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Zhou Y, Li S, Hu Y, Xu X, Cui J, Li S, Li Z, Ji J, Xing R. Multi-regional sequencing reveals the genetic and immune heterogeneity of non-cancerous tissues in gastric cancer. J Pathol 2024; 263:454-465. [PMID: 38845115 DOI: 10.1002/path.6297] [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: 09/10/2023] [Revised: 03/12/2024] [Accepted: 04/18/2024] [Indexed: 07/09/2024]
Abstract
Gastric cancer (GC) is one of the most heterogeneous tumors. However, research on normal tissue adjacent to the tumor (NAT) is very limited. We performed multi-regional omics sequencing on 150 samples to assess the genetic basis and immune microenvironment in NAT and matched primary tumor or lymph node metastases. NATs demonstrated different mutated genes compared with GC, and NAT genomes underwent independent evolution with low variant allele frequency. Mutation profiles were predominated by aging and smoking-associated signatures in NAT instead of signatures associated with genetic instability. Although the immune microenvironment within NATs shows substantial intra-patient heterogeneity, the proportion of shared TCR clones among NATs is five times higher than that of tumor regions. These findings support the notion that subclonal expansion is not pronounced in NATs. We also demonstrated remarkable intra-patient heterogeneity of GCs and revealed heterogeneity of focal amplification of CD274 (encoding PD-L1) that leads to differential expression. Finally, we identified that monoclonal seeding is predominant in GC, which is followed by metastasis-to-metastasis dissemination in individual lymph nodes. These results provide novel insights into GC carcinogenesis. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Yong Zhou
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Tumor Biology, Peking University Cancer Hospital & Institute, Beijing, PR China
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, PR China
| | - Shen Li
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Yingqi Hu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Tumor Biology, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Xiao Xu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Tumor Biology, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Jiantao Cui
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Tumor Biology, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Shuaicheng Li
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, PR China
| | - Ziyu Li
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Jiafu Ji
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, PR China
| | - Rui Xing
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Tumor Biology, Peking University Cancer Hospital & Institute, Beijing, PR China
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Dong W, Liu M, Liu B, Xiao Y, Liu X, Yang M, Yuan X, Zhang Y, Li G, Meng K. Isolation of Bacillus licheniformis and its protective effect on liver oxidative stress and apoptosis induced by aflatoxin B1. Poult Sci 2024; 103:104079. [PMID: 39098297 DOI: 10.1016/j.psj.2024.104079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/18/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024] Open
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. The use of probiotics is an effective approach to reduce aflatoxins content in foods. To find efficient bacterial species that can eliminate or detoxify AFB1, a bacterial strain S51 capable of degrading AFB1 was isolated from chicken intestine and soil samples by using a culture medium containing coumarin as the sole carbon source. Based on the results of 16S rRNA gene sequence analysis, this isolate (strain S51) was identified as Bacillus licheniformis strain QT338. Further characterization of strain S51 showed that it could degrade AFB1 by 61.3% after incubation at 30°C for 72 h. Additional studies demonstrated that S51 promoted good growth performance of the treated chickens, showed no hemolytic activity, carried few drug resistance genes, and exhibited a certain level of tolerance to acid and bile salts. Furthermore, to verify whether strain S51 exerts a protective effect on AFB1-induced liver injury in chickens and to elucidate the underlying mechanism, a chicken toxicity model was induced with AFB1 (100 μg/kg BW) and treated with S51(1×109CFU/mL) for 12 d. The results showed that S51 decreased the level of alanine transaminase, aspartate transaminase, and total bilirubin (P < 0.05); increased glutathione activity and total antioxidant capacityin the liver induced by AFB1, and decreased malondialdehyde production (P < 0.05). S51 also up-regulated the mRNA expression level of the antioxidant proteins HO-1 and Nrf2 and down-regulated the expression of the oxidation-related factor Keap1 in the Nrf2/Keap1 signaling pathway (P <0.05). S51 inhibited hepatocyte apoptosis induced by AFB1 and decreased the mRNA expression levels of the apoptosis-related genes Bax, caspase-3, caspase-9, and Cyt-C (P < 0.05). These results indicate that S51 regulates apoptosis and alleviates AFB1-induced oxidative stress in chicken liver by controlling the Nrf2/Keap1 signaling pathway.
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Affiliation(s)
- Wenwen Dong
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China
| | - Mingchao Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, PR China
| | - Bei Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China; College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, PR China
| | - Yaqing Xiao
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China; College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, PR China
| | - Xia Liu
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China; Research Center for Animal Disease Control Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Menghao Yang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China; Research Center for Animal Disease Control Engineering, Shandong Agricultural University, Taian, 271018, Shandong, PR China
| | - Xiaoyuan Yuan
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China
| | - Yuxia Zhang
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China
| | - Guiming Li
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China
| | - Kai Meng
- Poultry Breeding Engineering Technology Center of Shandong Province, Poultry Institute, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan Key Laboratory for Agricultural Experimental Animal and Comparative Medicine, Jinan 250023, PR China.
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3
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Zuckerman JT, Jackson AS, Minko IG, Kant M, Jaruga P, Stone MP, Dizdaroglu M, McCullough AK, Lloyd RS. Functional characterization of single nucleotide polymorphic variants of DNA repair enzyme NEIL1 in South Asian populations. DNA Repair (Amst) 2024; 139:103695. [PMID: 38795603 PMCID: PMC11218669 DOI: 10.1016/j.dnarep.2024.103695] [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: 02/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/28/2024]
Abstract
The base excision repair (BER) pathway is a precise and versatile mechanism of DNA repair that is initiated by DNA glycosylases. Endonuclease VIII-like 1 (NEIL1) is a bifunctional glycosylase/abasic site (AP) lyase that excises a damaged base and subsequently cleaves the phosphodiester backbone. NEIL1 is able to recognize and hydrolyze a broad range of oxidatively-induced base lesions and substituted ring-fragmented guanines, including aflatoxin-induced 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua). Due to NEIL1's protective role against these and other pro-mutagenic lesions, it was hypothesized that naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 could increase human risk for aflatoxin-induced hepatocellular carcinoma (HCC). Given that populations in South Asia experience high levels of dietary aflatoxin exposures and hepatitis B viral infections that induce oxidative stress, investigations on SNP variants of NEIL1 that occur in this region may have clinical implications. In this study, the most common South Asian variants of NEIL1 were expressed, purified, and functionally characterized. All tested variants exhibited activities and substrate specificities similar to wild type (wt)-NEIL1 on high-molecular weight DNA containing an array of oxidatively-induced base lesions. On short oligodeoxynucleotides (17-mers) containing either a site-specific apurinic/apyrimidinic (AP) site, thymine glycol (ThyGly), or AFB1-FapyGua, P206L-NEIL1 was catalytically comparable to wt-NEIL1, while the activities of NEIL1 variants Q67K and T278I on these substrates were ≈2-fold reduced. Variant T103A had a greatly diminished ability to bind to 17-mer DNAs, limiting the subsequent glycosylase and lyase reactions. Consistent with this observation, the rate of excision by T103A on 17-mer oligodeoxynucleotides containing ThyGly or AFB1-FapyGua could not be measured. However, the ability of T103A to excise ThyGly was improved on longer oligodeoxynucleotides (51-mers), with ≈7-fold reduced activity compared to wt-NEIL1. Our studies suggest that NEIL1 variant T103A may present a pathogenic phenotype that is limited in damage recognition, potentially increasing human risk for HCC.
