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Hong K, Zhang Y, Yao L, Zhang J, Sheng X, Song L, Guo Y, Guo Y. Pan-cancer analysis of the angiotensin II receptor-associated protein as a prognostic and immunological gene predicting immunotherapy responses in pan-cancer. Front Cell Dev Biol 2022; 10:913684. [PMID: 36060798 PMCID: PMC9437438 DOI: 10.3389/fcell.2022.913684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Understanding interior molecular mechanisms of tumorigenesis and cancer progression contributes to antitumor treatments. The angiotensin II receptor-associated protein (AGTRAP) has been confirmed to be related with metabolic products in metabolic diseases and can drive the progression of hepatocellular carcinoma and colon carcinoma. However, functions of AGTRAP in other kinds of cancers are unclear, and a pan-cancer analysis of AGTRAP has not been carried out. Methods and materials: We downloaded data from The Cancer Genome Atlas and Genotype-Tissue Expression dataset and The Human Protein Atlas databases and then used R software (version 4.1.1) and several bioinformatic tools to conduct the analysis. Results: In our study, we evaluated the expression of AGTRAP in cancers, such as high expression in breast cancer, lung adenocarcinoma, and glioma and low expression in kidney chromophobe. Furthermore, our study revealed that high expression of AGTRAP is significantly related with poor prognosis in glioma, liver cancer, kidney chromophobe, and so on. We also explored the putative functional mechanisms of AGTRAP across pan-cancer, such as endoplasmic reticulum pathway, endocytosis pathway, and JAK-STAT signaling pathway. In addition, the connection between AGTRAP and tumor microenvironment, tumor mutation burden, and immune-related genes was proven. Conclusion: Our study provided comprehensive evidence of the roles of AGTRAP in different kinds of cancers and supported the relationship of AGTRAP and tumorous immunity.
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Affiliation(s)
- Kai Hong
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
- Medicine School, Ningbo University, Ningbo, Zhejiang, China
| | - Yingjue Zhang
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Lingli Yao
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
- Medicine School, Ningbo University, Ningbo, Zhejiang, China
| | - Jiabo Zhang
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
| | - Xianneng Sheng
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
| | - Lihua Song
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
- Medicine School, Ningbo University, Ningbo, Zhejiang, China
| | - Yu Guo
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
- *Correspondence: Yu Guo, ; Yangyang Guo,
| | - Yangyang Guo
- Department of Thyroid and Breast Surgery, Ningbo City First Hospital, Ningbo, Zhejiang, China
- *Correspondence: Yu Guo, ; Yangyang Guo,
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2
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Feng Y, Martin A. Mutagenic repair during antibody diversification: emerging insights. Trends Immunol 2022; 43:604-607. [PMID: 35701290 DOI: 10.1016/j.it.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
Abstract
Deoxyuracils (dUs) produced by activation-induced cytidine deaminase (AID) during antibody diversification are processed by base excision repair (BER) and mismatch repair (MMR) pathways that paradoxically expand this lesion within jawed vertebrate immunoglobulin (Ig) genes. We highlight new findings describing mechanisms that allow B cells to carry out mutagenic DNA repair, an essential process for antibody maturation with implications in cancer pathogenesis.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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3
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Feng Y, Seija N, Di Noia JM, Martin A. AID in Antibody Diversification: There and Back Again. Trends Immunol 2020; 41:586-600. [PMID: 32434680 PMCID: PMC7183997 DOI: 10.1016/j.it.2020.04.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023]
Abstract
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic hypermutation (SHM) and class switch recombination (CSR). AID thus potentiates the humoral response to clear pathogens. Marking the 20th anniversary of the discovery of AID, we review the current understanding of AID function. We discuss AID biochemistry and how error-free forms of DNA repair are co-opted to prioritize mutagenesis over accuracy during antibody diversification. We discuss the regulation of DNA double-strand break (DSB) repair pathways during CSR. We describe genomic targeting of AID as a multilayered process involving chromatin architecture, cis- and trans-acting factors, and determining mutagenesis – distinct from AID occupancy at loci that are spared from mutation. Subverted base excision repair (BER) and mismatch repair (MMR) pathways act concertedly to generate antibody sequence diversity during SHM. In CSR, DNA DSBs are repaired by the nonhomologous end-joining pathway involving the 53BP1–Rif1–Shieldin axis, and by an alternative end-joining pathway involving HMCES (5-Hydroxymethylcytosine binding, ES-cell-specific) that binds and protects resected DSB ends. Genomic targeting of AID appears to be multilayered, with inbuilt redundancy, but robust enough to ensure that most of the genome is spared from AID activity. Cis elements and genome topology act together with trans-acting factors involved in transcription and RNA processing to determine AID activity at specific Ig regions. Other loci sharing genomic and transcriptional features with the Ig are collaterally targeted during SHM and CSR.