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Nishie R, Tanaka T, Hirosuna K, Miyamoto S, Murakami H, Tsuchihashi H, Toji A, Ueda S, Morita N, Hashida S, Daimon A, Terada S, Maruoka H, Konishi H, Kogata Y, Taniguchi K, Komura K, Ohmichi M. Creation and Validation of Patient-Derived Cancer Model Using Peritoneal and Pleural Effusion in Patients with Advanced Ovarian Cancer: An Early Experience. J Clin Med 2024; 13:2718. [PMID: 38731247 PMCID: PMC11084603 DOI: 10.3390/jcm13092718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Background: The application of personalized cancer treatment based on genetic information and surgical samples has begun in the field of cancer medicine. However, a biopsy may be painful for patients with advanced diseases that do not qualify for surgical resection. Patient-derived xenografts (PDXs) are cancer models in which patient samples are transplanted into immunodeficient mice. PDXs are expected to be useful for personalized medicine. The aim of this study was to establish a PDX from body fluid (PDX-BF), such as peritoneal and pleural effusion samples, to provide personalized medicine without surgery. Methods: PDXs-BF were created from patients with ovarian cancer who had positive cytology findings based on peritoneal and pleural effusion samples. PDXs were also prepared from each primary tumor. The pathological findings based on immunohistochemistry were compared between the primary tumor, PDX, and PDX-BF. Further, genomic profiles and gene expression were evaluated using DNA and RNA sequencing to compare primary tumors, PDXs, and PDX-BF. Results: Among the 15 patients, PDX-BF was established for 8 patients (5 high-grade serous carcinoma, 1 carcinosarcoma, 1 low-grade serous carcinoma, and 1 clear cell carcinoma); the success rate was 53%. Histologically, PDXs-BF have features similar to those of primary tumors and PDXs. In particular, PDXs-BF had similar gene mutations and expression patterns to primary tumors and PDXs. Conclusions: PDX-BF reproduced primary tumors in terms of pathological features and genomic profiles, including gene mutation and expression. Thus, PDX-BF may be a potential alternative to surgical resection for patients with advanced disease.
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Affiliation(s)
- Ruri Nishie
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Tomohito Tanaka
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
- Center for Medical Research & Development, Division of Translational Research, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (K.T.); (K.K.)
| | - Kensuke Hirosuna
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kitaku, Okayama 700-8558, Okayama, Japan;
| | - Shunsuke Miyamoto
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
- Center for Medical Research & Development, Division of Translational Research, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (K.T.); (K.K.)
| | - Hikaru Murakami
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Hiromitsu Tsuchihashi
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Akihiko Toji
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Shoko Ueda
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Natsuko Morita
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Sousuke Hashida
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Atsushi Daimon
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Shinichi Terada
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Hiroshi Maruoka
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Hiromi Konishi
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Yuhei Kogata
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
| | - Kohei Taniguchi
- Center for Medical Research & Development, Division of Translational Research, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (K.T.); (K.K.)
| | - Kazumasa Komura
- Center for Medical Research & Development, Division of Translational Research, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (K.T.); (K.K.)
| | - Masahide Ohmichi
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki 569-8686, Osaka, Japan; (R.N.); (S.M.); (H.M.); (H.T.); (A.T.); (S.U.); (N.M.); (S.H.); (A.D.); (S.T.); (H.M.); (H.K.); (Y.K.); (M.O.)
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2
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Dennis M, Hurley A, Bray N, Cordero C, Ilagan J, Mertz TM, Roberts SA. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells. PLoS Genet 2024; 20:e1011293. [PMID: 38805570 PMCID: PMC11161071 DOI: 10.1371/journal.pgen.1011293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.
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Affiliation(s)
- Madeline Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Alyssa Hurley
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Nicholas Bray
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Cameron Cordero
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Jose Ilagan
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
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3
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Liu WJ, Song R, Zou XR, Li DL, Xu Q, Zhang CY. Enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of cytosine deaminase activity in cancer cells. Anal Chim Acta 2023; 1281:341895. [PMID: 38783732 DOI: 10.1016/j.aca.2023.341895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 05/25/2024]
Abstract
APOBEC3A (A3A) is a cytidine deaminase with critical roles in molecular diagnostics. Herein, we demonstrate the enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of A3A activity in cancer cells. Target A3A can convert cytosine (C) in substrate probe to uracil (U), and then the template binds with substrate probe to form a dsDNA containing U/A base pairs. Uracil DNA glycosylase (UDG) excises the U base to produce an apurinic/apyrimidinic (AP) site that can be cleaved by apurinic/apyrimidic endonuclease 1 (APE1) to obtain the substrate fragment with 3'-OH end. Subsequently, the substrate fragment initiates cyclic enzymatic repairing amplification (ERA), releasing trigger-1 and trigger-2. The resultant trigger-1 can act as the primer to induce multiple cycles of cyclic ERA, producing numerous trigger-1 and trigger-2. The hybridization of trigger-2 with signal probe forms the dsDNA duplexes with an AP site, inducing the cyclic cleavage of signal probes by APE1 to release abundant Cy5 molecules from the AuNPs. Released Cy5 molecules can be easily quantified by single-molecule imaging. This nanosensor allows for specific and sensitive detection of A3A activity with a detection limit of 0.855 aM, and it can further measure kinetic parameters, screen inhibitors, and quantify endogenous A3A activity at the single-cell level, with prospect application in disease diagnostics and therapy.
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Affiliation(s)
- Wen-Jing Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Rui Song
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Xiao-Ran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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4
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Schnack TH, Oliveira DVNP, Christiansen AP, Høgdall C, Høgdall E. Prognostic impact of molecular profiles and molecular signatures in clear cell ovarian cancer. Cancer Genet 2023; 278-279:9-16. [PMID: 37567101 DOI: 10.1016/j.cancergen.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
OBJECTIVE Ovarian Clear cell carcinomas (OCCC) are characterized by low response to chemotherapy and a poor prognosis in advanced stages. Several studies have demonstrated that OCCC are heterogenous entities. We have earlier identified four molecular profiles based on the mutational status of ARID1A and PIK3CA. In this study we aimed to examine the association between molecular profiles, Tumor Mutational Burden (TMB), and molecular signatures with the clinical outcome in OCCC METHODS: We identified 55 OCCC cases with corresponding data and biological tissue samples in the Danish Gynecological Cancer Database during 2005-2016. Mutational profiling and TMB were performed using the Oncomine Tumor Mutational Load Assay. Chi-square and Cox regression analyses were used. P-values < 0.05 were considered statistically significant. RESULTS Mutations in the PIK3CA gene (p=0.04) and low TMB (p=0.05) were associated with disease progression. In multivariate analyses adjusted for stage, patients with tumor mutations in the ARID1A and/or PIK3CA genes had a significantly impaired Progression Free Survival (PFS) and Overall Survival (OS) compared to patients who were wildtype ARID1A and PIK3CA (undetermined subgroup) (HR= 5.42 and HR= 2.77, respectively). High TMB status was associated with an improved PFS (HR= 0.36) and OS (HR= 0.46). A trend towards an improved PFS in patients with APOBEC enrichment was observed (HR 0.45). CONCLUSION TMB-High was associated with decreased risk of progression and with an improved PFS and OS. Furthermore, OCCC with mutations in either ARID1A and/or PIK3CA genes had a significantly impaired prognosis compared to the undetermined subgroup in stage adjusted analyses.
