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Fukushima R, Suzuki T, Kobayakawa A, Kamiya H. Action-at-a-distance mutations induced by 8-oxo-7,8-dihydroguanine are dependent on APOBEC3. Mutagenesis 2024; 39:24-31. [PMID: 37471265 DOI: 10.1093/mutage/gead023] [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: 04/04/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
DNA oxidation is a serious threat to genome integrity and is involved in mutations and cancer initiation. The G base is most frequently damaged, and 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the predominant damaged bases. In human cells, GO causes a G:C→T:A transversion mutation at the modified site, and also induces untargeted substitution mutations at the G bases of 5'-GpA-3' dinucleotides (action-at-a-distance mutations). The 5'-GpA-3' sequences are complementary to the 5'-TpC-3' sequences, the preferred substrates for apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) cytosine deaminases, and thus their contribution to mutagenesis has been considered. In this study, APOBEC3B, the most abundant APOBEC3 protein in human U2OS cells, was knocked down in human U2OS cells, and a GO-shuttle plasmid was then transfected into the cells. The action-at-a-distance mutations were reduced to ~25% by the knockdown, indicating that GO-induced action-at-a-distance mutations are highly dependent on APOBEC3B in this cell line.
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Affiliation(s)
- Ruriko Fukushima
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Akari Kobayakawa
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
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2
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Carpenter MA, Temiz NA, Ibrahim MA, Jarvis MC, Brown MR, Argyris PP, Brown WL, Starrett GJ, Yee D, Harris RS. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer. PLoS Genet 2023; 19:e1011043. [PMID: 38033156 PMCID: PMC10715669 DOI: 10.1371/journal.pgen.1011043] [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: 07/31/2023] [Revised: 12/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.
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Affiliation(s)
- Michael A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mahmoud A. Ibrahim
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Matthew C. Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret R. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Gabriel J. Starrett
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
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3
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Bong IPN, Esa E. Molecular genetic aberrations in the pathogenesis of multiple myeloma. ASIAN BIOMED 2023; 17:152-162. [PMID: 37860676 PMCID: PMC10584387 DOI: 10.2478/abm-2023-0056] [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] [Indexed: 10/21/2023]
Abstract
Multiple myeloma (MM) is the second most common form of blood cancer characterized by clonal expansion of malignant plasma cells within the bone marrow. MM is a complex, progressive, and highly heterogeneous malignancy, which occurs via a multistep transformation process involving primary and secondary oncogenic events. Recent advances in molecular techniques have further expanded our understanding of the mutational landscape, clonal composition, and dynamic evolution patterns of MM. The first part of this review describes the key oncogenic events involved in the initiation and progression of MM, together with their prognostic impact. The latter part highlights the most prominent findings concerning genomic aberrations promoted by gene expression profiling (GEP) and next-generation sequencing (NGS) in MM. This review provides a concise understanding of the molecular pathogenesis of the MM genome and the importance of adopting emerging molecular technology in future clinical management of MM.