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Affiliation(s)
- Jamie T Zuckerman
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Asia Sage Jackson
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Math & Sciences, Corban University, Salem, OR 97317, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Melis Kant
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, United States
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States.
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4
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Senkin S, Moody S, Díaz-Gay M, Abedi-Ardekani B, Cattiaux T, Ferreiro-Iglesias A, Wang J, Fitzgerald S, Kazachkova M, Vangara R, Le AP, Bergstrom EN, Khandekar A, Otlu B, Cheema S, Latimer C, Thomas E, Atkins JR, Smith-Byrne K, Cortez Cardoso Penha R, Carreira C, Chopard P, Gaborieau V, Keski-Rahkonen P, Jones D, Teague JW, Ferlicot S, Asgari M, Sangkhathat S, Attawettayanon W, Świątkowska B, Jarmalaite S, Sabaliauskaite R, Shibata T, Fukagawa A, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Bartlett JMS, Albert M, Phouthavongsy L, Ashton-Prolla P, Botton MR, Silva Neto B, Bezerra SM, Curado MP, Zequi SDC, Reis RM, Faria EF, de Menezes NS, Ferrari RS, Banks RE, Vasudev NS, Zaridze D, Mukeriya A, Shangina O, Matveev V, Foretova L, Navratilova M, Holcatova I, Hornakova A, Janout V, Purdue MP, Rothman N, Chanock SJ, Ueland PM, Johansson M, McKay J, Scelo G, Chanudet E, Humphreys L, de Carvalho AC, Perdomo S, Alexandrov LB, Stratton MR, Brennan P. Geographic variation of mutagenic exposures in kidney cancer genomes. Nature 2024; 629:910-918. [PMID: 38693263 PMCID: PMC11111402 DOI: 10.1038/s41586-024-07368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.
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Affiliation(s)
- Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thomas Cattiaux
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aida Ferreiro-Iglesias
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Anh Phuong Le
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Saamin Cheema
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Emily Thomas
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Joshua Ronald Atkins
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Priscilia Chopard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Ferlicot
- Service d'Anatomie Pathologique, Assistance Publique-Hôpitaux de Paris, Univeristé Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Mojgan Asgari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Surasak Sangkhathat
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Worapat Attawettayanon
- Division of Urology, Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Sonata Jarmalaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
- Department of Botany and Genetics, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Rasa Sabaliauskaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Dana Mates
- Occupational Health and Toxicology Department, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, University Hospital Dr D. Misovic Clinical Center, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - John M S Bartlett
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Monique Albert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patricia Ashton-Prolla
- Experimental Research Center, Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariana R Botton
- Transplant Immunology and Personalized Medicine Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Brasil Silva Neto
- Service of Urology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Medicine: Surgical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Paula Curado
- Department of Epidemiology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stênio de Cássio Zequi
- Department of Urology, A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, A.C. Camargo Cancer Center, São Paulo, Brazil
- Latin American Renal Cancer Group (LARCG), São Paulo, Brazil
- Department of Surgery, Division of Urology, Sao Paulo Federal University (UNIFESP), São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Minho University, Braga, Portugal
| | - Eliney Ferreira Faria
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
- Department of Urology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David Zaridze
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeriya
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Oxana Shangina
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Vsevolod Matveev
- Department of Urology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Estelle Chanudet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Ana Carolina de Carvalho
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
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5
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Minko IG, Kellum AH, Stone MP, Lloyd RS. The aflatoxin B 1-induced imidazole ring-opened guanine adduct: High mutagenic potential that is minimally affected by sequence context. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:9-13. [PMID: 37303259 PMCID: PMC10711146 DOI: 10.1002/em.22556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Dietary exposure to aflatoxin B1 (AFB1) is a recognized risk factor for developing hepatocellular carcinoma. The mutational signature of AFB1 is characterized by high-frequency base substitutions, predominantly G>T transversions, in a limited subset of trinucleotide sequences. The 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) has been implicated as the primary DNA lesion responsible for AFB1-induced mutations. This study evaluated the mutagenic potential of AFB1-FapyGua in four sequence contexts, including hot- and cold-spot sequences as apparent in the mutational signature. Vectors containing site-specific AFB1-FapyGua lesions were replicated in primate cells and the products of replication were isolated and sequenced. Consistent with the role of AFB1-FapyGua in AFB1-induced mutagenesis, AFB1-FapyGua was highly mutagenic in all four sequence contexts, causing G>T transversions and other base substitutions at frequencies of ~80%-90%. These data suggest that the unique mutational signature of AFB1 is not explained by sequence-dependent fidelity of replication past AFB1-FapyGua lesions.
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Affiliation(s)
- Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
| | | | | | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
- Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
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6
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Minko I, Luzadder M, Vartanian V, Rice SM, Nguyen M, Sanchez-Contreras M, Van P, Kennedy S, McCullough A, Lloyd R. Frequencies and spectra of aflatoxin B 1-induced mutations in liver genomes of NEIL1-deficient mice as revealed by duplex sequencing. NAR MOLECULAR MEDICINE 2024; 1:ugae006. [PMID: 38779538 PMCID: PMC11105970 DOI: 10.1093/narmme/ugae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Increased risk for the development of hepatocellular carcinoma (HCC) is driven by a number of etiological factors including hepatitis viral infection and dietary exposures to foods contaminated with aflatoxin-producing molds. Intracellular metabolic activation of aflatoxin B1 (AFB1) to a reactive epoxide generates highly mutagenic AFB1-Fapy-dG adducts. Previously, we demonstrated that repair of AFB1-Fapy-dG adducts can be initiated by the DNA glycosylase NEIL1 and that male Neil1-/- mice were significantly more susceptible to AFB1-induced HCC relative to wild-type mice. To investigate the mechanisms underlying this enhanced carcinogenesis, WT and Neil1-/- mice were challenged with a single, 4 mg/kg dose of AFB1 and frequencies and spectra of mutations were analyzed in liver DNAs 2.5 months post-injection using duplex sequencing. The analyses of DNAs from AFB1-challenged mice revealed highly elevated mutation frequencies in the nuclear genomes of both males and females, but not the mitochondrial genomes. In both WT and Neil1-/- mice, mutation spectra were highly similar to the AFB1-specific COSMIC signature SBS24. Relative to wild-type, the NEIL1 deficiency increased AFB1-induced mutagenesis with concomitant elevated HCCs in male Neil1-/- mice. Our data establish a critical role of NEIL1 in limiting AFB1-induced mutagenesis and ultimately carcinogenesis.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Michael M Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Vladimir L Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Sean P M Rice
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- School of Public Health, Oregon Health & Science University - Portland State University, Portland, OR, USA
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Phu Van
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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7
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Sanz-Serrano J, Callewaert E, De Boever S, Drees A, Verhoeven A, Vinken M. Chemical-induced liver cancer: an adverse outcome pathway perspective. Expert Opin Drug Saf 2024; 23:425-438. [PMID: 38430529 DOI: 10.1080/14740338.2024.2326479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/29/2024] [Indexed: 03/04/2024]
Abstract
INTRODUCTION The evaluation of the potential carcinogenicity is a key consideration in the risk assessment of chemicals. Predictive toxicology is currently switching toward non-animal approaches that rely on the mechanistic understanding of toxicity. AREAS COVERED Adverse outcome pathways (AOPs) present toxicological processes, including chemical-induced carcinogenicity, in a visual and comprehensive manner, which serve as the conceptual backbone for the development of non-animal approaches eligible for hazard identification. The current review provides an overview of the available AOPs leading to liver cancer and discusses their use in advanced testing of liver carcinogenic chemicals. Moreover, the challenges related to their use in risk assessment are outlined, including the exploitation of available data, the need for semantic ontologies, and the development of quantitative AOPs. EXPERT OPINION To exploit the potential of liver cancer AOPs in the field of risk assessment, 3 immediate prerequisites need to be fulfilled. These include developing human relevant AOPs for chemical-induced liver cancer, increasing the number of AOPs integrating quantitative toxicodynamic and toxicokinetic data, and developing a liver cancer AOP network. As AOPs and other areas in the field continue to evolve, liver cancer AOPs will progress into a reliable and robust tool serving future risk assessment and management.