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Affiliation(s)
- Tine Henrichsen Schnack
- Department of Gynecology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 København Ø, Denmark; Department of Gynecology and Obstetrics, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense.
| | | | - Anne Pernille Christiansen
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 København Ø, Denmark
| | - Claus Høgdall
- Department of Gynecology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 København Ø, Denmark
| | - Estrid Høgdall
- Department of Pathology, unit of Molecular Medicine, Herlev University Hospital
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5
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, Alonso de la Vega A, Proehl J, Holzhauer AM, Seeman ZJ, Liu X, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases. Cell Rep Med 2023; 4:101211. [PMID: 37797615 PMCID: PMC10591044 DOI: 10.1016/j.xcrm.2023.101211] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many cancers. However, despite years of work, a causal relationship has yet to be established in vivo. Here, we report a murine model that expresses tumor-like levels of human APOBEC3B. Animals expressing full-body APOBEC3B appear to develop normally. However, adult males manifest infertility, and older animals of both sexes show accelerated rates of carcinogenesis, visual and molecular tumor heterogeneity, and metastasis. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Enrichment for APOBEC3B-attributable single base substitution mutations also associates with elevated levels of insertion-deletion mutations and structural variations. APOBEC3B catalytic activity is required for all of these phenotypes. Together, these studies provide a cause-and-effect demonstration that human APOBEC3B is capable of driving both tumor initiation and evolution in vivo.
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Lene Alsøe
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xingyu Liu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hilde Nilsen
- Department of Microbiology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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6
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Zong C, Zhang Z, Gao L, He J, Wang Y, Li Q, Liu X, Yang J, Chen D, Huang R, Zheng G, Jin X, Wei W, Jia R, Shen J. APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors. Cell Death Dis 2023; 14:348. [PMID: 37270643 DOI: 10.1038/s41419-023-05867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023]
Abstract
The cytidine deaminase, Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B, herein termed A3B), is a critical mutation driver that induces genomic instability in cancer by catalyzing cytosine-to-thymine (C-to-T) conversion and promoting replication stress (RS). However, the detailed function of A3B in RS is not fully determined and it is not known whether the mechanism of A3B action can be exploited for cancer therapy. Here, we conducted an immunoprecipitation-mass spectrometry (IP-MS) study and identified A3B to be a novel binding component of R-loops, which are RNA:DNA hybrid structures. Mechanistically, overexpression of A3B exacerbated RS by promoting R-loop formation and altering the distribution of R-loops in the genome. This was rescued by the R-loop gatekeeper, Ribonuclease H1 (RNASEH1, herein termed RNH1). In addition, a high level of A3B conferred sensitivity to ATR/Chk1 inhibitors (ATRi/Chk1i) in melanoma cells, which was dependent on R-loop status. Together, our results provide novel insights into the mechanistic link between A3B and R-loops in the promotion of RS in cancer. This will inform the development of markers to predict the response of patients to ATRi/Chk1i.
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Affiliation(s)
- Chunyan Zong
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Li Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiran Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoting Liu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Di Chen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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7
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Long X, Lu H, Cai MC, Zang J, Zhang Z, Wu J, Liu X, Cheng L, Cheng J, Cheung LWT, Shen Z, Zhou Y, Di W, Zhuang G, Yin X. APOBEC3B stratifies ovarian clear cell carcinoma with distinct immunophenotype and prognosis. Br J Cancer 2023; 128:2054-2062. [PMID: 36997661 PMCID: PMC10206171 DOI: 10.1038/s41416-023-02239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Ovarian clear cell carcinoma (OCCC) is a challenging disease due to its intrinsic chemoresistance. Immunotherapy is an emerging treatment option but currently impeded by insufficient understanding of OCCC immunophenotypes and their molecular determinants. METHODS Whole-genome sequencing on 23 pathologically confirmed patients was employed to depict the genomic profile of primary OCCCs. APOBEC3B expression and digital pathology-based Immunoscore were assessed by performing immunohistochemistry and correlated with clinical outcomes. RESULTS An APOBEC-positive (APOBEC+) subtype was identified based on the characteristic mutational signature and prevalent kataegis events. APOBEC + OCCC displayed favourable prognosis across one internal and two external patient cohorts. The improved outcome was ascribable to increased lymphocytic infiltration. Similar phenomena of APOBEC3B expression and T-cell accumulation were observed in endometriotic tissues, suggesting that APOBEC-induced mutagenesis and immunogenicity could occur early during OCCC pathogenesis. Corroborating these results, a case report was presented for an APOBEC + patient demonstrating inflamed tumour microenvironment and clinical response to immune checkpoint blockade. CONCLUSIONS Our findings implicate APOBEC3B as a novel mechanism of OCCC stratification with prognostic value and as a potential predictive biomarker that may inform immunotherapeutic opportunities.
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Affiliation(s)
- Xiaoran Long
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaiwu Lu
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mei-Chun Cai
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyu Zang
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuqing Zhang
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Wu
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoshi Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Cheng
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiejun Cheng
- Department of Radiology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lydia W T Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhen Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen Di
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xia Yin
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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8
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Naumann JA, Argyris PP, Carpenter MA, Gupta HB, Chen Y, Temiz NA, Zhou Y, Durfee C, Proehl J, Koniar BL, Conticello SG, Largaespada DA, Brown WL, Aihara H, Vogel RI, Harris RS. DNA Deamination Is Required for Human APOBEC3A-Driven Hepatocellular Carcinoma In Vivo. Int J Mol Sci 2023; 24:9305. [PMID: 37298259 PMCID: PMC10253583 DOI: 10.3390/ijms24119305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Although the APOBEC3 family of single-stranded DNA cytosine deaminases is well-known for its antiviral factors, these enzymes are rapidly gaining attention as prominent sources of mutation in cancer. APOBEC3's signature single-base substitutions, C-to-T and C-to-G in TCA and TCT motifs, are evident in over 70% of human malignancies and dominate the mutational landscape of numerous individual tumors. Recent murine studies have established cause-and-effect relationships, with both human APOBEC3A and APOBEC3B proving capable of promoting tumor formation in vivo. Here, we investigate the molecular mechanism of APOBEC3A-driven tumor development using the murine Fah liver complementation and regeneration system. First, we show that APOBEC3A alone is capable of driving tumor development (without Tp53 knockdown as utilized in prior studies). Second, we show that the catalytic glutamic acid residue of APOBEC3A (E72) is required for tumor formation. Third, we show that an APOBEC3A separation-of-function mutant with compromised DNA deamination activity and wildtype RNA-editing activity is defective in promoting tumor formation. Collectively, these results demonstrate that APOBEC3A is a "master driver" that fuels tumor formation through a DNA deamination-dependent mechanism.
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Affiliation(s)
- Jordan A. Naumann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Harshita B. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yufan Zhou
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Brenda L. Koniar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, 50139 Florence, Italy;
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Rachel I. Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Obstetrics, Gynecology, and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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9
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Roelofs PA, Martens JW, Harris RS, Span PN. Clinical Implications of APOBEC3-Mediated Mutagenesis in Breast Cancer. Clin Cancer Res 2023; 29:1658-1669. [PMID: 36478188 PMCID: PMC10159886 DOI: 10.1158/1078-0432.ccr-22-2861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Over recent years, members of the APOBEC3 family of cytosine deaminases have been implicated in increased cancer genome mutagenesis, thereby contributing to intratumor and intertumor genomic heterogeneity and therapy resistance in, among others, breast cancer. Understanding the available methods for clinical detection of these enzymes, the conditions required for their (dysregulated) expression, the clinical impact they have, and the clinical implications they may offer is crucial in understanding the current impact of APOBEC3-mediated mutagenesis in breast cancer. Here, we provide a comprehensive review of recent developments in the detection of APOBEC3-mediated mutagenesis and responsible APOBEC3 enzymes, summarize the pathways that control their expression, and explore the clinical ramifications and opportunities they pose. We propose that APOBEC3-mediated mutagenesis can function as a helpful predictive biomarker in several standard-of-care breast cancer treatment plans and may be a novel target for treatment.