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Noé Seija
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Javier M Di Noia
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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4
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Ennishi D, Takata K, Béguelin W, Duns G, Mottok A, Farinha P, Bashashati A, Saberi S, Boyle M, Meissner B, Ben-Neriah S, Woolcock BW, Telenius A, Lai D, Teater M, Kridel R, Savage KJ, Sehn LH, Morin RD, Marra MA, Shah SP, Connors JM, Gascoyne RD, Scott DW, Melnick AM, Steidl C. Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition. Cancer Discov 2019; 9:546-563. [PMID: 30705065 DOI: 10.1158/2159-8290.cd-18-1090] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
We performed a genomic, transcriptomic, and immunophenotypic study of 347 patients with diffuse large B-cell lymphoma (DLBCL) to uncover the molecular basis underlying acquired deficiency of MHC expression. Low MHC-II expression defines tumors originating from the centroblast-rich dark zone of the germinal center (GC) that was associated with inferior prognosis. MHC-II-deficient tumors were characterized by somatically acquired gene mutations reducing MHC-II expression and a lower amount of tumor-infiltrating lymphocytes. In particular, we demonstrated a strong enrichment of EZH2 mutations in both MHC-I- and MHC-II-negative primary lymphomas, and observed reduced MHC expression and T-cell infiltrates in murine lymphoma models expressing mutant Ezh2 Y641. Of clinical relevance, EZH2 inhibitors significantly restored MHC expression in EZH2-mutated human DLBCL cell lines. Hence, our findings suggest a tumor progression model of acquired immune escape in GC-derived lymphomas and pave the way for development of complementary therapeutic approaches combining immunotherapy with epigenetic reprogramming. SIGNIFICANCE: We demonstrate how MHC-deficient lymphoid tumors evolve in a cell-of-origin-specific context. Specifically, EZH2 mutations were identified as a genetic mechanism underlying acquired MHC deficiency. The paradigmatic restoration of MHC expression by EZH2 inhibitors provides the rationale for synergistic therapies combining immunotherapies with epigenetic reprogramming to enhance tumor recognition and elimination.See related commentary by Velcheti et al., p. 472.This article is highlighted in the In This Issue feature, p. 453.
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Affiliation(s)
- Daisuke Ennishi
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Bruce W Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Daniel Lai
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Robert Kridel
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Laurie H Sehn
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marco A Marra
- Genome Science Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.
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5
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Deficiency in the DNA glycosylases UNG1 and OGG1 does not potentiate c-Myc-induced B-cell lymphomagenesis. Exp Hematol 2018; 61:52-58. [PMID: 29496532 DOI: 10.1016/j.exphem.2018.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022]
Abstract
C-Myc overexpression mediates lymphomagenesis; however, secondary genetic lesions are required for its full oncogenic potential. The origin and the mechanism of formation of these mutations are unclear. Using the lacI mutation detection system, we show that secondary mutations occur early in B-cell development and are repaired by Msh2. The mutations at the lacI gene were predominantly at C:G base pairs and CpG motifs, suggesting that they were formed due to cytosine deamination or oxidative damage of G. Therefore, we investigated the role of Ogg1 and UNG glycosylases in c-Myc-driven lymphomagenesis but found that their deficiencies did not influence disease outcome in the Eµ c-Myc mouse model. We also show that Rag proteins do not contribute to secondary lesions in this model. Our work suggests that mutations at C:G base pairs that are repaired primarily by the mismatch repair system arise early in B-cell ontogeny to promote c-Myc-driven lymphomagenesis.