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Affiliation(s)
- Julen Sanz-Serrano
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen Callewaert
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sybren De Boever
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Annika Drees
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anouk Verhoeven
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- In Vitro Toxicology and Dermato-Cosmetology Research Group, Vrije Universiteit Brussel, Brussels, Belgium
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8
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Hu Y, Yang X, Tai B, Wang G, Zhang X, Yin Y, Xing F. Bacillus amyloliquefaciens A-1 inhibiting fungal spoilage in agricultural products is improved by metabolic engineering of enhancing surfactin yield. Food Res Int 2024; 175:113752. [PMID: 38129052 DOI: 10.1016/j.foodres.2023.113752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Fungi and subsequent mycotoxins contamination in agricultural products have caused enormous losses and great harm to human and animal health. Biological control has attracted the attention of researchers due to its advantages, including mild conditions, low cost, high efficiency and low nutrient loss. In this study, a newly isolated strain Bacillus amyloliquefaciens A-1 (A-1), was screened for its ability to inhibit the growth and Aflatoxin B1 (AFB1) production of Aspergillus flavus NRRL 3357. Electron microscopy results revealed that mycelium and conidia of A. flavus were destroyed by A-1, affecting hyphae, cell walls, cell membranes and organelles. RNA-seq analysis indicated disturbance in gene expression profiles of A. flavus, including amino acid degradation and starch and sucrose metabolism pathways. Importantly, the biosynthesis of AFB1 was significantly inhibited by the down-regulation of key regulatory genes, aflR and aflS, and the simultaneous down-regulation of most structural genes. Genome analysis predicted six secondary metabolites biosynthetic gene clusters. Then, four surfactin synthesized by cluster C were identified as the main active substance of A-1 using HPLC-Q-TOF-MS. The addition of alanine, threonine, Fe2+ increased surfactin production. Notably, the overexpression of comX also improved surfactin production. The vivo test results indicated that A-1 could significantly inhibit the decay of pear by Aspergillus westerdijkiae, and the mildew of maize and peanuts. Especially, the overexpression of comX in A-1 could enhance the inhibitory activity. In conclusion, the inhibition mechanism of A-1 was revealed, and comX was found can improve the production of surfactin and subsequent activities, which provides the scientific basis for the development of biocontrol agents to reduce spoilage in agricultural products.
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Affiliation(s)
- Yafan Hu
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xu Yang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Bowen Tai
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Gang Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Xinlong Zhang
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Yixuan Yin
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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9
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Sukowati CH, El-Khobar K, Jasirwan COM, Kurniawan J, Gani RA. Stemness markers in hepatocellular carcinoma of Eastern vs. Western population: Etiology matters? Ann Hepatol 2024; 29:101153. [PMID: 37734662 DOI: 10.1016/j.aohep.2023.101153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers with a high mortality rate. HCC development is associated with its underlying etiologies, mostly caused by infection of chronic hepatitis B virus (HBV) and hepatitis C virus (HCV), alcohol, non-alcoholic fatty liver disease, and exposure to aflatoxins. These variables, together with human genetic susceptibility, contribute to HCC molecular heterogeneity, including at the cellular level. HCC initiation, tumor recurrence, and drug resistance rates have been attributed to the presence of liver cancer stem cells (CSC). This review summarizes available data regarding whether various HCC etiologies may be associated to the appearance of CSC biomarkers. It also described the genetic variations of tumoral tissues obtained from Western and Eastern populations, in particular to the oncogenic effect of HBV in the human genome.
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Affiliation(s)
- Caecilia Hc Sukowati
- Liver Cancer Unit, Fondazione Italiana Fegato ONLUS, AREA Science Park campus Basovizza, SS14 km 163.5, Trieste 34149, Italy; Eijkman Research Center for Molecular Biology, National Research and Innovation Agency of Indonesia (BRIN), B.J. Habibie Building, Jl. M.H. Thamrin No. 8, Jakarta Pusat 10340, Indonesia.
| | - Korri El-Khobar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency of Indonesia (BRIN), B.J. Habibie Building, Jl. M.H. Thamrin No. 8, Jakarta Pusat 10340, Indonesia
| | - Chyntia Olivia Maurine Jasirwan
- Hepatobiliary Division, Medical Staff Group of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jl. Pangeran Diponegoro No.71, Jakarta 10430, Indonesia
| | - Juferdy Kurniawan
- Hepatobiliary Division, Medical Staff Group of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jl. Pangeran Diponegoro No.71, Jakarta 10430, Indonesia
| | - Rino Alvani Gani
- Hepatobiliary Division, Medical Staff Group of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jl. Pangeran Diponegoro No.71, Jakarta 10430, Indonesia
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10
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Chevalier A, Guo T, Gurevich NQ, Xu J, Yajima M, Campbell JD. Characterization of highly active mutational signatures in tumors from a large Chinese population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.03.23297964. [PMID: 37961450 PMCID: PMC10635259 DOI: 10.1101/2023.11.03.23297964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The majority of mutational signatures have been characterized in tumors from Western countries and the degree to which mutational signatures are similar or different in Eastern populations has not been fully explored. We leveraged a large-scale clinical sequencing cohort of tumors from a Chinese population containing 25 tumor types and found that the highly active mutational signatures were similar to those previously characterized1,2. The aristolochic acid signature SBS22 was observed in four soft tissue sarcomas and the POLE-associated signature SBS10 was observed in a gallbladder carcinoma. In lung adenocarcinoma, the polycyclic aromatic hydrocarbon (PAH) signature SBS4 was significantly higher in males compared to females but not associated with smoking status. The UV-associated signature SBS7 was significantly lower in cutaneous melanomas from the Chinese population compared to a similar American cohort. Overall, these results add to our understanding of the mutational processes that contribute to tumors from the Chinese population.