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Affiliation(s)
- Ivyna Pau Ni Bong
- Hematology Unit, Cancer Research Center, Institute for Medical Research, National Institute of Health, Ministry of Health, Malaysia
| | - Ezalia Esa
- Hematology Unit, Cancer Research Center, Institute for Medical Research, National Institute of Health, Ministry of Health, Malaysia
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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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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6
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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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Anoshkin K, Zosen D, Karandasheva K, Untesco M, Volodin I, Alekseeva E, Parfenenkova A, Snegova E, Kim A, Dorofeeva M, Kutsev S, Strelnikov V. Pediatric chordoma associated with tuberous sclerosis complex: A rare case report with a thorough analysis of potential therapeutic molecular targets. Heliyon 2022; 8:e10291. [PMID: 36051260 PMCID: PMC9424951 DOI: 10.1016/j.heliyon.2022.e10291] [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] [Received: 05/20/2022] [Revised: 07/27/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Chordoma associated with tuberous sclerosis complex (TSC) is an extremely rare tumor that was described only in 13 cases since 1975. Сhordoma itself is a malignant slow-growing bone tumor thought to arise from vestigial or ectopic notochordal tissue. Chordoma associated with TSC differs from chordoma in the general pediatric population in the median age, where the diagnosis of TSC-associated chordoma is 6.2 months, whereas for chordoma in the general pediatric population it is set to 12 years. The majority of TSC-associated chordomas are localized in skull-based and sacrum regions, and rare in the spine. Chordomas are genetically heterogeneous tumors characterized by chromosomal instability (CIN), and alterations involving PI3K-AKT signaling pathway genes and chromatin remodeling genes. Here we present the 14th case of chordoma associated with TSC in a 1-year-old pediatric patient. Alongside biallelic inactivation of the TSC1 gene, molecular genetic analysis revealed CIN and involvement of epigenetic regulation genes. In addition, we found the engagement of CBX7 and apolipoprotein B editing complex (APOBEC3) genes that were not yet seen in chordomas before. Amplification of CBX7 may epigenetically silence the CDKN2A gene, whereas amplification of APOBEC3 genes can explain the frequent occurrence of CIN in chordomas. We also found that KRAS gene is located in the region with gain status, which may suggest the ineffectiveness of potential EGFR monotherapy. Thus, molecular genetic analysis carried out in this study broadens the horizons of possible approaches for targeted therapies with potential applications for personalized medicine.
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Affiliation(s)
- Kirill Anoshkin
- Research Centre for Medical Genetics, Moskvorechye Str. 1, 115522 Moscow, Russia
| | - Denis Zosen
- Faculty of Mathematics and Natural Sciences, University of Oslo, PO Box 1068, Blindern, 0316 Oslo, Norway
| | | | - Maxim Untesco
- UNIM LLC, Podsosensky Lane 23, 105062 Moscow, Russia.,Pathology Department, Telemark HF Hospital, Ulefossveien 55, PO Box 2900 Kjørbekk, 3710 Skien, Norway
| | - Ilya Volodin
- Research Centre for Medical Genetics, Moskvorechye Str. 1, 115522 Moscow, Russia
| | - Ekaterina Alekseeva
- Research Centre for Medical Genetics, Moskvorechye Str. 1, 115522 Moscow, Russia.,I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Str. 8-2, 119991 Moscow, Russia
| | - Anna Parfenenkova
- Saint Petersburg State University, University emb. 7-9, 199034 Saint Petersburg, Russia
| | - Eugenia Snegova
- Saint Petersburg State Budget Healthcare Facility "Advisory and Diagnostic Center for Children", Oleko Dundicha Str. 36/2, 192289 Saint Petersburg, Russia
| | - Aleksandr Kim
- Almazov National Medical Research Centre, Akkuratova Str. 2, 197341 Saint Petersburg, Russia
| | - Marina Dorofeeva
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Taldomskaya Str. 2, 125412 Moscow, Russia
| | - Sergei Kutsev
- Research Centre for Medical Genetics, Moskvorechye Str. 1, 115522 Moscow, Russia
| | - Vladimir Strelnikov
- Research Centre for Medical Genetics, Moskvorechye Str. 1, 115522 Moscow, Russia
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8
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Prognostic Value of HPV E6 and APOBEC3B in Upper Urinary Tract Urothelial Carcinoma. DISEASE MARKERS 2022; 2022:2147494. [PMID: 35903294 PMCID: PMC9325345 DOI: 10.1155/2022/2147494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022]
Abstract
Background APOBEC mutation signature is common in upper urinary tract urothelial carcinoma (UTUC). When virus infection occurs, upregulated APOBEC plays an antiviral role by deoxycytidine deaminase activity. However, the carcinogenic roles of HPV E6 protein and APOBEC mutation signature in UTUC have not been investigated. Aims This study explored the relationship among HPV E6, APOBEC, and clinicopathological characteristics in patients with UTUC and impacts of their expression on the prognosis. Methods The expression of HPV E6 and APOBEC3B of 78 patients with UTUC was detected by immunohistochemistry. Correlation of HPV E6 and APOBEC3B expression levels with clinicopathological characteristics was statistically analyzed. Univariate and multivariate Cox regression analyses were used to evaluate the prognosis of HPV E6 and APOBEC3B for disease-free survival (DFS); survival analysis was performed using Kaplan-Meier methods. Results The expression of APOBEC3B was positively correlated with the expression of HPV E6 (r = 0.383, P = 0.001). HPV E6 was significantly increased in patients with stage I (χ2 = 4.938, P = 0.026) and low-grade urothelial carcinoma (χ2 = 3.939, P = 0.047), as well as in patients without LVI (χ2 = 4.064, P = 0.044). Meanwhile, APOBEC3B was highly expressed in patients with stage I (χ2 = 4.057, P = 0.044) and low-grade urothelial carcinoma (χ2 = 7.153, P = 0.007). Multivariate Cox regression analysis revealed the APOBEC3B expression was the independent prognostic factor for DFS, Kaplan-Meier survival analysis showed that low expression of APOBEC3B and HPV E6 was significantly associated with the poor prognosis of UTUC patients. Conclusion HPV E6 expression is positively associated with APOBEC3B expression, and the high expression of HPV E6 and APOBEC3B is associated with favorable prognosis of patients with UTUC.