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Affiliation(s)
- Pieter A. Roelofs
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - John W.M. Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul N. Span
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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10
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Roelofs PA, Timmermans MAM, Stefanovska B, den Boestert MA, van den Borne AWM, Balcioglu HE, Trapman AM, Harris RS, Martens JWM, Span PN. Aberrant APOBEC3B Expression in Breast Cancer Is Linked to Proliferation and Cell Cycle Phase. Cells 2023; 12:cells12081185. [PMID: 37190094 DOI: 10.3390/cells12081185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
APOBEC3B (A3B) is aberrantly overexpressed in a subset of breast cancers, where it associates with advanced disease, poor prognosis, and treatment resistance, yet the causes of A3B dysregulation in breast cancer remain unclear. Here, A3B mRNA and protein expression levels were quantified in different cell lines and breast tumors and related to cell cycle markers using RT-qPCR and multiplex immunofluorescence imaging. The inducibility of A3B expression during the cell cycle was additionally addressed after cell cycle synchronization with multiple methods. First, we found that A3B protein levels within cell lines and tumors are heterogeneous and associate strongly with the proliferation marker Cyclin B1 characteristic of the G2/M phase of the cell cycle. Second, in multiple breast cancer cell lines with high A3B, expression levels were observed to oscillate throughout the cell cycle and again associate with Cyclin B1. Third, induction of A3B expression is potently repressed throughout G0/early G1, likely by RB/E2F pathway effector proteins. Fourth, in cells with low A3B, induction of A3B through the PKC/ncNF-κB pathway occurs predominantly in actively proliferating cells and is largely absent in cells arrested in G0. Altogether, these results support a model in which dysregulated A3B overexpression in breast cancer is the cumulative result of proliferation-associated relief from repression with concomitant pathway activation during the G2/M phase of the cell cycle.
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Affiliation(s)
- Pieter A Roelofs
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mieke A M Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Bojana Stefanovska
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Myrthe A den Boestert
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Amber W M van den Borne
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anita M Trapman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Paul N Span
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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11
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Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
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Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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12
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Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
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13
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Durfee C, Temiz NA, Levin-Klein R, Argyris PP, Alsøe L, Carracedo S, de la Vega AA, Proehl J, Holzhauer AM, Seeman ZJ, Lin YHT, Vogel RI, Sotillo R, Nilsen H, Harris RS. Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529970. [PMID: 36865194 PMCID: PMC9980288 DOI: 10.1101/2023.02.24.529970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The antiviral DNA cytosine deaminase APOBEC3B has been implicated as a source of mutation in many different cancers. Despite over 10 years of work, a causal relationship has yet to be established between APOBEC3B and any stage of carcinogenesis. Here we report a murine model that expresses tumor-like levels of human APOBEC3B after Cre-mediated recombination. Animals appear to develop normally with full-body expression of APOBEC3B. However, adult males manifest infertility and older animals of both sexes show accelerated rates of tumorigenesis (mostly lymphomas or hepatocellular carcinomas). Interestingly, primary tumors also show overt heterogeneity, and a subset spreads to secondary sites. Both primary and metastatic tumors exhibit increased frequencies of C-to-T mutations in TC dinucleotide motifs consistent with the established biochemical activity of APOBEC3B. Elevated levels of structural variation and insertion-deletion mutations also accumulate in these tumors. Together, these studies provide the first cause-and-effect demonstration that human APOBEC3B is an oncoprotein capable of causing a wide range of genetic changes and driving tumor formation in vivo .
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Affiliation(s)
- Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Prokopios P Argyris
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, Ohio, USA, 43210
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Anna M Holzhauer
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Zachary J Seeman
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Yu-Hsiu T Lin
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL)
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA, 78229
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14
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Wong L, Sami A, Chelico L. Competition for DNA binding between the genome protector replication protein A and the genome modifying APOBEC3 single-stranded DNA deaminases. Nucleic Acids Res 2022; 50:12039-12057. [PMID: 36444883 PMCID: PMC9757055 DOI: 10.1093/nar/gkac1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/30/2022] Open
Abstract
The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing evolution of antibody genes, and innate immunity through inactivation of viral genomes. These benefits come at a cost where some family members, primarily from the APOBEC3 subfamily (APOBEC3A-H, excluding E), can cause off-target deaminations of cytosine to form uracil on transiently single-stranded genomic DNA, which induces mutations that are associated with cancer evolution. Since uracil is only promutagenic, the mutations observed in cancer genomes originate only when uracil is not removed by uracil DNA glycosylase (UNG) or when the UNG-induced abasic site is erroneously repaired. However, when ssDNA is present, replication protein A (RPA) binds and protects the DNA from nucleases or recruits DNA repair proteins, such as UNG. Thus, APOBEC enzymes must compete with RPA to access their substrate. Certain APOBEC enzymes can displace RPA, bind and scan ssDNA efficiently to search for cytosines, and can become highly overexpressed in tumor cells. Depending on the DNA replication conditions and DNA structure, RPA can either be in excess or deficient. Here we discuss the interplay between these factors and how despite RPA, multiple cancer genomes have a mutation bias at cytosines indicative of APOBEC activity.
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Affiliation(s)
- Lai Wong
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Alina Sami
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Linda Chelico
- To whom correspondence should be addressed. Tel: +1 306 966 4318; Fax: +1 306 966 4298;
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15
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Chen C, Sui X, Ning H, Sun Y, Du J, Chen X, Zhou X, Chen G, Shen W, Pang L, Zhou X, Shi R, Li W, Wang H, Zhao W, Zhai W, Qi Y, Wu Y, Gao Y. Identification of natural product 3, 5-diiodotyrosine as APOBEC3B inhibitor to prevent somatic mutation accumulation and cancer progression. J Immunother Cancer 2022; 10:jitc-2022-005503. [PMID: 36323433 PMCID: PMC9639148 DOI: 10.1136/jitc-2022-005503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The development of cancer is largely dependent on the accumulation of somatic mutations, indicating the potential to develop cancer chemoprevention agents targeting mutation drivers. However, ideal cancer chemoprevention agents that can effectively inhibit the mutation drivers have not been identified yet. METHODS The somatic mutation signatures and expression analyses of APOBEC3B were performed in patient with pan-cancer. The computer-aided screening and skeleton-based searching were performed to identify natural products that can inhibit the activity of APOBEC3B. 4-nitroquinoline-1-oxide (4-NQO)-induced spontaneous esophageal squamous cell carcinoma (ESCC) and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced spontaneous colon cancer mouse models were conducted to investigate the influences of APOBEC3B inhibitor on the prevention of somatic mutation accumulation and cancer progression. RESULTS Here, we discovered that the cytidine deaminase APOBEC3B correlated somatic mutations were widely observed in a variety of cancers, and its overexpression indicated poor survival. SMC247 (3, 5-diiodotyrosine), as a source of kelp iodine without side effects, could strongly bind APOBEC3B (KD=65 nM) and effectively inhibit its deaminase activity (IC50=1.69 µM). Interestingly, 3, 5-diiodotyrosine could significantly reduce the clusters of mutations, prevent the precancerous lesion progression, and prolong the survival in 4-NQO-induced spontaneous ESCC and AOM/DSS-induced spontaneous colon cancer mouse models. Furthermore, 3, 5-diiodotyrosine could reduce colitis, increase the proportion and function of T lymphocytes via IL-15 in tumor microenvironment. The synergistic cancer prevention effects were observed when 3, 5-diiodotyrosine combined with PD-1/PD-L1 blockade. CONCLUSIONS This is the first prove-of-concept study to elucidate that the natural product 3, 5-diiodotyrosine could prevent somatic mutation accumulation and cancer progression through inhibiting the enzymatic activity of APOBEC3B. In addition, 3, 5-diiodotyrosine could reduce the colitis and increase the infiltration and function of T lymphocytes via IL-15 in tumor microenvironment. 3, 5-diiodotyrosine combined with PD-1/PD-L1 blockade could elicit synergistic cancer prevention effects, indicating a novel strategy for both prevent the somatic mutation accumulation and the immune-suppressive microenvironment exacerbation.