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Affiliation(s)
- Aaron Chevalier
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Tao Guo
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Natasha Q. Gurevich
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | - Jingwen Xu
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Masanao Yajima
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts
| | - Joshua D. Campbell
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Bioinformatics Program, Boston University, Boston, Massachusetts
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11
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Smaoui S, D’Amore T, Tarapoulouzi M, Agriopoulou S, Varzakas T. Aflatoxins Contamination in Feed Commodities: From Occurrence and Toxicity to Recent Advances in Analytical Methods and Detoxification. Microorganisms 2023; 11:2614. [PMID: 37894272 PMCID: PMC10609407 DOI: 10.3390/microorganisms11102614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Synthesized by the secondary metabolic pathway in Aspergilli, aflatoxins (AFs) cause economic and health issues and are culpable for serious harmful health and economic matters affecting consumers and global farmers. Consequently, the detection and quantification of AFs in foods/feeds are paramount from food safety and security angles. Nowadays, incessant attempts to develop sensitive and rapid approaches for AFs identification and quantification have been investigated, worldwide regulations have been established, and the safety of degrading enzymes and reaction products formed in the AF degradation process has been explored. Here, occurrences in feed commodities, innovative methods advanced for AFs detection, regulations, preventive strategies, biological detoxification, removal, and degradation methods were deeply reviewed and presented. This paper showed a state-of-the-art and comprehensive review of the recent progress on AF contamination in feed matrices with the intention of inspiring interests in both academia and industry.
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Affiliation(s)
- Slim Smaoui
- Laboratory of Microbial, Enzymatic Biotechnology and Biomolecules (LBMEB), Center of Biotechnology of Sfax, University of Sfax-Tunisia, Sfax 3029, Tunisia
| | - Teresa D’Amore
- IRCCS CROB, Centro di Riferimento Oncologico della Basilicata, 85028 Rionero in Vulture, Italy;
| | - Maria Tarapoulouzi
- Department of Chemistry, Faculty of Pure and Applied Science, University of Cyprus, P.O. Box 20537, Nicosia CY-1678, Cyprus;
| | - Sofia Agriopoulou
- Department of Food Science and Technology, University of the Peloponnese, Antikalamos, 24100 Kalamata, Greece;
| | - Theodoros Varzakas
- Department of Food Science and Technology, University of the Peloponnese, Antikalamos, 24100 Kalamata, Greece;
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12
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Wu Y, Adeel MM, Sancar A, Li W. Nucleotide Excision Repair of Aflatoxin-induced DNA Damage within the 3D Human Genome Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559858. [PMID: 37808841 PMCID: PMC10557652 DOI: 10.1101/2023.09.27.559858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aflatoxin B1 (AFB1), a potent mycotoxin, is one of the two primary risk factors that cause liver cancer. In the liver, the bioactivated AFB1 intercalates into the DNA double helix to form a bulky DNA adduct which will lead to mutation if left unrepaired. We have adapted the tXR-seq method to measure the nucleotide excision repair of AFB1-induced DNA adducts. We have found that transcription-coupled repair plays a major role in the damage removal process and the released excision products have a distinctive length distribution pattern. We further analyzed the impact of 3D genome organization on the repair of AFB1-induced DNA adducts. We have revealed that chromosomes close to the nuclear center and A compartments undergo expedited repair processes. Notably, we observed an accelerated repair around both TAD boundaries and loop anchors. These findings provide insights into the complex interplay between repair, transcription, and 3D genome organization, shedding light on the mechanisms underlying AFB1-induced liver cancer.
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Affiliation(s)
- Yiran Wu
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
| | - Muhammad Muzammal Adeel
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Wentao Li
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602
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13
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Gu M, Fu J, Yan H, Yue X, Zhao S, Zhang Q, Li P. Approach for quick exploration of highly effective broad-spectrum biocontrol strains based on PO8 protein inhibition. NPJ Sci Food 2023; 7:45. [PMID: 37658048 PMCID: PMC10474023 DOI: 10.1038/s41538-023-00210-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/03/2023] [Indexed: 09/03/2023] Open
Abstract
Aflatoxin is a group of strongly toxic and carcinogenic mycotoxins produced by Aspergillus flavus and other Aspergillus species, which caused food contamination and food loss problems widely across the world especially in developing countries, thus threatening human health and sustainable development. So, it is important to develop new, green, and broad-spectrum biocontrol technology for the prevention of aflatoxin contamination sources. Previously, we found that the PO8 protein from aflatoxigenic A. flavus could be used as a biomarker to predict aflatoxin production in peanuts (so the PO8 is named as an early warning molecule), which infers that the PO8 is relative to aflatoxin production. Therefore, in the study, based on inhibiting the PO8, a new and quick strategy for screening aflatoxin biocontrol strains for developing control agents was presented. With the PO8 inhibition method, four biocontrol strains (2 strains were isolated from peanut kernels with sterilized surface and another 2 strains from peanut rhizosphere soil) were selected and combined to increase prevention wide-spectrum. As a result, the combination showed over 90% inhibition to all tested aflatoxigenic A. flavus isolated from three different peanut production areas (north, middle, and south areas of China), and better than any single strain. The field experiments located in five provinces of China showed that the practice prevention effects (inhibition of aflatoxigenic fungi on the surface of the peanuts) were from 50% to over 80%. The results indicated that the strategy of inhibiting the early warning molecule PO8 can be used to develop aflatoxin control agents well.
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Affiliation(s)
- Mei Gu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China
| | - Jiayun Fu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China
| | - Honglin Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China
| | - Xiaofeng Yue
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China
- Hubei Hongshan Laboratory, Wuhan, 430061, China
| | - Shancang Zhao
- Institute of Quality Standards and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, P. R. China.
| | - Qi Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China.
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China.
- Hubei Hongshan Laboratory, Wuhan, 430061, China.
- Institute of Food Safety, Hubei University, Wuhan, 430061, China.
- Ministry of Agriculture and Rural Affairs and Key Laboratory of Detection for Mycotoxins, Wuhan, 430061, China.
| | - Peiwu Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430061, China.
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430061, China.
- Hubei Hongshan Laboratory, Wuhan, 430061, China.
- Ministry of Agriculture and Rural Affairs and Key Laboratory of Detection for Mycotoxins, Wuhan, 430061, China.
- Xianghu Laboratory, Hangzhou, 311231, P. R. China.