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Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A. A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron. Commun Biol 2022; 5:669. [PMID: 35794202 PMCID: PMC9257560 DOI: 10.1038/s42003-022-03630-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies. A panel of nanobodies are presented that can detect the spike proteins of five SARS-CoV-2 variants of concern and structural analyses show that one clone targets conserved epitopes on the receptor-binding domain and contacts the N-terminal domain.
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10
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Zhang X, Wu Z, Hao Y, Yu T, Li X, Liang Y, Li J, Huang L, Xu Y, Li X, Xu X, Wang W, Xu G, Zhang X, Lv Q, Fang Y, Xu R, Qian W. Aberrantly Activated APOBEC3B Is Associated With Mutant p53-Driven Refractory/Relapsed Diffuse Large B-Cell Lymphoma. Front Immunol 2022; 13:888250. [PMID: 35592333 PMCID: PMC9112561 DOI: 10.3389/fimmu.2022.888250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Tumor protein 53 (TP53) mutation predicts an unfavorable prognosis in diffuse large B-cell lymphoma (DLBCL), but the molecular basis for this association remains unclear. In several malignancies, the cytidine deaminase apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) has been reported to be associated with the TP53 G/C-to-A/T mutation. Here, we show that the frequency of this mutation was significantly higher in relapsed/refractory (R/R) than in non-R/R DLBCL, which was positively associated with the APOBEC3B expression level. APOBEC3B overexpression induced the TP53 G/C-to-A/T mutation in vitro, resulting in a phenotype similar to that of DLBCL specimens. Additionally, APOBEC3B-induced p53 mutants promoted the growth of DLBCL cells and enhanced drug resistance. These results suggest that APOBEC3B is a critical factor in mutant p53-driven R/R DLBCL and is therefore a potential therapeutic target.
