopoietic stem cell activity. Overexpression of ten of these factors resulted in an increased repopulating activity compared to unmanipulated cells. Interestingly, at least four of the 18 factors, Fos, Tcfec, Hmgb1, and Sfpi1, show non-cell-autonomous functions. The utilization of this screening method together with the creation of a database enriched for potential determinants of hematopoietic stem cell self-renewal will serve as a resource to uncover regulatory networks in these cells.
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Affiliation(s)
- Eric Deneault
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Sonia Cellot
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Amélie Faubert
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Mélanie Fréchette
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Jalila Chagraoui
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Nadine Mayotte
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Martin Sauvageau
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Stephen B. Ting
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Guy Sauvageau
- Molecular Genetics of Stem Cells Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec H3C 3J7, Canada
- Division of Hematology and Leukemia Cell Bank of Quebec (BCLQ), Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada
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