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14
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Zuckerman JT, Minko IG, Kant M, Jaruga P, Stone MP, Dizdaroglu M, McCullough AK, Lloyd RS. Functional analyses of single nucleotide polymorphic variants of the DNA glycosylase NEIL1 in sub-Saharan African populations. DNA Repair (Amst) 2023; 129:103544. [PMID: 37517321 PMCID: PMC10546947 DOI: 10.1016/j.dnarep.2023.103544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Nei-like glycosylase 1 (NEIL1) is a DNA repair enzyme that initiates the base excision repair (BER) pathway to cleanse the human genome of damage. The substrate specificity of NEIL1 includes several common base modifications formed under oxidative stress conditions, as well as the imidazole ring open adducts that are induced by alkylating agents following initial modification at N7 guanine. An example of the latter is the persistent and mutagenic 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adduct, resulting from the alkylating agent aflatoxin B1 (AFB1) exo-8-9-epoxide. Naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 are hypothesized to be associated with an increased risk for development of early-onset hepatocellular carcinoma (HCC), especially in environments with high exposures to aflatoxins and chronic inflammation from viral infections and alcohol consumption. Given that AFB1 exposures and hepatitis B viral (HBV) infections represent a major problem in the developing countries of sub-Saharan Africa, it is pertinent to study SNP NEIL1 variants that are present in this geographic region. In this investigation, we characterized the three most common NEIL1 variants found in this region: P321A, R323G, and I182M. Biochemical analyses were conducted to determine the proficiencies of these variants in initiating the repair of DNA lesions. Our data show that damage recognition and excision activities of P321A and R323G were near that of wild-type (WT) NEIL1 for both thymine glycol (ThyGly) and AFB1-FapyGua. The substrate specificities of these variants with respect to various oxidatively-induced base lesions were also similar to that of WT. In contrast, the I182M variant was unstable, such that it precipitated under a variety of conditions and underwent rapid inactivation at a biologically relevant temperature, with partial stabilization being observed in the presence of undamaged DNA. This study provides insight regarding the potential increased risk for early-onset HCC in human populations carrying the NEIL1 I182M variant.
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Affiliation(s)
- Jamie T Zuckerman
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Melis Kant
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Pawel Jaruga
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, United States
| | - Miral Dizdaroglu
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States.
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15
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Otlu B, Díaz-Gay M, Vermes I, Bergstrom EN, Zhivagui M, Barnes M, Alexandrov LB. Topography of mutational signatures in human cancer. Cell Rep 2023; 42:112930. [PMID: 37540596 PMCID: PMC10507738 DOI: 10.1016/j.celrep.2023.112930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.
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Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ian Vermes
- COSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA.
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16
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Dhanasekaran R, Suzuki H, Lemaitre L, Kubota N, Hoshida Y. Molecular and immune landscape of hepatocellular carcinoma to guide therapeutic decision-making. Hepatology 2023:01515467-990000000-00480. [PMID: 37300379 PMCID: PMC10713867 DOI: 10.1097/hep.0000000000000513] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
Liver cancer, primarily HCC, exhibits highly heterogeneous histological and molecular aberrations across tumors and within individual tumor nodules. Such intertumor and intratumor heterogeneities may lead to diversity in the natural history of disease progression and various clinical disparities across the patients. Recently developed multimodality, single-cell, and spatial omics profiling technologies have enabled interrogation of the intertumor/intratumor heterogeneity in the cancer cells and the tumor immune microenvironment. These features may influence the natural history and efficacy of emerging therapies targeting novel molecular and immune pathways, some of which had been deemed undruggable. Thus, comprehensive characterization of the heterogeneities at various levels may facilitate the discovery of biomarkers that enable personalized and rational treatment decisions, and optimize treatment efficacy while minimizing the risk of adverse effects. Such companion biomarkers will also refine HCC treatment algorithms across disease stages for cost-effective patient management by optimizing the allocation of limited medical resources. Despite this promise, the complexity of the intertumor/intratumor heterogeneity and ever-expanding inventory of therapeutic agents and regimens have made clinical evaluation and translation of biomarkers increasingly challenging. To address this issue, novel clinical trial designs have been proposed and incorporated into recent studies. In this review, we discuss the latest findings in the molecular and immune landscape of HCC for their potential and utility as biomarkers, the framework of evaluation and clinical application of predictive/prognostic biomarkers, and ongoing biomarker-guided therapeutic clinical trials. These new developments may revolutionize patient care and substantially impact the still dismal HCC mortality.
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Affiliation(s)
| | - Hiroyuki Suzuki
- Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, Fukuoka
| | - Lea Lemaitre
- Division of Gastroenterology and Hepatology, Stanford University, Stanford, California
| | - Naoto Kubota
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
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17
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Mingard C, Battey JND, Takhaveev V, Blatter K, Hürlimann V, Sierro N, Ivanov NV, Sturla SJ. Dissection of Cancer Mutational Signatures with Individual Components of Cigarette Smoking. Chem Res Toxicol 2023; 36:714-723. [PMID: 36976926 PMCID: PMC10114081 DOI: 10.1021/acs.chemrestox.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Tobacco smoke delivers a complex mixture of hazardous and potentially hazardous chemicals. Some of these may induce the formation of DNA mutations, which increases the risk of various cancers that display characteristic patterns of accumulated mutations arising from the causative exposures. Tracking the contributions of individual mutagens to mutational signatures present in human cancers can help understand cancer etiology and advance disease prevention strategies. To characterize the potential contributions of individual constituents of tobacco smoke to tobacco exposure-associated mutational signatures, we first assessed the toxic potential of 13 tobacco-relevant compounds by determining their impact on the viability of a human bronchial lung epithelial cell line (BEAS-2B). Experimentally derived high-resolution mutational profiles were characterized for the seven most potent compounds by sequencing the genomes of clonally expanded mutants that arose after exposure to the individual chemicals. Analogous to the classification of mutagenic processes on the basis of signatures from human cancers, we extracted mutational signatures from the mutant clones. We confirmed the formation of previously characterized benzo[a]pyrene mutational signatures. Furthermore, we discovered three novel mutational signatures. The mutational signatures arising from benzo[a]pyrene and norharmane were similar to human lung cancer signatures attributed to tobacco smoking. However, the signatures arising from N-methyl-N'-nitro-N-nitrosoguanidine and 4-(acetoxymethyl)nitrosamino]-1-(3-pyridyl)-1-butanone were not directly related to known tobacco-linked mutational signatures from human cancers. This new data set expands the scope of the in vitro mutational signature catalog and advances understanding of how environmental agents mutate DNA.