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Belcheva A, Irrazabal T, Robertson SJ, Streutker C, Maughan H, Rubino S, Moriyama EH, Copeland JK, Surendra A, Kumar S, Green B, Geddes K, Pezo RC, Navarre WW, Milosevic M, Wilson BC, Girardin SE, Wolever TMS, Edelmann W, Guttman DS, Philpott DJ, Martin A. Gut microbial metabolism drives transformation of MSH2-deficient colon epithelial cells. Cell 2014; 158:288-299. [PMID: 25036629 DOI: 10.1016/j.cell.2014.04.051] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 03/24/2014] [Accepted: 04/28/2014] [Indexed: 02/08/2023]
Abstract
The etiology of colorectal cancer (CRC) has been linked to deficiencies in mismatch repair and adenomatous polyposis coli (APC) proteins, diet, inflammatory processes, and gut microbiota. However, the mechanism through which the microbiota synergizes with these etiologic factors to promote CRC is not clear. We report that altering the microbiota composition reduces CRC in APC(Min/+)MSH2(-/-) mice, and that a diet reduced in carbohydrates phenocopies this effect. Gut microbes did not induce CRC in these mice through an inflammatory response or the production of DNA mutagens but rather by providing carbohydrate-derived metabolites such as butyrate that fuel hyperproliferation of MSH2(-/-) colon epithelial cells. Further, we provide evidence that the mismatch repair pathway has a role in regulating β-catenin activity and modulating the differentiation of transit-amplifying cells in the colon. These data thereby provide an explanation for the interaction between microbiota, diet, and mismatch repair deficiency in CRC induction. PAPERCLIP:
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Affiliation(s)
- Antoaneta Belcheva
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Thergiory Irrazabal
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Susan J Robertson
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Catherine Streutker
- Department of Laboratory Medicine, St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
| | | | - Stephen Rubino
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eduardo H Moriyama
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON M5G 1L7, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Anu Surendra
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Sachin Kumar
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Blerta Green
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kaoru Geddes
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rossanna C Pezo
- Department of Medical Oncology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - William W Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael Milosevic
- Department of Radiation Oncology, Princess Margaret Hospital, Toronto, ON M5G 2M9, Canada
| | - Brian C Wilson
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Thomas M S Wolever
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 3E2, Canada
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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7
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Belcheva A, Green B, Weiss A, Streutker C, Martin A. Elevated incidence of polyp formation in APC(Min/⁺)Msh2⁻/⁻ mice is independent of nitric oxide-induced DNA mutations. PLoS One 2013; 8:e65204. [PMID: 23741483 PMCID: PMC3669241 DOI: 10.1371/journal.pone.0065204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/21/2013] [Indexed: 01/19/2023] Open
Abstract
Gut microbiota has been linked to a number of human diseases including colon cancer. However, the mechanism through which gut bacteria influence colon cancer development and progression remains unclear. Perturbation of the homeostasis between the host immune system and microbiota leads to inflammation and activation of macrophages which produce large amounts of nitric oxide that acts as a genotoxic effector molecule to suppress bacterial growth. However, nitric oxide also has genotoxic effects to host cells by producing mutations that can predispose to colon cancer development. The major DNA lesions caused by nitric oxide are 8oxoG and deamination of deoxycytosine bases. Cellular glycosylases that belong to the base excision repair pathway have been demonstrated to repair these mutations. Recent evidence suggests that the mismatch repair pathway (MMR) might also repair nitric oxide-induced DNA damage. Since deficiency in MMR predisposes to colon cancer, we hypothesized that MMR-deficient colon epithelial cells are incapable of repairing nitric-oxide induced genetic lesions that can promote colon cancer. Indeed, we found that the MMR pathway repairs nitric oxide-induced DNA mutations in cell lines. To test whether nitric oxide promotes colon cancer, we genetically ablated the inducible nitric oxide synthase (iNOS) or inhibited iNOS activity in the APC(Min/+)Msh2(-/-) mouse model of colon cancer. However, despite the fact that nitric oxide production was strongly reduced in the colon using both approaches, colon cancer incidence was not affected. These data show that nitric oxide and iNOS do not promote colon cancer in APC(Min/+)Msh2(-/-) mice.
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Affiliation(s)
- Antoaneta Belcheva
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Blerta Green
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ashley Weiss
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Catherine Streutker
- Department of Laboratory Medicine, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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8
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The biochemistry of activation-induced deaminase and its physiological functions. Semin Immunol 2012; 24:255-63. [DOI: 10.1016/j.smim.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 05/18/2012] [Indexed: 01/26/2023]
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9
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AIDing antibody diversity by error-prone mismatch repair. Semin Immunol 2012; 24:293-300. [PMID: 22703640 DOI: 10.1016/j.smim.2012.05.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 05/18/2012] [Indexed: 11/20/2022]
Abstract
The creation of a highly diverse antibody repertoire requires the synergistic activity of a DNA mutator, known as activation-induced deaminase (AID), coupled with an error-prone repair process that recognizes the DNA mismatch catalyzed by AID. Instead of facilitating the canonical error-free response, which generally occurs throughout the genome, DNA mismatch repair (MMR) participates in an error-prone repair mode that promotes A:T mutagenesis and double-strand breaks at the immunoglobulin (Ig) genes. As such, MMR is capable of compounding the mutation frequency of AID activity as well as broadening the spectrum of base mutations; thereby increasing the efficiency of antibody maturation. We here review the current understanding of this MMR-mediated process and describe how the MMR signaling cascade downstream of AID diverges in a locus dependent manner and even within the Ig locus itself to differentially promote somatic hypermutation (SHM) and class switch recombination (CSR) in B cells.
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