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https://www.readbyqxmd.com/read/29324969/apobec-mutagenesis-in-drug-resistance-and-immune-escape-in-hiv-and-cancer-evolution
#1
S Venkatesan, R Rosenthal, N Kanu, N McGranahan, J Bartek, S A Quezada, J Hare, R S Harris, C Swanton
The APOBEC mutational signature has only recently been detected in a multitude of cancers through next-generation sequencing. In contrast, APOBEC has been a focus of virology research for over a decade. Many lessons learnt regarding APOBEC within virology are likely to be applicable to cancer. In this review, we explore the parallels between the role of APOBEC enzymes in HIV and cancer evolution. We discuss data supporting the role of APOBEC mutagenesis in creating HIV genome heterogeneity, drug resistance, and immune escape variants...
January 8, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29323274/apobec3-induces-mutations-during-repair-of-crispr-cas9-generated-dna-breaks
#2
Liqun Lei, Hongquan Chen, Wei Xue, Bei Yang, Bian Hu, Jia Wei, Lijie Wang, Yiqiang Cui, Wei Li, Jianying Wang, Lei Yan, Wanjing Shang, Jimin Gao, Jiahao Sha, Min Zhuang, Xingxu Huang, Bin Shen, Li Yang, Jia Chen
The APOBEC-AID family of cytidine deaminase prefers single-stranded nucleic acids for cytidine-to-uridine deamination. Single-stranded nucleic acids are commonly involved in the DNA repair system for breaks generated by CRISPR-Cas9. Here, we show in human cells that APOBEC3 can trigger cytidine deamination of single-stranded oligodeoxynucleotides, which ultimately results in base substitution mutations in genomic DNA through homology-directed repair (HDR) of Cas9-generated double-strand breaks. In addition, the APOBEC3-catalyzed deamination in genomic single-stranded DNA formed during the repair of Cas9 nickase-generated single-strand breaks in human cells can be further processed to yield mutations mainly involving insertions or deletions (indels)...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29209044/biological-and-prognostic-impact-of-apobec-induced-mutations-in-the-spectrum-of-plasma-cell-dyscrasias-and-multiple-myeloma-cell-lines
#3
F Maura, M Petljak, M Lionetti, I Cifola, W Liang, E Pinatel, L Alexandrov, A Fullam, I Martincorena, K J Dawson, N Angelopoulos, M K Samur, R Szalat, J Zamora, P Tarpey, H Davies, P Corradini, K Anderson, S Minvielle, A Neri, H Avet-Loiseau, J J Keats, P J Campbell, N Munshi, N Bolli
Leukemia accepted article preview online, 06 December 2017. doi:10.1038/leu.2017.345.
December 6, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29198328/the-role-of-nuclear-factor-kappa-b-signaling-in-human-cervical-cancer
#4
REVIEW
Sam Tilborghs, Jerome Corthouts, Yannick Verhoeven, David Arias, Christian Rolfo, Xuan Bich Trinh, Peter A van Dam
Background The Nuclear Factor kappaB (NF-kB) family consists of transcription factors that play a complex and essential role in the regulation of immune responses and inflammation. NF-kB has recently generated considerable interest as it has been implicated in human cancer initiation, progression and resistance to treatment. In the present comprehensive review the different aspects of NF-kB signaling in the carcinogenesis of cancer of the uterine cervix are discussed. NF-kB functions as part of a network, which determines the pattern of its effects on the expression of several other genes (such as crosstalks with reactive oxygen species, p53, STAT3 and miRNAS) and thus its function...
December 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29180607/small-cell-carcinomas-of-the-bladder-and-lung-are-characterized-by-a-convergent-but-distinct-pathogenesis
#5
Matthew T Chang, Alexander V Penson, Neil B Desai, Nicholas D Socci, Ronglai Shen, Venkatraman Seshan, Ritika Kundra, Adam A Abeshouse, Agnes Viale, Eugene K Cha, Xueli Hao, Victor Reuter, Charles M Rudin, Bernard H Bochner, Jonathan E Rosenberg, Dean F Bajorin, Nikolaus Schultz, Michael F Berger, Gopa Iyer, David B Solit, Hikmat A Al-Ahmadie, Barry S Taylor
Background Small cell carcinoma of the bladder (SCCB) is a rare and aggressive neuroendocrine tumor with a dismal prognosis and limited treatment options. As SCCB is histologically indistinguishable from small cell lung cancer, a shared pathogenesis and cell of origin has been proposed. The aim of this study is to determine whether SCCBs arise from a pre-existent urothelial carcinoma or share a molecular pathogenesis in common with small cell lung cancer. Results We performed an integrative analysis of 61 SCCB tumors to identify histology- and organ-specific similarities and differences...