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Affiliation(s)
- Chunxia Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinghua Sui
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Haoming Ning
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yixuan Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaotong Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiuman Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Guanyu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Wenhui Shen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Liwei Pang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaowen Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ranran Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wanqiong Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
| | - Hongfei Wang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenshan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanming Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University - Shenzhen Campus, Shenzhen, Guangdong, China
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16
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Leung RWT, Jiang X, Zong X, Zhang Y, Hu X, Hu Y, Qin J. CORN-Condition Orientated Regulatory Networks: bridging conditions to gene networks. Brief Bioinform 2022; 23:6702670. [PMID: 36124777 PMCID: PMC9677472 DOI: 10.1093/bib/bbac402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/14/2022] Open
Abstract
A transcriptional regulatory network (TRN) is a collection of transcription regulators with their associated downstream genes, which is highly condition-specific. Understanding how cell states can be programmed through small molecules/drugs or conditions by modulating the whole gene expression system granted us the potential to amend abnormal cells and cure diseases. Condition Orientated Regulatory Networks (CORN, https://qinlab.sysu.edu.cn/home) is a library of condition (small molecule/drug treatments and gene knockdowns)-based transcriptional regulatory sub-networks (TRSNs) that come with an online TRSN matching tool. It allows users to browse condition-associated TRSNs or match those TRSNs by inputting transcriptomic changes of interest. CORN utilizes transcriptomic changes data after specific conditional treatment in cells, and in vivo transcription factor (TF) binding data in cells, by combining TF binding information and calculations of significant expression alterations of TFs and genes after the conditional treatments, TRNs under the effect of different conditions were constructed. In short, CORN associated 1805 different types of specific conditions (small molecule/drug treatments and gene knockdowns) to 9553 TRSNs in 25 human cell lines, involving 204TFs. By linking and curating specific conditions to responsive TRNs, the scientific community can now perceive how TRNs are altered and controlled by conditions alone in an organized manner for the first time. This study demonstrated with examples that CORN can aid the understanding of molecular pathology, pharmacology and drug repositioning, and screened drugs with high potential for cancer and coronavirus disease 2019 (COVID-19) treatments.
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Affiliation(s)
| | | | | | - Yanhong Zhang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xinlin Hu
- College of Mathematics and Statistics, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University, Shenzhen 518060, China,Department of Applied Mathematics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Yaohua Hu
- Corresponding authors: Yaohua Hu, College of Mathematics and Statistics, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University, Shenzhen 518060, China; Jing Qin, School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China. E-mail:
| | - Jing Qin
- Corresponding authors: Yaohua Hu, College of Mathematics and Statistics, Shenzhen Key Laboratory of Advanced Machine Learning and Applications, Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University, Shenzhen 518060, China; Jing Qin, School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China. E-mail:
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17
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Qin T, Fan J, Lu F, Zhang L, Liu C, Xiong Q, Zhao Y, Chen G, Sun C. Harnessing preclinical models for the interrogation of ovarian cancer. J Exp Clin Cancer Res 2022; 41:277. [PMID: 36114548 PMCID: PMC9479310 DOI: 10.1186/s13046-022-02486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022] Open
Abstract
Ovarian cancer (OC) is a heterogeneous malignancy with various etiology, histopathology, and biological feature. Despite accumulating understanding of OC in the post-genomic era, the preclinical knowledge still undergoes limited translation from bench to beside, and the prognosis of ovarian cancer has remained dismal over the past 30 years. Henceforth, reliable preclinical model systems are warranted to bridge the gap between laboratory experiments and clinical practice. In this review, we discuss the status quo of ovarian cancer preclinical models which includes conventional cell line models, patient-derived xenografts (PDXs), patient-derived organoids (PDOs), patient-derived explants (PDEs), and genetically engineered mouse models (GEMMs). Each model has its own strengths and drawbacks. We focus on the potentials and challenges of using these valuable tools, either alone or in combination, to interrogate critical issues with OC.
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18
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Jafarpour S, Yazdi M, Nedaeinia R, Ghobakhloo S, Salehi R. Unfavorable prognosis and clinical consequences of APOBEC3B expression in breast and other cancers: A systematic review and meta-analysis. Tumour Biol 2022; 44:153-169. [DOI: 10.3233/tub-211577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION: Controversy exists regarding the association of apolipoprotein B mRNA editing enzyme catalytic subunit 3B APOBEC3B, (A3B) overexpression and poor prognosis, metastasis, and chemotherapy drug resistance in cancers. Here we conducted a systematic review and meta-analysis to determine its prognostic value and clinicopathological features in breast cancer and some other malignancies. MATERIALS AND METHODS: PubMed, Scopus, Cochrane Library, Web of Science, and EMBASE were searched up to Feb 2022 for the association of A3B with breast, ovarian, gastrointestinal and lung cancers. The pooled hazard ratios with 95% confidence interval (CI) were evaluated to assess disease-free survival (DFS), overall survival (OS), and recurrence-free survival (RFS) in cancers under study. RESULTS: Over 3700 patients were included in this meta-survey. Elevated levels of A3B were significantly related to low OS (pooled HR = 1.30; 95% CI:1.09–1.55, P < 0.01), poor DFS (pooled HR = 1.66; 95% CI:1.17–2.35, P < 0.01) and poor RFS (HR = 1.51, 95% CI:1.11–2.04, P = 0.01). Subgroup analysis revealed that high A3B expression was associated with poor OS in lung (HR = 1.85, 95% CI: 1.40–2.45), and breast cancers (HR = 1.38, 95% CI: 1.00–1.89). High expression of A3B did not display any significant association with clinicopathologic features. CONCLUSION: APOBEC3B overexpression is related to poor OS, DFS and RFS only in some cancer types and no generalized role could be predicted for all cancers.
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Affiliation(s)
- Sima Jafarpour
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Yazdi
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sepideh Ghobakhloo
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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19
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The Role of ATR Inhibitors in Ovarian Cancer: Investigating Predictive Biomarkers of Response. Cells 2022; 11:cells11152361. [PMID: 35954206 PMCID: PMC9367423 DOI: 10.3390/cells11152361] [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: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
Ataxia telangiectasia and Rad-3 related kinase (ATR) signals DNA lesions and replication stress (RS) to the S and G2/M checkpoints and DNA repair pathways making it a promising target to exploit the dysregulated DNA damage response in cancer. ATR inhibitors (ATRi) are under clinical investigation as monotherapy and in combination with other anticancer agents. Molecular determinants of sensitivity to ATRi are common in ovarian cancer, suggesting the therapeutic potential of ATRi. We investigated the cytotoxicity of the ATRi, VE-821, in a panel of human ovarian cancer cell lines. High grade serous (HGS) cell lines were significantly more sensitive to VE-821 than non-HGS (p ≤ 0.0001) but previously identified determinants of sensitivity (TP53, ATM and BRCA1) were not predictive. Only low RAD51 (p = 0.041), TopBP1 (p = 0.026) and APOBEC3B (p = 0.015) protein expression were associated with increased VE-821 sensitivity. HGS cells had increased levels of RS (pRPASer4/8 and γH2AX nuclear immunofluorescence), and elevated RS predicted sensitivity to VE-821 independently of the cell line subtype. These data suggest that functional assessment of RS biomarkers may be a better predictive biomarker of ATRi response than any single aberrant gene in ovarian cancer and potentially other cancers.