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Affiliation(s)
- Xuzhao Zhang
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Zhaoxing Wu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yuanyuan Hao
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Teng Yu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xian Li
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yun Liang
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Liansheng Huang
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Xu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiuzhen Li
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohua Xu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Weiqin Wang
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Genbo Xu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohong Zhang
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qinghua Lv
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yongming Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Rongzhen Xu
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wenbin Qian
- Department of Hematology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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11
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Farswan A, Gupta A, Jena L, Ruhela V, Kaur G, Gupta R. Characterizing the mutational landscape of MM and its precursor MGUS. Am J Cancer Res 2022; 12:1919-1933. [PMID: 35530275 PMCID: PMC9077084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023] Open
Abstract
Mutational Signatures and Tumor mutational burden (TMB) have emerged as prognostic biomarkers in cancer genomics. However, the association of TMB with overall survival (OS) is still unknown in newly diagnosed multiple myeloma (NDMM) patients. Further, the change in the mutational spectrum involving both synonymous and non-synonymous mutations as MGUS progresses to MM is unexplored. This study addresses both these aspects via extensive evaluation of the mutations in MGUS and NDMM. WES data of 1018 NDMM patients and 61 MGUS patients collected from three different global regions were analyzed in this study. Single base substitutions, mutational signatures and TMB were inferred from the variants identified in MGUS and MM patients. The cutoff value for TMB was estimated to divide patients into low TMB and high TMB (hypermutators) groups. This study finds a change in the mutational spectrum with a statistically significant increase from MGUS to MM. There was a statistically significant increase in the frequency of all the three categories of variants, non-synonymous (NS), synonymous (SYN), and others (OTH), from MGUS to MM (P<0.05). However, there was a statistically significant rise in the TMB values for TMB_NS and TMB_SYN only. We also observed that 3' and 5'UTR mutations were more frequent in MM and might be responsible for driving MGUS to MM via regulatory binding sites. NDMM patients were also examined separately along with their survival outcomes. The frequency of hypermutators was low in MM with poor OS and PFS outcome. We observed a statistically significant rise in the frequency of C>A and C>T substitutions and a statistically significant decline in T>G substitutions in the MM patients with poor outcomes. Additionally, there was a statistically significant increase in the TMB of the patients with poor outcome compared to patients with a superior outcome. A statistically significant association between the APOBEC activity and poor overall survival in MM was discovered. These findings have potential clinical relevance and can assist in designing risk-adapted therapies to inhibit the progression of MGUS to MM and prolong the overall survival in high-risk MM patients.
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Affiliation(s)
- Akanksha Farswan
- SBILab, Department of ECE, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi)New Delhi 110020, India
| | - Anubha Gupta
- SBILab, Department of ECE, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi)New Delhi 110020, India
| | - Lingaraja Jena
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
| | - Vivek Ruhela
- Department of Computational Biology, IIIT-DelhiNew Delhi 110020, India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, AIIMSNew Delhi 110029, India
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12
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ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells. Sci Rep 2022; 12:2278. [PMID: 35145187 PMCID: PMC8831623 DOI: 10.1038/s41598-022-06226-3] [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: 07/27/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022] Open
Abstract
DNA cytosine deaminase APOBEC3B (A3B) is an endogenous source of mutations in many human cancers, including multiple myeloma. A3B proteins form catalytically inactive high molecular mass (HMM) complexes in nuclei, however, the regulatory mechanisms of A3B deaminase activity in HMM complexes are still unclear. Here, we performed mass spectrometry analysis of A3B-interacting proteins from nuclear extracts of myeloma cell lines and identified 30 putative interacting proteins. These proteins are involved in RNA metabolism, including RNA binding, mRNA splicing, translation, and regulation of gene expression. Except for SAFB, these proteins interact with A3B in an RNA-dependent manner. Most of these interacting proteins are detected in A3B HMM complexes by density gradient sedimentation assays. We focused on two interacting proteins, ILF2 and SAFB. We found that overexpressed ILF2 enhanced the deaminase activity of A3B by 30%, while SAFB did not. Additionally, siRNA-mediated knockdown of ILF2 suppressed A3B deaminase activity by 30% in HEK293T cell lysates. Based on these findings, we conclude that ILF2 can interact with A3B and enhance its deaminase activity in HMM complexes.
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13
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APOBEC mediated mutagenesis drives genomic heterogeneity in endometriosis. J Hum Genet 2022; 67:323-329. [PMID: 35017684 DOI: 10.1038/s10038-021-01003-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
Endometriosis is a benign gynecologic condition, acting as a precursor of certain histological subtypes of ovarian cancers. The epithelial cells of endometriotic tissues and normal uterine endometrium accumulated somatic mutations in cancer-associated genes such as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and Kirsten rat sarcoma (KRAS) proto-oncogene. To determine the genomic characteristic of endometriotic epithelial cells and normal uterine endometrium and to identify the predominant mutational process acting on them, we studied the somatic mutation profiles obtained from whole exome sequencing of 14 endometriotic epithelium and 11 normal uterine endometrium tissues and classified them into mutational signatures. We observed that single base substitutions 2/13 (SBS), attributed to Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit (APOBEC) induced mutagenesis, were significant in endometriotic tissues, but not in the normal uterine endometrium. Additionally, the larger number and wider allele frequency distribution of APOBEC signature mutations, compared to cancer-associated driver mutations in endometriotic epithelium suggested APOBEC mutagenesis as an important source of mutational burden and heterogeneity in endometriosis. Further, the relative risk of enriched APOBEC signature mutations was higher in endometriosis patients who were carriers of APOBEC3A/3B germline deletion, a common polymorphism in East Asians which involves the complete loss of APOBEC3B coding region. Our results illustrate the significance of APOBEC induced mutagenesis in driving the genomic heterogeneity of endometriosis.