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Affiliation(s)
- Cécile Mingard
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - James N D Battey
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Katharina Blatter
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Vera Hürlimann
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products SA, Quai Jeanrenaud 5, Neuchâtel, CH 2000, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, Zürich, CH 8092, Switzerland
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18
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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A versatile nanozyme integrated colorimetric and photothermal lateral flow immunoassay for highly sensitive and reliable Aspergillus flavus detection. Biosens Bioelectron 2022; 213:114435. [DOI: 10.1016/j.bios.2022.114435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/28/2022]
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20
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Zhang CH, Cheng Y, Zhang S, Fan J, Gao Q. Changing epidemiology of hepatocellular carcinoma in Asia. Liver Int 2022; 42:2029-2041. [PMID: 35319165 DOI: 10.1111/liv.15251] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/06/2021] [Accepted: 03/19/2022] [Indexed: 12/24/2022]
Abstract
Liver cancer is the fifth most common cancer and the second leading cause of malignant death in Asia, and Asia reports 72.5% of the world's cases in 2020. As the most common histological type, hepatocellular carcinoma (HCC) accounts for the majority of incidence and mortality of liver cancer cases. This review presents the changing epidemiology of HCC in Asian countries in recent years. Globally, aged, male and Asian populations remain the group with the highest risk of HCC. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are still the leading risk factors of HCC with a slight decline in most Asian countries, which is mainly attributed to HBV vaccination of newborns, prevention of HCV horizontal transmission and treatment of chronic hepatitis. However, the prevalence of HCC caused by metabolic factors, including metabolic syndrome, obesity and non-alcoholic fatty liver diseases, is increasing rapidly in Asian countries, which may eventually become the major cause of HCC. Excessive alcohol consumption continues to be an important risk factor as the average consumption of alcohol is still growing. Hopefully, great effort has been made to better prevention and treatment of HCC in most Asian regions, which significantly prolongs the survival of HCC patients. Asian countries tend to use more aggressive intervention than European and American countries, but it remains unclear whether this preference is related to a better prognosis. In conclusion, HCC remains a major disease burden in Asia, and the management of HCC should be adjusted dynamically based on the changing epidemiology.
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Affiliation(s)
- Chen-Hao Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yifei Cheng
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
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21
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Mycotoxin-Linked Mutations and Cancer Risk: A Global Health Issue. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137754. [PMID: 35805411 PMCID: PMC9266006 DOI: 10.3390/ijerph19137754] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 12/04/2022]
Abstract
Humans continue to be constantly exposed to mycotoxins, mainly through oral exposure (dietary), inhalation, or dermal contact. Recently, it has been of increasing interest to investigate mycotoxin-linked carcinogenicity. This systematic review was conducted to synthesize evidence of the association between mycotoxin-linked mutations and the risk of cancer, to provide an overview of the data linking exposure to different mycotoxins with human cancer risk, and to provide an update on current research on the risk of cancer associated with human exposure to mycotoxins. PRISMA guidelines were used when conducting the systematic review. PubMed, MEDLINE, and CINAHL electronic databases were comprehensively searched to extract the relevant studies published from inception to May 2022. A total of sixteen relevant studies (4907 participants) were identified and included in this review. Of these, twelve studies were from Asia, while four of the studies were conducted in Africa. The overall meta-analysis result found no significant association, although some of the studies confirmed an association between mycotoxin-linked mutations and primary liver cancer risk. Mainly, the experimental studies have shown associations between mycotoxin-linked mutations and cancer risk, and there is a need for researchers to confirm these links in epidemiological studies in order to guide public health policies and interventions.
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22
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Steele CD, Pillay N, Alexandrov LB. An overview of mutational and copy number signatures in human cancer. J Pathol 2022; 257:454-465. [PMID: 35420163 PMCID: PMC9324981 DOI: 10.1002/path.5912] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022]
Abstract
The genome of each cell in the human body is constantly under assault from a plethora of exogenous and endogenous processes that can damage DNA. If not successfully repaired, DNA damage generally becomes permanently imprinted in cells, and all their progenies, as somatic mutations. In most cases, the patterns of these somatic mutations contain the tell‐tale signs of the mutagenic processes that have imprinted and are termed mutational signatures. Recent pan‐cancer genomic analyses have elucidated the compendium of mutational signatures for all types of small mutational events, including (1) single base substitutions, (2) doublet base substitutions, and (3) small insertions/deletions. In contrast to small mutational events, where, in most cases, DNA damage is a prerequisite, aneuploidy, which refers to the abnormal number of chromosomes in a cell, usually develops from mistakes during DNA replication. Such mistakes include DNA replication stress, mitotic errors caused by faulty microtubule dynamics, or cohesion defects that contribute to chromosomal breakage and can lead to copy number (CN) alterations (CNAs) or even to structural rearrangements. These aberrations also leave behind genomic scars which can be inferred from sequencing as CN signatures and rearrangement signatures. The analyses of mutational signatures of small mutational events have been extensively reviewed, so we will not comprehensively re‐examine them here. Rather, our focus will be on summarising the existing knowledge for mutational signatures of CNAs. As studying CN signatures is an emerging field, we briefly summarise the utility that mutational signatures of small mutational events have provided in basic science, cancer treatment, and cancer prevention, and we emphasise the future role that CN signatures may play in each of these fields. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK.,Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, USA
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23
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Li S, Liu R, Xia S, Wei G, Ishfaq M, Zhang Y, Zhang X. Protective role of curcumin on aflatoxin B1-induced TLR4/RIPK pathway mediated-necroptosis and inflammation in chicken liver. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 233:113319. [PMID: 35189522 DOI: 10.1016/j.ecoenv.2022.113319] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
This study set out to assess the mitigative effects of curcumin on AFB1-induced necroptosis and inflammation in chicken liver. Ninety-six one-day-old AA broiler chickens were separated into four groups, including control group, AFB1 (1 mg/kg) group, curcumin (300 mg/kg) + AFB1 (1 mg/kg) group and curcumin (300 mg/kg) group. After 28 days treatment, livers were collected for different experimental analyses. The morphological observation results showed obvious necrotic characteristics, including cell swelling, rupture of cell and mitochondrial membranes and inflammation in chicken livers. AFB1 exposure increased oxidative stress index (ROS and MDA) and decreased the antioxidant activity markers (SOD, CAT and GSH) and ATPase activities in chickens' liver. ELISA results showed that AFB1 exposure significantly induced the cytokines (TNF-α, iNOS, IL-6 and IL-1β) release from the liver tissues. While, western blot and qRT-PCR results showed that the protein and mRNA expressions of inflammatory (TLR4/myd88/NF-κB) and necroptosis (RIPK1/RIPK3/MLKL) genes were up-regulated by AFB1 exposure. We suspect that signal crosstalk between TLR4 and TNF-α triggers inflammation and RIPK1/RIPK3 mediating necroptosis in AFB1-induced chicken liver injury. Curcumin can regulate the TLR4/RIPK signaling pathway, reduced oxidative stress biomarkers and inflammatory cytokines levels and attenuated the expression of necroptosis and inflammation genes altered by AFB1 to reduce necroptosis of chicken liver tissue. In conclusion, curcumin can protect against AFB1-induced necroptosis and inflammation by TLR4/RIPK pathway in chicken liver.
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Affiliation(s)
- Sihong Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China; Animal Genome Engineering Research Team, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Ruimeng Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Shun Xia
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Gaoqiang Wei
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Muhammad Ishfaq
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China; Huanggang Normal University, 438000 Huanggang, China
| | - Yixin Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China
| | - Xiuying Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang District, Harbin, China.