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20
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Jakobsdottir GM, Brewer DS, Cooper C, Green C, Wedge DC. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biol 2022; 20:117. [PMID: 35597990 PMCID: PMC9124393 DOI: 10.1186/s12915-022-01316-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes are activated in response to viral infection, and have been associated with increased mutation burden and TP53 mutation. In addition to this, it has been suggested that APOBEC3 activity may be responsible for mutations that do not fall into the classical APOBEC3 signatures (SBS2 and SBS13), through generation of double strand breaks.Previous work has mainly focused on the effects of APOBEC3 within individual tumour types using exome sequencing data. Here, we use whole genome sequencing data from 2451 primary tumours from 39 different tumour types in the Pan-Cancer Analysis of Whole Genomes (PCAWG) data set to investigate the relationship between APOBEC3 and genomic instability (GI). RESULTS AND CONCLUSIONS We found that the number of classical APOBEC3 signature mutations correlates with increased mutation burden across different tumour types. In addition, the number of APOBEC3 mutations is a significant predictor for six different measures of GI. Two GI measures (INDELs attributed to INDEL signatures ID6 and ID8) strongly suggest the occurrence and error prone repair of double strand breaks, and the relationship between APOBEC3 mutations and GI remains when SNVs attributed to kataegis are excluded.We provide evidence that supports a model of cancer genome evolution in which APOBEC3 acts as a causative factor in the development of diverse and widespread genomic instability through the generation of double strand breaks. This has important implications for treatment approaches for cancers that carry APOBEC3 mutations, and challenges the view that APOBECs only act opportunistically at sites of single stranded DNA.
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Affiliation(s)
- G Maria Jakobsdottir
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Colin Cooper
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK.
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21
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Farmanbar A, Firouzi S, Kneller R, Khiabanian H. Mutational signatures reveal ternary relationships between homologous recombination repair, APOBEC, and mismatch repair in gynecological cancers. J Transl Med 2022; 20:65. [PMID: 35109853 PMCID: PMC8812249 DOI: 10.1186/s12967-022-03259-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/17/2022] [Indexed: 01/29/2023] Open
Abstract
Background Revealing the impacts of endogenous and exogenous mutagenesis processes is essential for understanding the etiology of somatic genomic alterations and designing precise prognostication and treatment strategies for cancer. DNA repair deficiency is one of the main sources of endogenous mutagenesis and is increasingly recognized as a target for cancer therapeutics. The role and prevalence of mechanisms that underly different forms of DNA repair deficiencies and their interactions remain to be elucidated in gynecological malignancies. Methods We analyzed 1231 exomes and 268 whole-genomes from three major gynecological malignancies including uterine corpus endometrial carcinoma (UCEC) as well as ovarian and cervical cancers. We also analyzed data from 134 related cell lines. We extracted and compared de novo and refitted mutational signature profiles using complementary and confirmatory approaches and performed interaction analysis to detect co-occurring and mutually exclusive signatures. Results We found an inverse relationship between homologous recombination deficiency (HRd) and mismatch repair deficiency (MMRd). Moreover, APOBEC co-occurred with HRd but was mutually exclusive with MMRd. UCEC tumors were dominated by MMRd, yet a subset of them manifested the HRd and APOBEC signatures. Conversely, ovarian tumors were dominated by HRd, while a subset represented MMRd and APOBEC. In contrast to both, cervical tumors were dominated by APOBEC with a small subsets showing the POLE, HRd, and MMRd signatures. Although the type, prevalence, and heterogeneity of mutational signatures varied across the tumor types, the patterns of co-occurrence and exclusivity were consistently observed in all. Notably, mutational signatures in gynecological tumor cell lines reflected those detected in primary tumors. Conclusions Taken together, these analyses indicate that application of mutation signature analysis not only advances our understanding of mutational processes and their interactions, but also it has the potential to stratify patients that could benefit from treatments available for tumors harboring distinct mutational signatures and to improve clinical decision-making for gynecological malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03259-0.
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Affiliation(s)
- Amir Farmanbar
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08903, USA
| | - Sanaz Firouzi
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA.
| | - Robert Kneller
- Research Center for Advanced Science and Technology, University of Tokyo, Minato-ku, Tokyo, 153-8904, Japan
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08903, USA. .,Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, 08903, USA.
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22
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Liao X, Xia X, Su W, Yan H, Ma Y, Xu L, Luo H, Liu W, Yin D, Zhang WH, Chen HN, Deng Y, Ren Z, Yu Z, Liao F, Chen K, Cao M, Zhang Y, Zhang W, Wang W, Zhao JN, Xu H, Shu Y. Association of recurrent APOBEC3B alterations with the prognosis of gastric-type cervical adenocarcinoma. Gynecol Oncol 2022; 165:105-113. [DOI: 10.1016/j.ygyno.2022.01.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
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23
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Gao M, Qi Z, Feng W, Huang H, Xu Z, Dong Z, Xu M, Han J, Kloeber JA, Huang J, Lou Z, Liu S. m6A demethylation of cytidine deaminase APOBEC3B mRNA orchestrates arsenic-induced mutagenesis. J Biol Chem 2022; 298:101563. [PMID: 34998823 PMCID: PMC8814665 DOI: 10.1016/j.jbc.2022.101563] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
The cytidine deaminase APOBEC3B (A3B) is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in single-stranded DNA. Therefore, identification of factors and mechanisms that mediate A3B expression will be helpful for developing therapeutic approaches to decrease DNA mutagenesis. Arsenic (As) is one well-known mutagen and carcinogen, but the mechanisms by which it induces mutations have not been fully elucidated. Herein, we show that A3B is upregulated and required for As-induced DNA damage and mutagenesis. We found that As treatment causes a decrease of N6-methyladenosine (m6A) modification near the stop codon of A3B, consequently increasing the stability of A3B mRNA. We further reveal that the demethylase FTO is responsible for As-reduced m6A modification of A3B, leading to increased A3B expression and DNA mutation rates in a manner dependent on the m6A reader YTHDF2. Our in vivo data also confirm that A3B is a downstream target of FTO in As-exposed lung tissues. In addition, FTO protein is highly expressed and positively correlates with the protein levels of A3B in tumor samples from human non-small cell lung cancer patients. These findings indicate a previously unrecognized role of A3B in As-triggered somatic mutation and might open new avenues to reduce DNA mutagenesis by targeting the FTO/m6A axis.
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Affiliation(s)
- Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zijuan Qi
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Ji'nan, Shandong, China
| | - Wenya Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyang Huang
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhijie Xu
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jinxiang Han
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Ji'nan, Shandong, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA.