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14
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Talluri S, Samur MK, Buon L, Kumar S, Potluri LB, Shi J, Prabhala RH, Shammas MA, Munshi NC. Dysregulated APOBEC3G causes DNA damage and promotes genomic instability in multiple myeloma. Blood Cancer J 2021; 11:166. [PMID: 34625538 PMCID: PMC8501035 DOI: 10.1038/s41408-021-00554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/14/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
Multiple myeloma (MM) is a heterogeneous disease characterized by significant genomic instability. Recently, a causal role for the AID/APOBEC deaminases in inducing somatic mutations in myeloma has been reported. We have identified APOBEC/AID as a prominent mutational signature at diagnosis with further increase at relapse in MM. In this study, we identified upregulation of several members of APOBEC3 family (A3A, A3B, A3C, and A3G) with A3G, as one of the most expressed APOBECs. We investigated the role of APOBEC3G in MM and observed that A3G expression and APOBEC deaminase activity is elevated in myeloma cell lines and patient samples. Loss-of and gain-of function studies demonstrated that APOBEC3G significantly contributes to increase in DNA damage (abasic sites and DNA breaks) in MM cells. Evaluation of the impact on genome stability, using SNP arrays and whole genome sequencing, indicated that elevated APOBEC3G contributes to ongoing acquisition of both the copy number and mutational changes in MM cells over time. Elevated APOBEC3G also contributed to increased homologous recombination activity, a mechanism that can utilize increased DNA breaks to mediate genomic rearrangements in cancer cells. These data identify APOBEC3G as a novel gene impacting genomic evolution and underlying mechanisms in MM.
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Affiliation(s)
- Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | | | - Leutz Buon
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
| | - Subodh Kumar
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Lakshmi B Potluri
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Jialan Shi
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Rao H Prabhala
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
- Harvard Medical School, Boston, MA, 02215, USA
| | - Masood A Shammas
- Dana Farber Cancer Institute, Boston, MA, 02115, USA
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA
| | - Nikhil C Munshi
- Dana Farber Cancer Institute, Boston, MA, 02115, USA.
- Veterans Administration Boston Healthcare System, West Roxbury, MA, 02132, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
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15
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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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16
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Wiecek AJ, Jacobson DH, Lason W, Secrier M. Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes. Front Cell Dev Biol 2021; 9:698659. [PMID: 34307377 PMCID: PMC8299471 DOI: 10.3389/fcell.2021.698659] [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] [Received: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Tumor mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterize. Little is understood of its prevalence across cancer types and of the mutational background that may favor such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumor mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumor mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumor mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumors, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumors, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that aging-induced mutations were relatively depleted in these tumors, while patterns of smoking and defective base excision repair were linked with increased tumor mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumor mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumor mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.