November 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29166639/apobec3a-expression-in-penile-squamous-cell-carcinoma
#6
Martina Heller, Elena-Sophie Prigge, Adam Kaczorowski, Magnus von Knebel Doeberitz, Markus Hohenfellner, Stefan Duensing
BACKGROUND: APOBECs (apolipoprotein B mRNA-editing catalytic polypeptides) are cytidine deaminases that have been implicated in the host defense against viruses by blocking viral replication. They have also been shown to play a role in genome hypermutation in several human cancers. An APOBEC3 hypermutation signature has been discovered in cervical cancer, which is intimately associated with infection by high-risk human papillomaviruses (HPVs). At the same time, HPV genomes themselves are subject to DNA editing by APOBECs...
November 23, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29153851/apobec-enzymes-as-targets-for-virus-and-cancer-therapy
#7
REVIEW
Margaret E Olson, Reuben S Harris, Daniel A Harki
Human DNA cytosine-to-uracil deaminases catalyze mutations in both pathogen and cellular genomes. APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H restrict human immunodeficiency virus 1 (HIV-1) infection in cells deficient in the viral infectivity factor (Vif), and have the potential to catalyze sublethal levels of mutation in viral genomes in Vif-proficient cells. At least two APOBEC3 enzymes, and in particular APOBEC3B, are sources of somatic mutagenesis in cancer cells that drive tumor evolution and may manifest clinically as recurrence, metastasis, and/or therapy resistance...
November 14, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/29140415/apobec3a-b-deletion-polymorphism-and-cancer-risk
#8
Liv B Gansmo, Paal Romundstad, Kristian Hveem, Lars Vatten, Serena Nik-Zainal, Per Eystein Lønning, Stian Knappskog
Activity of the APOBEC enzymes has been linked to specific mutational processes in human cancer genomes. A germline APOBEC3A/B deletion polymorphism is associated with APOBEC-dependent mutational signatures, and the deletion allele has been reported to confer an elevated risk of some cancers in Asian populations, while the results in European populations, so far, have been conflicting. We genotyped the APOBEC3A/B deletion polymorphism in a large population based sample consisting of 11,106 Caucasian (Norwegian) individuals, including 7,279 incident cancer cases (1,769 breast- , 1,360 lung-, 1,585 colon-, and 2,565 prostate cancer) and a control group of 3,827 matched individuals without cancer (1,918 females and 1,909 males) from the same population...
November 13, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29107330/allele-specific-hla-loss-and-immune-escape-in-lung-cancer-evolution
#9
Nicholas McGranahan, Rachel Rosenthal, Crispin T Hiley, Andrew J Rowan, Thomas B K Watkins, Gareth A Wilson, Nicolai J Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero, Charles Swanton
Immune evasion is a hallmark of cancer. Losing the ability to present neoantigens through human leukocyte antigen (HLA) loss may facilitate immune evasion. However, the polymorphic nature of the locus has precluded accurate HLA copy-number analysis. Here, we present loss of heterozygosity in human leukocyte antigen (LOHHLA), a computational tool to determine HLA allele-specific copy number from sequencing data. Using LOHHLA, we find that HLA LOH occurs in 40% of non-small-cell lung cancers (NSCLCs) and is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity...
November 30, 2017: Cell
https://www.readbyqxmd.com/read/29103756/multi-modality-analysis-supports-apobec-as-a-major-source-of-mutations-in-head-and-neck-squamous-cell-carcinoma
#10
Daniel L Faden, Sean Thomas, Paul G Cantalupo, Nishant Agrawal, Jeffrey Myers, Joseph DeRisi
OBJECTIVES: The mutagenic processes underlying head and neck squamous cell carcinoma (HNSCC) are poorly understood. Pan-cancer mutational signature analyses have identified a signature for APOBEC, a cytosine deaminase, in a subset of cancers, including HNSCC. The role of APOBEC activity in HNSCC remains poorly understood. Therefore, we sought to determine the role of APOBEC in HNSCC pathogenesis. MATERIAL AND METHODS: Utilizing bioinformatic approaches we explored the role of APOBEC mediated mutations in tumor exomes, transcriptomes and germline exomes from 511HNSCC patients in the TCGA...