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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Xu F, Liu T, Zhou Z, Zou C, Xu S. Comprehensive Analyses Identify APOBEC3A as a Genomic Instability-Associated Immune Prognostic Biomarker in Ovarian Cancer. Front Immunol 2021; 12:749369. [PMID: 34745121 PMCID: PMC8568129 DOI: 10.3389/fimmu.2021.749369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancer (OC) is one of the most malignant tumors whose mortality rate ranks first in gynecological tumors. Although immunotherapy sheds new light on clinical treatments, the low response still restricts its clinical use because of the unique characteristics of OC such as immunosuppressive microenvironment and unstable genomes. Further exploration on determining an efficient biomarker to predict the immunotherapy response of OC patients is of vital importance. In this study, integrative analyses were performed systematically using transcriptome profiles and somatic mutation data from The Cancer Genome Atlas (TCGA) based on the immune microenvironment and genomic instability of OC patients. Firstly, intersection analysis was conducted to identify immune-related differentially expressed genes (DEGs) and genomic instability-related DEGs. Secondly, Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3A (APOBEC3A) was recognized as a protective factor for OC, which was also verified through basic experiments such as quantitative reverse transcription PCR (RT-qPCR), immunohistochemistry (IHC), Cell Counting Kit-8 (CCK-8), and transwell assays. Thirdly, the correlation analyses of APOBEC3A expression with tumor-infiltrating immune cells (TICs), inhibitory checkpoint molecules (ICPs), Immunophenoscores (IPS), and response to anti-PD-L1 immunotherapy were further applied along with single-sample GSEA (ssGSEA), demonstrating APOBEC3A as a promising biomarker to forecast the immunotherapy response of OC patients. Last, the relationship between APOBEC3A expression with tumor mutation burden (TMB), DNA damage response (DDR) genes, and m6A-related regulators was also analyzed along with the experimental verification of immunofluorescence (IF) and RT-qPCR, comprehensively confirming the intimate association of APOBEC3A with genomic instability in OC. In conclusion, APOBEC3A was identified as a protective signature and a promising prognostic biomarker for forecasting the survival and immunotherapy effect of OC patients, which might accelerate the clinical application and improve immunotherapy effect.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tingwei Liu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhuonan Zhou
- Jianping Educational Center of International Curriculum, Shanghai Jianping High School, Shanghai, China
| | - Chang Zou
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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25
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Zhu Z, Ji X, Zhu W, Cai T, Xu C, Huang C, He S, Gong Y, Li X, Lin J, Zhou L. Comprehensive bioinformatics analyses of APOBECs family and identification of APOBEC3D as the unfavorable prognostic biomarker in clear cell renal cell carcinoma. J Cancer 2021; 12:7101-7110. [PMID: 34729111 PMCID: PMC8558646 DOI: 10.7150/jca.61972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/03/2021] [Indexed: 01/22/2023] Open
Abstract
Purpose: At present, how early screening for ccRCC is still a thorny issue for urologists. Probing the mechanisms underlying the development of ccRCC and finding relevant prognostic biomarkers remains crucial. Therefore, we systematically analyzed the APOBEC family in this study and identified APOBEC3D as a prognostic biomarker. Methods: In this study, based on the TCGA database, we systematically assessed the expression and prognosis of the APOBEC family and analyzed potential bioinformatic pathways. We then constructed nomograms to predict the prognosis of ccRCC patients better. Afterward, we further focused on APOBEC3D in our data on ccRCC specimens. The APOBEC3D should be extensively studied in ccRCC in the future. Results: The results showed that the APOBEC family showed the most significant changes in expression in ccRCC. The pathway enrichment analysis showed that APOBEC3 family members mainly regulated cytidine and cytosine-related processes. Subsequently, the Cox regression was used to construct prognostic signature, and validated in ICGC and GEO databases. Next, a nomogram was created integrating clinical parameters showing good predictive performance. Finally, we screened for APOBEC3D and found in our clinical sample that patients with high expression of APOBEC3D had a worse prognosis. Conclusion: Based on these results, APOBEC family members play important roles in the development of ccRCC, and APOBEC3D could serve as the biomarker for predicting patient prognosis.
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Affiliation(s)
- Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xing Ji
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Weijie Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Tianyu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Cong Huang
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
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26
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Xia S, Gu Y, Zhang H, Fei Y, Cao Y, Fang H, Wang J, Lin C, Zhang H, Li H, He H, Xu J, Li R, Liu H, Zhang W. Immune inactivation by APOBEC3B enrichment predicts response to chemotherapy and survival in gastric cancer. Oncoimmunology 2021; 10:1975386. [PMID: 34552824 PMCID: PMC8451457 DOI: 10.1080/2162402x.2021.1975386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic polypeptide 3B (APOBEC3B) plays an important role in tumor mutagenesis. However, its clinical significance in gastric cancer (GC) remains largely unknown. We enrolled a total of 482 GC patients from Zhongshan Hospital, Fudan University for immunohistochemistry (IHC) staining to evaluate the prognostic and predictive values of APOBEC3B. Genomic and phenotypic datasets from the Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG) cohort were downloaded for external validation and complementary bioinformatic analysis. Fresh specimens of additional 60 patients from Zhongshan Hospital, Fudan University were collected to detect CD8+ T cell phenotype with flow cytometry (FCM). The high expression of APOBEC3B indicated inferior overall survival (OS, P < .001 and P = .003) and disease-free survival (DFS, P < .001 and P < .001), yet superior therapeutic responsiveness to fluorouracil-based adjuvant chemotherapy (ACT) in TNM stage II patients. The tumor microenvironment (TME) of APOBEC3B-enriched tumors was characterized by reduced infiltration of tumor reactive CD8+ T cells expressing both effector molecules and immune checkpoints. APOBEC3B high CD8+ T cell high GC patients were most likely to benefit from ACT and PD-1 blockade. Our study demonstrates that APOBEC3B was an independent prognostic and predictive factor in GC. The potential interplay between APOBEC3B and CD8+ T cells merited further investigations.
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Affiliation(s)
- Siyu Xia
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Gu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuchao Fei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yifan Cao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hanji Fang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jieti Wang
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao Lin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Heng Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - He Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongyong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ruochen Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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27
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Wang B, Zhang X, Wang Y, Chen K, Wang F, Weng X, Zhou X. One-pot fluorescent assay for sensitive detection of APOBEC3A activity. RSC Chem Biol 2021; 2:1201-1205. [PMID: 34458832 PMCID: PMC8341802 DOI: 10.1039/d1cb00076d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/30/2021] [Indexed: 01/03/2023] Open
Abstract
We reported a one-pot fluorescence-based assay to quantitively detect A3A activity combined with cytosine deamination and uracil excision. After deamination by A3A and USER enzyme treatment, the fluorescent turn-on effect at 520 nm was observed, which can be used to evaluate the A3A activity and screen inhibitors.
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Affiliation(s)
- Bingyao Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
| | - Xiong Zhang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
| | - Yafen Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
| | - Kun Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Xiaocheng Weng
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
| | - Xiang Zhou
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University Wuhan Hubei 430072 China +86-27-68756663 +86-27-68756663
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28
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APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet 2021; 37:1028-1043. [PMID: 34353635 DOI: 10.1016/j.tig.2021.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts.
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29
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Chen Z, Eggerman TL, Bocharov AV, Baranova IN, Vishnyakova TG, Patterson AP. APOBEC3-induced mutation of the hepatitis virus B DNA genome occurs during its viral RNA reverse transcription into (-)-DNA. J Biol Chem 2021; 297:100889. [PMID: 34181944 PMCID: PMC8321922 DOI: 10.1016/j.jbc.2021.100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
APOBEC3s are innate single-stranded DNA cytidine-to-uridine deaminases that catalyze mutations in both pathogen and human genomes with significant roles in human disease. However, how APOBEC3s mutate a single-stranded DNA that is available momentarily during DNA transcription or replication in vivo remains relatively unknown. In this study, utilizing hepatitis B virus (HBV) viral mutations, we evaluated the mutational characteristics of individual APOBEC3s with reference to the HBV replication process through HBV whole single-strand (-)-DNA genome mutation analyses. We found that APOBEC3s induced C-to-T mutations from the HBV reverse transcription start site continuing through the whole (-)-DNA transcript to the termination site with variable efficiency, in an order of A3B >> A3G > A3H-II or A3C. A3B had a 3-fold higher mutation efficiency than A3H-II or A3C with up to 65% of all HBV genomic cytidines being converted into uridines in a single mutation event, consistent with the A3B localized hypermutation signature in cancer, namely, kataegis. On the other hand, A3C expression led to a 3-fold higher number of mutation-positive HBV genome clones, although each individual clone had a lower number of C-to-T mutations. Like A3B, A3C preferred both 5'-TC and 5'-CC sequences, but to a lesser degree. The APOBEC3-induced HBV mutations were predominantly detected in the HBV rcDNA but were not detectable in other intermediates including HBV cccDNA and pgRNA by primer extension of their PCR amplification products. These data demonstrate that APOBEC3-induced HBV genome mutations occur predominantly when the HBV RNA genome was reversely transcribed into (-)-DNA in the viral capsid.