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Affiliation(s)
- Anna Julia Wiecek
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Daniel Hadar Jacobson
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom.,UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Wojciech Lason
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
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17
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Taiana E, Gallo Cantafio ME, Favasuli VK, Bandini C, Viglietto G, Piva R, Neri A, Amodio N. Genomic Instability in Multiple Myeloma: A "Non-Coding RNA" Perspective. Cancers (Basel) 2021; 13:cancers13092127. [PMID: 33924959 PMCID: PMC8125142 DOI: 10.3390/cancers13092127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Genomic instability (GI) plays an important role in the pathobiology of multiple myeloma (MM) by promoting the acquisition of several tumor hallmarks. Molecular determinants of GI in MM are continuously emerging and will be herein discussed, with specific regard to non-coding RNAs. Targeting non-coding RNA molecules known to be involved in GI indeed provides novel routes to dampen such oncogenic mechanisms in MM. Abstract Multiple myeloma (MM) is a complex hematological malignancy characterized by abnormal proliferation of malignant plasma cells (PCs) within a permissive bone marrow microenvironment. The pathogenesis of MM is unequivocally linked to the acquisition of genomic instability (GI), which indicates the tendency of tumor cells to accumulate a wide repertoire of genetic alterations. Such alterations can even be detected at the premalignant stages of monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM) and, overall, contribute to the acquisition of the malignant traits underlying disease progression. The molecular basis of GI remains unclear, with replication stress and deregulation of DNA damage repair pathways representing the most documented mechanisms. The discovery that non-coding RNA molecules are deeply dysregulated in MM and can target pivotal components of GI pathways has introduced a further layer of complexity to the GI scenario in this disease. In this review, we will summarize available information on the molecular determinants of GI in MM, focusing on the role of non-coding RNAs as novel means to tackle GI for therapeutic intervention.
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Affiliation(s)
- Elisa Taiana
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
| | - Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
| | - Vanessa Katia Favasuli
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
| | - Cecilia Bandini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (C.B.); (R.P.)
- Città Della Salute e della Scienza Hospital, 10126 Torino, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
| | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (C.B.); (R.P.)
- Città Della Salute e della Scienza Hospital, 10126 Torino, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (E.T.); (V.K.F.)
- Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy
- Correspondence: (A.N.); (N.A.)
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (M.E.G.C.); (G.V.)
- Correspondence: (A.N.); (N.A.)
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18
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Zhang H, Chen Z, Wang Z, Dai Z, Hu Z, Zhang X, Hu M, Liu Z, Cheng Q. Correlation Between APOBEC3B Expression and Clinical Characterization in Lower-Grade Gliomas. Front Oncol 2021; 11:625838. [PMID: 33842328 PMCID: PMC8033027 DOI: 10.3389/fonc.2021.625838] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background As the most aggressive tumors in the central nervous system, gliomas have poor prognosis and limited therapy methods. Immunotherapy has become promising in the treatment of gliomas. Here, we explored the expression pattern of APOBEC3B, a genomic mutation inducer, in gliomas to assess its value as an immune biomarker and immunotherapeutic target. Methods We mined transcriptional data from two publicly available genomic datasets, TCGA and CGGA, to investigate the relevance between APOBEC3B and clinical characterizations including tumor classifications, patient prognosis, and immune infiltrating features in gliomas. We especially explored the correlation between APOBEC3B and tumor mutations. Samples from Xiangya cohort were used for immunohistochemistry staining. Results Our findings demonstrated that APOBEC3B expression level was relatively high in advanced gliomas and other cancer types, which indicated poorer prognosis. APOBEC3B also stratified patients’ survival in Xiangya cohort. APOBEC3B was significantly associated with infiltrating immune and stromal cell types in the tumor microenvironment. Notably, APOBEC3B was involved in tumor mutation and strongly correlated with the regulation of oncogenic genes. Conclusion Our findings identified that APOBEC3B could be a latent molecular target in gliomas.
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiyang Chen
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhengang Hu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xun Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Min Hu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
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19
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Law EK, Levin-Klein R, Jarvis MC, Kim H, Argyris PP, Carpenter MA, Starrett GJ, Temiz NA, Larson LK, Durfee C, Burns MB, Vogel RI, Stavrou S, Aguilera AN, Wagner S, Largaespada DA, Starr TK, Ross SR, Harris RS. APOBEC3A catalyzes mutation and drives carcinogenesis in vivo. J Exp Med 2021; 217:152061. [PMID: 32870257 PMCID: PMC7953736 DOI: 10.1084/jem.20200261] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/08/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members, including APOBEC3B, fail to promote liver tumor formation. Tumor DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor datasets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.