November 2017: Oral Oncology
https://www.readbyqxmd.com/read/29076965/mutational-and-epigenetic-signatures-in-cancer-tissue-linked-to-environmental-exposures-and-lifestyle
#11
Vittorio Perduca, Hanane Omichessan, Laura Baglietto, Gianluca Severi
PURPOSE OF REVIEW: In this article, we describe how recent advances in the study of mutational and epigenetic signatures in tumours provide new opportunities to understand the role of the environment and lifestyle in cancer development. RECENT FINDINGS: Cancer-related mutational events have been investigated for decades but only recently the wide availability of genomic sequences and epigenomic data from thousands of cancer genomes has made it possible to identify numerous distinct mutational and epigenetic signatures through the application of advanced mathematical models...
October 25, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29044863/identification-of-somatic-genetic-alterations-in-ovarian-clear-cell-carcinoma-with-next-generation-sequencing
#12
Yusuke Shibuya, Hideki Tokunaga, Sakae Saito, Kazurou Shimokawa, Fumiki Katsuoka, Li Bin, Kaname Kojima, Masao Nagasaki, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda
Ovarian clear cell carcinoma (OCCC) is the most refractory subtype of ovarian cancer and more prevalent in Japanese than Caucasians (25% and 5% of all ovarian cancer, respectively). The aim of this study is to discover the genomic alterations that may cause OCCC and effective molecular targets for chemotherapy. Paired genomic DNAs of 48 OCCC tissues and corresponding non-cancerous tissues were extracted from formalin-fixed, paraffin embedded specimens collected between 2007 and 2015 at Tohoku University Hospital...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28988769/comprehensive-molecular-characterization-of-muscle-invasive-bladder-cancer
#13
A Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D Cherniack, Toshinori Hinoue, Peter W Laird, Katherine A Hoadley, Rehan Akbani, Mauro A A Castro, Ewan A Gibb, Rupa S Kanchi, Dmitry A Gordenin, Sachet A Shukla, Francisco Sanchez-Vega, Donna E Hansel, Bogdan A Czerniak, Victor E Reuter, Xiaoping Su, Benilton de Sa Carvalho, Vinicius S Chagas, Karen L Mungall, Sara Sadeghi, Chandra Sekhar Pedamallu, Yiling Lu, Leszek J Klimczak, Jiexin Zhang, Caleb Choo, Akinyemi I Ojesina, Susan Bullman, Kristen M Leraas, Tara M Lichtenberg, Catherine J Wu, Nicholaus Schultz, Gad Getz, Matthew Meyerson, Gordon B Mills, David J McConkey, John N Weinstein, David J Kwiatkowski, Seth P Lerner
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology...
October 19, 2017: Cell
https://www.readbyqxmd.com/read/28983111/ifn-%C3%AE-mediated-base-excision-repair-pathway-correlates-with-antiviral-response-against-hepatitis-b-virus-infection
#14
Yong Li, Yuchen Xia, Meifang Han, Guang Chen, Dake Zhang, Wolfgang E Thasler, Ulrike Protzer, Qin Ning
Previous studies identified APOBEC deaminases as enzymes targeting hepatitis B virus (HBV) DNA in the nucleus thus affecting its persistence. Interferon (IFN)-α treated chimpanzees and hepatitis C patients showed elevated APOBEC expression. We thus hypothesized that the responses to IFN-α treatment of chronic hepatitis B (CHB) patients is influenced by IFN-induced base excision repair (BER). CHB-treatment naïve patients, patients treated with PEGylated IFN-α, and patients with sequential treatment of Entecavior and PEGylated IFN-α were recruited...