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24
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Awuchi CG, Ondari EN, Nwozo S, Odongo GA, Eseoghene IJ, Twinomuhwezi H, Ogbonna CU, Upadhyay AK, Adeleye AO, Okpala COR. Mycotoxins’ Toxicological Mechanisms Involving Humans, Livestock and Their Associated Health Concerns: A Review. Toxins (Basel) 2022; 14:toxins14030167. [PMID: 35324664 PMCID: PMC8949390 DOI: 10.3390/toxins14030167] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 12/21/2022] Open
Abstract
Mycotoxins are well established toxic metabolic entities produced when fungi invade agricultural/farm produce, and this happens especially when the conditions are favourable. Exposure to mycotoxins can directly take place via the consumption of infected foods and feeds; humans can also be indirectly exposed from consuming animals fed with infected feeds. Among the hundreds of mycotoxins known to humans, around a handful have drawn the most concern because of their occurrence in food and severe effects on human health. The increasing public health importance of mycotoxins across human and livestock environments mandates the continued review of the relevant literature, especially with regard to understanding their toxicological mechanisms. In particular, our analysis of recently conducted reviews showed that the toxicological mechanisms of mycotoxins deserve additional attention to help provide enhanced understanding regarding this subject matter. For this reason, this current work reviewed the mycotoxins’ toxicological mechanisms involving humans, livestock, and their associated health concerns. In particular, we have deepened our understanding about how the mycotoxins’ toxicological mechanisms impact on the human cellular genome. Along with the significance of mycotoxin toxicities and their toxicological mechanisms, there are associated health concerns arising from exposures to these toxins, including DNA damage, kidney damage, DNA/RNA mutations, growth impairment in children, gene modifications, and immune impairment. More needs to be done to enhance the understanding regards the mechanisms underscoring the environmental implications of mycotoxins, which can be actualized via risk assessment studies into the conditions/factors facilitating mycotoxins’ toxicities.
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Affiliation(s)
- Chinaza Godseill Awuchi
- Department of Biochemistry, Kampala International University, Bushenyi P.O. Box 20000, Uganda; (E.N.O.); (S.N.); (G.A.O.); (I.J.E.)
- Correspondence: (C.G.A.); (C.O.R.O.)
| | - Erick Nyakundi Ondari
- Department of Biochemistry, Kampala International University, Bushenyi P.O. Box 20000, Uganda; (E.N.O.); (S.N.); (G.A.O.); (I.J.E.)
| | - Sarah Nwozo
- Department of Biochemistry, Kampala International University, Bushenyi P.O. Box 20000, Uganda; (E.N.O.); (S.N.); (G.A.O.); (I.J.E.)
| | - Grace Akinyi Odongo
- Department of Biochemistry, Kampala International University, Bushenyi P.O. Box 20000, Uganda; (E.N.O.); (S.N.); (G.A.O.); (I.J.E.)
| | - Ifie Josiah Eseoghene
- Department of Biochemistry, Kampala International University, Bushenyi P.O. Box 20000, Uganda; (E.N.O.); (S.N.); (G.A.O.); (I.J.E.)
| | | | - Chukwuka U. Ogbonna
- Department of Biochemistry, Federal University of Agriculture, P.M.B. 2240, Abeokuta 110124, Ogun State, Nigeria;
| | - Anjani K. Upadhyay
- Heredity Healthcare & Lifesciences, 206-KIIT TBI, Patia, Bhubaneswar 751024, Odisha, India;
| | - Ademiku O. Adeleye
- Faith Heroic Generation, No. 36 Temidire Street, Azure 340251, Ondo State, Nigeria;
| | - Charles Odilichukwu R. Okpala
- Department of Functional Foods Product Development, Wrocław University of Environmental and Life Sciences, 51-630 Wrocław, Poland
- Correspondence: (C.G.A.); (C.O.R.O.)
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25
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Xie H, Wang X, van der Hooft JJ, Medema MH, Chen ZY, Yue X, Zhang Q, Li P. Fungi population metabolomics and molecular network study reveal novel biomarkers for early detection of aflatoxigenic Aspergillus species. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127173. [PMID: 34597924 DOI: 10.1016/j.jhazmat.2021.127173] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Mycotoxins threaten global food safety, public health and cause huge socioeconomic losses. Early detection is an effective preventive strategy, yet efficient biomarkers for early detection of aflatoxigenic Aspergillus species are lacking. Here, we proposed to use untargeted metabolomics and machine learning to mine biomarkers of aflatoxigenic Aspergillus species. We systematically delineated metabolic differences across 568 extensive field sampling A. flavus and performed biomarker analysis. Versicolorin B, 11-hydroxy-O-methylsterigmatocystin et.al metabolites shown a high correlation (from 0.71 to 0.95) with strains aflatoxin-producing capacity. Molecular networking analysis deciphered the connection of aflatoxins and biomarkers as well as potential emerging mycotoxins. We then developed a model using the biomarkers as variables to discern aflatoxigenic Aspergillus species with 97.8% accuracy. A validation dataset and metabolome from other 16 fungal isolates confirmed the robustness and specificity of these biomarkers. We further demonstrated the solution feasibility in agricultural products by early detection of biomarkers, which predicted aflatoxin contamination risk 35-47 days in advance. A developed operable decision rule by the XGBoost algorithm help regulators to intuitively assess the risk prioritization with 87.2% accuracy. Our research provides novel insights into global food safety risk assessment which will be crucial for early prevention and control of mycotoxins.
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Affiliation(s)
- Huali Xie
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Key laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China; Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Xiupin Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China; Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, China
| | | | - Marnix H Medema
- Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Xiaofeng Yue
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China
| | - Qi Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Key laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China; Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Peiwu Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Key laboratory of Detection for Aflatoxins, Ministry of Agriculture, Wuhan, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China; Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430061, China; Hubei Hongshan Laboratory, Wuhan, China.
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26
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Wu Y, Chua EHZ, Ng AWT, Boot A, Rozen SG. Accuracy of mutational signature software on correlated signatures. Sci Rep 2022; 12:390. [PMID: 35013428 PMCID: PMC8748538 DOI: 10.1038/s41598-021-04207-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
Mutational signatures are characteristic patterns of mutations generated by exogenous mutagens or by endogenous mutational processes. Mutational signatures are important for research into DNA damage and repair, aging, cancer biology, genetic toxicology, and epidemiology. Unsupervised learning can infer mutational signatures from the somatic mutations in large numbers of tumors, and separating correlated signatures is a notable challenge for this task. To investigate which methods can best meet this challenge, we assessed 18 computational methods for inferring mutational signatures on 20 synthetic data sets that incorporated varying degrees of correlated activity of two common mutational signatures. Performance varied widely, and four methods noticeably outperformed the others: hdp (based on hierarchical Dirichlet processes), SigProExtractor (based on multiple non-negative matrix factorizations over resampled data), TCSM (based on an approach used in document topic analysis), and mutSpec.NMF (also based on non-negative matrix factorization). The results underscored the complexities of mutational signature extraction, including the importance and difficulty of determining the correct number of signatures and the importance of hyperparameters. Our findings indicate directions for improvement of the software and show a need for care when interpreting results from any of these methods, including the need for assessing sensitivity of the results to input parameters.