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Affiliation(s)
- Zhigang Chen
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas L Eggerman
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; Division of Diabetes, Endocrinology and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexander V Bocharov
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Irina N Baranova
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Tatyana G Vishnyakova
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Amy P Patterson
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA; National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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30
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Periyasamy M, Singh AK, Gemma C, Farzan R, Allsopp RC, Shaw JA, Charmsaz S, Young LS, Cunnea P, Coombes RC, Győrffy B, Buluwela L, Ali S. Induction of APOBEC3B expression by chemotherapy drugs is mediated by DNA-PK-directed activation of NF-κB. Oncogene 2021; 40:1077-1090. [PMID: 33323971 PMCID: PMC7116738 DOI: 10.1038/s41388-020-01583-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/06/2020] [Accepted: 11/20/2020] [Indexed: 12/24/2022]
Abstract
The mutagenic APOBEC3B (A3B) cytosine deaminase is frequently over-expressed in cancer and promotes tumour heterogeneity and therapy resistance. Hence, understanding the mechanisms that underlie A3B over-expression is important, especially for developing therapeutic approaches to reducing A3B levels, and consequently limiting cancer mutagenesis. We previously demonstrated that A3B is repressed by p53 and p53 mutation increases A3B expression. Here, we investigate A3B expression upon treatment with chemotherapeutic drugs that activate p53, including 5-fluorouracil, etoposide and cisplatin. Contrary to expectation, these drugs induced A3B expression and concomitant cellular cytosine deaminase activity. A3B induction was p53-independent, as chemotherapy drugs stimulated A3B expression in p53 mutant cells. These drugs commonly activate ATM, ATR and DNA-PKcs. Using specific inhibitors and gene knockdowns, we show that activation of DNA-PKcs and ATM by chemotherapeutic drugs promotes NF-κB activity, with consequent recruitment of NF-κB to the A3B gene promoter to drive A3B expression. Further, we find that A3B knockdown re-sensitises resistant cells to cisplatin, and A3B knockout enhances sensitivity to chemotherapy drugs. Our data highlight a role for A3B in resistance to chemotherapy and indicate that stimulation of A3B expression by activation of DNA repair and NF-κB pathways could promote cancer mutations and expedite chemoresistance.
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Affiliation(s)
| | - Anup K Singh
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Carolina Gemma
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Raed Farzan
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rebecca C Allsopp
- Department of Cancer Studies and Cancer Research UK, Leicester Centre, University of Leicester, Leicester, UK
| | - Jacqueline A Shaw
- Department of Cancer Studies and Cancer Research UK, Leicester Centre, University of Leicester, Leicester, UK
| | - Sara Charmsaz
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Paula Cunnea
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - R Charles Coombes
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Balázs Győrffy
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Lakjaya Buluwela
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, London, W12 0NN, UK.
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Endogenous APOBEC3B overexpression characterizes HPV-positive and HPV-negative oral epithelial dysplasias and head and neck cancers. Mod Pathol 2021; 34:280-290. [PMID: 32632179 PMCID: PMC8261524 DOI: 10.1038/s41379-020-0617-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022]
Abstract
The DNA cytosine deaminase APOBEC3B (A3B) is a newly recognized endogenous source of mutations in a range of human tumors, including head/neck cancer. A3B inflicts C-to-T and C-to-G base substitutions in 5'-TCA/T trinucleotide motifs, contributes to accelerated rates of tumor development, and affects clinical outcomes in a variety of cancer types. High-risk human papillomavirus (HPV) infection causes A3B overexpression, and HPV-positive cervical and head/neck cancers are among tumor types with the highest degree of APOBEC signature mutations. A3B overexpression in HPV-positive tumor types is caused by the viral E6/E7 oncoproteins and may be an early off-to-on switch in tumorigenesis. In comparison, less is known about the molecular mechanisms responsible for A3B overexpression in HPV-negative head/neck cancers. Here, we utilize an immunohistochemical approach to determine whether A3B is turned from off-to-on or if it undergoes a more gradual transition to overexpression in HPV-negative head/neck cancers. As positive controls, almost all HPV-positive oral epithelial dysplasias and oropharyngeal cancers showed high levels of nuclear A3B staining regardless of diagnosis. As negative controls, A3B levels were low in phenotypically normal epithelium adjacent to cancer and oral epithelial hyperplasias. Interestingly, HPV-negative and low-grade oral epithelial dysplasias showed intermediate A3B levels, while high-grade oral dysplasias showed high A3B levels similar to oral squamous cell carcinomas. A3B levels were highest in grade 2 and grade 3 oral squamous cell carcinomas. In addition, a strong positive association was found between nuclear A3B and Ki67 scores suggesting a linkage to the cell cycle. Overall, these results support a model in which gradual activation of A3B expression occurs during HPV-negative tumor development and suggest that A3B overexpression may provide a marker for advanced grade oral dysplasia and cancer.
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32
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Wong L, Vizeacoumar FS, Vizeacoumar FJ, Chelico L. APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A. Nucleic Acids Res 2021; 49:322-339. [PMID: 33330905 PMCID: PMC7797036 DOI: 10.1093/nar/gkaa1201] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Many APOBEC cytidine deaminase members are known to induce ‘off-target’ cytidine deaminations in 5′TC motifs in genomic DNA that contribute to cancer evolution. In this report, we characterized APOBEC1, which is a possible cancer related APOBEC since APOBEC1 mRNA is highly expressed in certain types of tumors, such as lung adenocarcinoma. We found a low level of APOBEC1-induced DNA damage, as measured by γH2AX foci, in genomic DNA of a lung cancer cell line that correlated to its inability to compete in vitro with replication protein A (RPA) for ssDNA. This suggests that RPA can act as a defense against off-target deamination for some APOBEC enzymes. Overall, the data support the model that the ability of an APOBEC to compete with RPA can better predict genomic damage than combined analysis of mRNA expression levels in tumors and analysis of mutation signatures.
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Affiliation(s)
- Lai Wong
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon S7N 5E5, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan S7S 0A6, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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Granadillo Rodríguez M, Flath B, Chelico L. The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead. Open Biol 2020; 10:200188. [PMID: 33292100 PMCID: PMC7776566 DOI: 10.1098/rsob.200188] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Conner KL, Shaik AN, Marshall KA, Floyd AM, Ekinci E, Lindquist J, Sawant A, Lei W, Adolph MB, Chelico L, Siriwardena SU, Bhagwat A, Kim S, Cote ML, Patrick SM. APOBEC3 enzymes mediate efficacy of cisplatin and are epistatic with base excision repair and mismatch repair in platinum response. NAR Cancer 2020; 2:zcaa033. [PMID: 33196045 PMCID: PMC7646253 DOI: 10.1093/narcan/zcaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023] Open
Abstract
Identifying the mechanisms mediating cisplatin response is essential for improving patient response. Previous research has identified base excision repair (BER) and mismatch repair (MMR) activity in sensitizing cells to cisplatin. Cisplatin forms DNA adducts including interstrand cross-links (ICLs) that distort the DNA helix, forcing adjacent cytosines to become extrahelical. These extrahelical cytosines provide a substrate for cytosine deaminases. Herein, we show that APOBEC3 (A3) enzymes are capable of deaminating the extrahelical cytosines to uracils and sensitizing breast cancer cells to cisplatin. Knockdown of A3s results in resistance to cisplatin and induction of A3 expression in cells with low A3 expression increases sensitivity to cisplatin. We show that the actions of A3s are epistatic with BER and MMR. We propose that A3-induced cytosine deamination to uracil at cisplatin ICLs results in repair of uracils by BER, which blocks ICL DNA repair and enhances cisplatin efficacy and improves breast cancer outcomes.