October 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28981865/enzyme-cycling-contributes-to-efficient-induction-of-genome-mutagenesis-by-the-cytidine-deaminase-apobec3b
#15
Madison B Adolph, Robin P Love, Yuqing Feng, Linda Chelico
The single-stranded DNA cytidine deaminases APOBEC3B, APOBEC3H haplotype I, and APOBEC3A can contribute to cancer through deamination of cytosine to form promutagenic uracil in genomic DNA. The enzymes must access single-stranded DNA during the dynamic processes of DNA replication or transcription, but the enzymatic mechanisms enabling this activity are not known. To study this, we developed a method to purify full length APOBEC3B and characterized it in comparison to APOBEC3A and APOBEC3H on substrates relevant to cancer mutagenesis...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977491/p53-controls-expression-of-the-dna-deaminase-apobec3b-to-limit-its-potential-mutagenic-activity-in-cancer-cells
#16
Manikandan Periyasamy, Anup K Singh, Carolina Gemma, Christian Kranjec, Raed Farzan, Damien A Leach, Naveenan Navaratnam, Hajnalka L Pálinkás, Beata G Vértessy, Tim R Fenton, John Doorbar, Frances Fuller-Pace, David W Meek, R Charles Coombes, Laki Buluwela, Simak Ali
Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression...
August 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28964683/apobec-from-mutator-to-editor
#17
REVIEW
Bei Yang, Xiaosa Li, Liqun Lei, Jia Chen
APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) are a family of cytidine deaminases that prefer single-stranded nucleic acids as substrates. Besides their physiological functions, APOBEC family members have been found to cause hypermutations of cancer genomes, which could be correlated with cancer development and poor prognosis. Recently, APOBEC family members have been combined with the versatile CRISPR/Cas9 system to perform targeted base editing or induce hypermutagenesis. This combination improved the CRISPR/Cas9-mediated gene editing at single-base precision, greatly enhancing its usefulness...
August 7, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28956761/apobec3a-is-upregulated-by-human-cytomegalovirus-hcmv-in-the-maternal-fetal-interface-acting-as-an-innate-anti-hcmv-effector
#18
Yiska Weisblum, Esther Oiknine-Djian, Zichria Zakay-Rones, Olesya Vorontsov, Ronit Haimov-Kochman, Yuval Nevo, David Stockheim, Simcha Yagel, Amos Panet, Dana G Wolf
Human cytomegalovirus (HCMV) is the leading cause of congenital infection and is associated with a wide range of neurodevelopmental disabilities and intrauterine growth restriction. Yet our current understanding of the mechanisms modulating transplacental HCMV transmission is poor. The placenta, given its critical function in protecting the fetus, has evolved effective yet largely uncharacterized innate immune barriers against invading pathogens. Here we show that the intrinsic cellular restriction factor apolipoprotein B editing catalytic subunit-like 3A (APOBEC3A [A3A]) is profoundly upregulated following ex vivo HCMV infection in human decidual tissues-constituting the maternal aspect of the placenta...
December 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28904067/whole-genome-sequencing-reveals-breast-cancers-with-mismatch-repair-deficiency
#19
Helen Davies, Sandro Morganella, Colin A Purdie, Se Jin Jang, Elin Borgen, Hege Russnes, Dominik Glodzik, Xueqing Zou, Alain Viari, Andrea L Richardson, Anne-Lise Børresen-Dale, Alastair Thompson, Jorunn E Eyfjord, Gu Kong, Michael R Stratton, Serena Nik-Zainal
Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients...
September 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28878238/apobec3a-is-an-oral-cancer-prognostic-biomarker-in-taiwanese-carriers-of-an-apobec-deletion-polymorphism
#20
Ting-Wen Chen, Chi-Ching Lee, Hsuan Liu, Chi-Sheng Wu, Curtis R Pickering, Po-Jung Huang, Jing Wang, Ian Yi-Feng Chang, Yuan-Ming Yeh, Chih-De Chen, Hsin-Pai Li, Ji-Dung Luo, Bertrand Chin-Ming Tan, Timothy En Haw Chan, Chuen Hsueh, Lichieh Julie Chu, Yi-Ting Chen, Bing Zhang, Chia-Yu Yang, Chih-Ching Wu, Chia-Wei Hsu, Lai-Chu See, Petrus Tang, Jau-Song Yu, Wei-Chao Liao, Wei-Fan Chiang, Henry Rodriguez, Jeffrey N Myers, Kai-Ping Chang, Yu-Sun Chang
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0...
September 6, 2017: Nature Communications
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