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Affiliation(s)
- Emily K Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Matthew C Jarvis
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Hyoung Kim
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Prokopios P Argyris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Division of Oral and Maxillofacial Pathology, School of Dentistry, University of Minnesota, Minneapolis, MN
| | - Michael A Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Gabriel J Starrett
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Health Informatics, University of Minnesota, Minneapolis, MN
| | - Lindsay K Larson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Cameron Durfee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Michael B Burns
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Department of Biology, Loyola University, Chicago, IL
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Spyridon Stavrou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Sandra Wagner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Susan R Ross
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
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20
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Hirabayashi S, Shirakawa K, Horisawa Y, Matsumoto T, Matsui H, Yamazaki H, Sarca AD, Kazuma Y, Nomura R, Konishi Y, Takeuchi S, Stanford E, Kawaji H, Murakawa Y, Takaori-Kondo A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochem Biophys Res Commun 2021; 546:178-184. [PMID: 33592502 DOI: 10.1016/j.bbrc.2021.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
APOBEC3B (A3B) is a cytosine deaminase that converts cytosine to uracil in single-stranded DNA. Cytosine-to-thymine and cytosine-to-guanine base substitution mutations in trinucleotide motifs (APOBEC mutational signatures) were found in various cancers including lymphoid hematological malignancies such as multiple myeloma and A3B has been shown to be an enzymatic source of mutations in those cancers. Although the importance of A3B is being increasingly recognized, it is unclear how A3B expression is regulated in cancer cells as well as normal cells. To answer these fundamental questions, we analyzed 1276 primary myeloma cells using single-cell RNA-sequencing (scRNA-seq) and found that A3B was preferentially expressed at the G2/M phase, in sharp contrast to the expression patterns of other APOBEC3 genes. Consistently, we demonstrated that A3B protein was preferentially expressed at the G2/M phase in myeloma cells by cell sorting. We also demonstrated that normal blood cells expressing A3B were also enriched in G2/M-phase cells by analyzing scRNA-seq data from 86,493 normal bone marrow mononuclear cells. Furthermore, we revealed that A3B was expressed mainly in plasma cells, CD10+ B cells and erythroid cells, but not in granulocyte-macrophage progenitors. A3B expression profiling in normal blood cells may contribute to understanding the defense mechanism of A3B against viruses, and partially explain the bias of APOBEC mutational signatures in lymphoid but not myeloid malignancies. This study identified the cells and cellular phase in which A3B is highly expressed, which may help reveal the mechanisms behind carcinogenesis and cancer heterogeneity, as well as the biological functions of A3B in normal blood cells.
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Affiliation(s)
- Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Nomura
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshinobu Konishi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Suguru Takeuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Emani Stanford
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy; Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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21
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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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22
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Fujibayashi Y, Isa R, Nishiyama D, Sakamoto-Inada N, Kawasumi N, Yamaguchi J, Kuwahara-Ota S, Matsumura-Kimoto Y, Tsukamoto T, Chinen Y, Shimura Y, Kobayashi T, Horiike S, Taniwaki M, Handa H, Kuroda J. Aberrant BUB1 Overexpression Promotes Mitotic Segregation Errors and Chromosomal Instability in Multiple Myeloma. Cancers (Basel) 2020; 12:cancers12082206. [PMID: 32781708 PMCID: PMC7464435 DOI: 10.3390/cancers12082206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 01/02/2023] Open
Abstract
Chromosome instability (CIN), the hallmarks of cancer, reflects ongoing chromosomal changes caused by chromosome segregation errors and results in whole chromosomal or segmental aneuploidy. In multiple myeloma (MM), CIN contributes to the acquisition of tumor heterogeneity, and thereby, to disease progression, drug resistance, and eventual treatment failure; however, the underlying mechanism of CIN in MM remains unclear. Faithful chromosomal segregation is tightly regulated by a series of mitotic checkpoint proteins, such as budding uninhibited by benzimidazoles 1 (BUB1). In this study, we found that BUB1 was overexpressed in patient-derived myeloma cells, and BUB1 expression was significantly higher in patients in an advanced stage compared to those in an early stage. This suggested the involvement of aberrant BUB1 overexpression in disease progression. In human myeloma-derived cell lines (HMCLs), BUB1 knockdown reduced the frequency of chromosome segregation errors in mitotic cells. In line with this, partial knockdown of BUB1 showed reduced variations in chromosome number compared to parent cells in HMCLs. Finally, BUB1 overexpression was found to promote the clonogenic potency of HMCLs. Collectively, these results suggested that enhanced BUB1 expression caused an increase in mitotic segregation errors and the resultant emergence of subclones with altered chromosome numbers and, thus, was involved in CIN in MM.