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Affiliation(s)
- Kayla L Conner
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Asra N Shaik
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Katie A Marshall
- Department of Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ashley M Floyd
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Elmira Ekinci
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Jacob Lindquist
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Akshada Sawant
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Wen Lei
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | | | - Linda Chelico
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK S7N 5E5, Canada
| | | | - Ashok Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Seongho Kim
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Michele L Cote
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
| | - Steve M Patrick
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Institute, Detroit, MI 48201, USA
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35
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Revathidevi S, Murugan AK, Nakaoka H, Inoue I, Munirajan AK. APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett 2020; 496:104-116. [PMID: 33038491 PMCID: PMC7539941 DOI: 10.1016/j.canlet.2020.10.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/16/2020] [Accepted: 10/04/2020] [Indexed: 02/09/2023]
Abstract
Cervical cancer is one of the foremost common cancers in women. Human papillomavirus (HPV) infection remains a major risk factor of cervical cancer. In addition, numerous other genetic and epigenetic factors also are involved in the underlying pathogenesis of cervical cancer. Recently, it has been reported that apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. Particularly, the APOBEC3 family was shown to induce tumor mutations by aberrant DNA editing mechanism. In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidine to uridine in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. This review briefly describes the pathogenesis of cervical cancer and discusses in detail the recent findings on the role of APOBEC in the molecular pathogenesis of cervical cancer. APOBEC enzymes deaminate cytidine to uridine and control diverse biological processes including viral restriction. APOBEC3, DNA/RNA-editing enzyme plays an important role in the molecular pathogenesis of cervical cancer. APOBEC3-mediated DNA editing leads to the accumulation of somatic mutations in tumors and HPV genome. Deregulation of APOBEC3 family genes cause genomic instability and result in drug resistance, and immune-evasion in tumors.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India; Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India.
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Petljak M, Maciejowski J. Molecular origins of APOBEC-associated mutations in cancer. DNA Repair (Amst) 2020; 94:102905. [PMID: 32818816 PMCID: PMC7494591 DOI: 10.1016/j.dnarep.2020.102905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 01/03/2023]
Abstract
The APOBEC family of cytidine deaminases has been proposed to represent a major enzymatic source of mutations in cancer. Here, we summarize available evidence that links APOBEC deaminases to cancer mutagenesis. We also highlight newly identified human cell models of APOBEC mutagenesis, including cancer cell lines with suspected endogenous APOBEC activity and a cell system of telomere crisis-associated mutations. Finally, we draw on recent data to propose potential causes of APOBEC misregulation in cancer, including the instigating factors, the relevant mutator(s), and the mechanisms underlying generation of the genome-dispersed and clustered APOBEC-induced mutations.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 , USA.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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37
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Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA, McCann JL, McDougle RM, Carpenter MA, Martens JW, Span PN, Kappei D, Harris RS. Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. eLife 2020; 9:61287. [PMID: 32985974 PMCID: PMC7553775 DOI: 10.7554/elife.61287] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate the binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm the involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.
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Affiliation(s)
- Pieter A Roelofs
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Chai Yeen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States
| | - Teneale A Stewart
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Mater Research Institute, The University of Queensland, Faculty of Medicine, Brisbane, Australia
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - Rebecca M McDougle
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Hennepin Healthcare, Minneapolis, United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
| | - John Wm Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
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38
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Iida Y, Okamoto A, Hollis RL, Gourley C, Herrington CS. Clear cell carcinoma of the ovary: a clinical and molecular perspective. Int J Gynecol Cancer 2020; 31:605-616. [PMID: 32948640 DOI: 10.1136/ijgc-2020-001656] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell carcinoma of the ovary has distinct biology and clinical behavior. There are significant geographical and racial differences in the incidence of clear cell carcinoma compared with other epithelial ovarian tumors. Patients with clear cell carcinoma are younger, tend to present at an early stage, and their tumors are commonly associated with endometriosis, which is widely accepted as a direct precursor of clear cell carcinoma and has been identified pathologically in approximately 50% of clear cell carcinoma cases. The most frequent and important specific gene alterations in clear cell carcinoma are mutations of AT-rich interaction domain 1A (ARID1A) (~50% of cases) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) (~50% cases). More broadly, subgroups of clear cell carcinoma have been identified based on C-APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) and C-AGE (age-related) mutational signatures. Gene expression profiling shows upregulation of hepatocyte nuclear factor 1-beta (HNF1β) and oxidative stress-related genes, and has identified epithelial-like and mesenchymal-like tumor subgroups. Although the benefit of platinum-based chemotherapy is not clearly defined it remains the mainstay of first-line therapy. Patients with early-stage disease have a favorable clinical outcome but the prognosis of patients with advanced-stage or recurrent disease is poor. Alternative treatment strategies are required to improve patient outcome and the development of targeted therapies based on molecular characteristics is a promising approach. Improved specificity of the histological definition of this tumor type is helping these efforts but, due to the rarity of clear cell carcinoma, international collaboration will be essential to design appropriately powered, large-scale clinical trials.
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Affiliation(s)
- Yasushi Iida
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Robert L Hollis
- University of Edinburgh Cancer Research UK Centre, Edinburgh, UK
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, Edinburgh, UK
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39
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Hix MA, Wong L, Flath B, Chelico L, Cisneros GA. Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer. NAR Cancer 2020; 2:zcaa023. [PMID: 32984821 PMCID: PMC7503452 DOI: 10.1093/narcan/zcaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022] Open
Abstract
A number of APOBEC family DNA cytosine deaminases can induce mutations in tumor cells. APOBEC3H haplotype I is one of the deaminases that has been proposed to cause mutations in lung cancer. Here, we confirmed that APOBEC3H haplotype I can cause uracil-induced DNA damage in lung cancer cells that results in γH2AX foci. Interestingly, the database of cancer biomarkers in DNA repair genes (DNArCdb) identified a single-nucleotide polymorphism (rs139298) of APOBEC3H haplotype I that is involved in lung cancer. While we thought this may increase the activity of APOBEC3H haplotype I, instead we found through computational modeling and cell-based experiments that this single-nucleotide polymorphism causes the destabilization of APOBEC3H Haplotype I. Computational analysis suggests that the resulting K121E change affects the structure of APOBEC3H leading to active site disruption and destabilization of the RNA-mediated dimer interface. A K117E mutation in a K121E background stabilized the APOBEC3H haplotype I, thus enabling biochemical study. Subsequent analysis showed that K121E affected catalytic activity, single-stranded DNA binding and oligomerization on single-stranded DNA. The destabilization of a DNA mutator associated with lung cancer supports the model that too much APOBEC3-induced mutation could result in immune recognition or death of tumor cells.
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Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Lai Wong
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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40
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Alexandrova E, Pecoraro G, Sellitto A, Melone V, Ferravante C, Rocco T, Guacci A, Giurato G, Nassa G, Rizzo F, Weisz A, Tarallo R. An Overview of Candidate Therapeutic Target Genes in Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12061470. [PMID: 32512900 PMCID: PMC7352306 DOI: 10.3390/cancers12061470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Ovarian cancer (OC) shows the highest mortality rate among gynecological malignancies and, because of the absence of specific symptoms, it is frequently diagnosed at an advanced stage, mainly due to the lack of specific and early biomarkers, such as those based on cancer molecular signature identification. Indeed, although significant progress has been made toward improving the clinical outcome of other cancers, rates of mortality for OC are essentially unchanged since 1980, suggesting the need of new approaches to identify and characterize the molecular mechanisms underlying pathogenesis and progression of these malignancies. In addition, due to the low response rate and the high frequency of resistance to current treatments, emerging therapeutic strategies against OC focus on targeting single factors and pathways specifically involved in tumor growth and metastasis. To date, loss-of-function screenings are extensively applied to identify key drug targets in cancer, seeking for more effective, disease-tailored treatments to overcome lack of response or resistance to current therapies. We review here the information relative to essential genes and functional pathways recently discovered in OC, often strictly interconnected with each other and representing promising biomarkers and molecular targets to treat these malignancies.
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Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Viola Melone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Anna Guacci
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
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