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Affiliation(s)
- Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Reiko Isa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Daichi Nishiyama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Natsumi Sakamoto-Inada
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Norichika Kawasumi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Junko Yamaguchi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Saeko Kuwahara-Ota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
- Department of Hematology, Fukuchiyama City Hospital, Kyoto 620-8505, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan;
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (Y.F.); (R.I.); (D.N.); (N.S.-I.); (N.K.); (J.Y.); (S.K.-O.); (Y.M.-K.); (T.T.); (Y.C.); (Y.S.); (T.K.); (S.H.); (M.T.)
- Correspondence: ; Tel.: +81-75-251-5740
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23
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Alagpulinsa DA, Szalat RE, Poznansky MC, Shmookler Reis RJ. Genomic Instability in Multiple Myeloma. Trends Cancer 2020; 6:858-873. [PMID: 32487486 DOI: 10.1016/j.trecan.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Genomic instability (GIN), an increased tendency to acquire genomic alterations, is a cancer hallmark. However, its frequency, underlying causes, and disease relevance vary across different cancers. Multiple myeloma (MM), a plasma cell malignancy, evolves through premalignant phases characterized by genomic abnormalities. Next-generation sequencing (NGS) methods are deconstructing the genomic landscape of MM across the continuum of its development, inextricably linking malignant transformation and disease progression with increasing acquisition of genomic alterations, and illuminating the mechanisms that generate these alterations. Although GIN drives disease evolution, it also creates vulnerabilities such as dependencies on 'superfluous' repair mechanisms and the induction of tumor-specific antigens that can be targeted. We review the mechanisms of GIN in MM, the associated vulnerabilities, and therapeutic targeting strategies.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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24
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Furukawa Y, Kikuchi J. Molecular basis of clonal evolution in multiple myeloma. Int J Hematol 2020; 111:496-511. [DOI: 10.1007/s12185-020-02829-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022]
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25
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Yamazaki H, Shirakawa K, Matsumoto T, Kazuma Y, Matsui H, Horisawa Y, Stanford E, Sarca AD, Shirakawa R, Shindo K, Takaori-Kondo A. APOBEC3B reporter myeloma cell lines identify DNA damage response pathways leading to APOBEC3B expression. PLoS One 2020; 15:e0223463. [PMID: 31914134 PMCID: PMC6948746 DOI: 10.1371/journal.pone.0223463] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminase 3B (A3B) is a DNA editing enzyme which induces genomic DNA mutations in multiple myeloma and in various other cancers. APOBEC family proteins are highly homologous so it is especially difficult to investigate the biology of specifically A3B in cancer cells. To easily and comprehensively investigate A3B function in myeloma cells, we used CRISPR/Cas9 to generate A3B reporter cells that contain 3×FLAG tag and IRES-EGFP sequences integrated at the end of the A3B gene. These reporter cells stably express 3xFLAG tagged A3B and the reporter EGFP and this expression is enhanced by known stimuli, such as PMA. Conversely, shRNA knockdown of A3B decreased EGFP fluorescence and 3xFLAG tagged A3B protein levels. We screened a series of anticancer treatments using these cell lines and identified that most conventional therapies, such as antimetabolites or radiation, exacerbated endogenous A3B expression, but recent molecular targeted therapeutics, including bortezomib, lenalidomide and elotuzumab, did not. Furthermore, chemical inhibition of ATM, ATR and DNA-PK suppressed EGFP expression upon treatment with antimetabolites. These results suggest that DNA damage triggers A3B expression through ATM, ATR and DNA-PK signaling.
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Affiliation(s)
- Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Emani Stanford
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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