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Affiliation(s)
- Yang Wu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Ellora Hui Zhen Chua
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Alvin Wei Tian Ng
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Arnoud Boot
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore.
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore.
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Ji H, Li J, Zhang Q, Yang J, Duan J, Wang X, Ma B, Zhang Z, Pan W, Zhang H. Clinical feature-related single-base substitution sequence signatures identified with an unsupervised machine learning approach. BMC Med Genomics 2021; 14:298. [PMID: 34930241 PMCID: PMC8686331 DOI: 10.1186/s12920-021-01144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mutation processes leave different signatures in genes. For single-base substitutions, previous studies have suggested that mutation signatures are not only reflected in mutation bases but also in neighboring bases. However, because of the lack of a method to identify features of long sequences next to mutation bases, the understanding of how flanking sequences influence mutation signatures is limited. METHODS We constructed a long short-term memory-self organizing map (LSTM-SOM) unsupervised neural network. By extracting mutated sequence features via LSTM and clustering similar features with the SOM, single-base substitutions in The Cancer Genome Atlas database were clustered according to both their mutation site and flanking sequences. The relationship between mutation sequence signatures and clinical features was then analyzed. Finally, we clustered patients into different classes according to the composition of the mutation sequence signatures by the K-means method and then studied the differences in clinical features and survival between classes. RESULTS Ten classes of mutant sequence signatures (mutation blots, MBs) were obtained from 2,141,527 single-base substitutions via LSTM-SOM machine learning approach. Different features in mutation bases and flanking sequences were revealed among MBs. MBs reflect both the site and pathological features of cancers. MBs were related to clinical features, including age, sex, and cancer stage. The class of an MB in a given gene was associated with survival. Finally, patients were clustered into 7 classes according to the MB composition. Significant differences in survival and clinical features were observed among different patient classes. CONCLUSIONS We provided a method for analyzing the characteristics of mutant sequences. Result of this study showed that flanking sequences, together with mutation bases, shape the signatures of SBSs. MBs were shown related to clinical features and survival of cancer patients. Composition of MBs is a feasible predictive factor of clinical prognosis. Further study of the mechanism of MBs related to cancer characteristics is suggested.
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Affiliation(s)
- Hongchen Ji
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China
- Faculty of Hepatopancreatobiliary Surgery, Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing, China
| | - Junjie Li
- Department of Emergency, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, China
| | - Qiong Zhang
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China
| | - Jingyue Yang
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China
| | - Juanli Duan
- Department of Hepatoxbiliary Surgery, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, China
| | - Xiaowen Wang
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China
| | - Ben Ma
- Faculty of Hepatopancreatobiliary Surgery, Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing, China
| | - Zhuochao Zhang
- Faculty of Hepatopancreatobiliary Surgery, Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing, China
| | - Wei Pan
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China
| | - Hongmei Zhang
- Department of Oncology, Xijing Hospital, Fourth Military Medical University, No. 127 West Changle Road, Xi'an, 710032, China.
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Rosendahl Huber A, Van Hoeck A, Van Boxtel R. The Mutagenic Impact of Environmental Exposures in Human Cells and Cancer: Imprints Through Time. Front Genet 2021; 12:760039. [PMID: 34745228 PMCID: PMC8565797 DOI: 10.3389/fgene.2021.760039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
During life, the DNA of our cells is continuously exposed to external damaging processes. Despite the activity of various repair mechanisms, DNA damage eventually results in the accumulation of mutations in the genomes of our cells. Oncogenic mutations are at the root of carcinogenesis, and carcinogenic agents are often highly mutagenic. Over the past decade, whole genome sequencing data of healthy and tumor tissues have revealed how cells in our body gradually accumulate mutations because of exposure to various mutagenic processes. Dissection of mutation profiles based on the type and context specificities of the altered bases has revealed a variety of signatures that reflect past exposure to environmental mutagens, ranging from chemotherapeutic drugs to genotoxic gut bacteria. In this review, we discuss the latest knowledge on somatic mutation accumulation in human cells, and how environmental mutagenic factors further shape the mutation landscapes of tissues. In addition, not all carcinogenic agents induce mutations, which may point to alternative tumor-promoting mechanisms, such as altered clonal selection dynamics. In short, we provide an overview of how environmental factors induce mutations in the DNA of our healthy cells and how this contributes to carcinogenesis. A better understanding of how environmental mutagens shape the genomes of our cells can help to identify potential preventable causes of cancer.
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Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Arne Van Hoeck
- Oncode Institute, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Ruben Van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
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29
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Seplyarskiy VB, Sunyaev S. The origin of human mutation in light of genomic data. Nat Rev Genet 2021; 22:672-686. [PMID: 34163020 DOI: 10.1038/s41576-021-00376-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Despite years of active research into the role of DNA repair and replication in mutagenesis, surprisingly little is known about the origin of spontaneous human mutation in the germ line. With the advent of high-throughput sequencing, genome-scale data have revealed statistical properties of mutagenesis in humans. These properties include variation of the mutation rate and spectrum along the genome at different scales in relation to epigenomic features and dependency on parental age. Moreover, mutations originated in mothers are less frequent than mutations originated in fathers and have a distinct genomic distribution. Statistical analyses that interpret these patterns in the context of known biochemistry can provide mechanistic models of mutagenesis in humans.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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30
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Environmental exposure and clinical correlates of hepatocellular carcinoma in New York City: a case only study. Cancer Causes Control 2021; 33:153-159. [PMID: 34498221 DOI: 10.1007/s10552-021-01494-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022]
Abstract
In the U.S., Hepatocellular carcinoma (HCC) incidence rates have increased. We aimed to determine whether environmental exposure plays a role in the high incidence of HCC observed in New York City. We conducted a hospital-based case only study to examine the prevalence of aflatoxin B1 (AFB1)- and polycyclic aromatic hydrocarbon (PAH)-albumin adducts and the distribution of adducts by different characteristics of HCC patients. Blood samples were collected from 155 HCC patients for biomarker analyses. We observed that about 46% and 49% of cases had detectable AFB1- and PAH-albumin adducts, respectively. There were significant differences between AFB1-albumin adducts and selected factors such as HCV infection status (p = 0.04), diabetes (p = 0.03) and Barcelona Clinic Liver Cancer stage (p = 0.02). Cases with detectable PAH-albumin adducts had a smoking history compared with those with nondetectable levels (p = 0.04). The level of AFB1-albumin adducts was positively correlated with plasma bilirubin (rs = 0.32, p < 0.0001) and adiponectin concentrations (rs = 0.28, p = 0.0005). The level of aflatoxin B1-albumin adducts was negatively associated with blood albumin concentration (rs = - 0.28, p = 0.0009) and plasma DNA LINE-1 methylation (rs = - 0.16, p = 0.04). Our study provides additional evidence that environmental exposures including to aflatoxin might drive the high incidence of HCC observed in the New York City.
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31
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Guo J, Zhou Y, Xu C, Chen Q, Sztupinszki Z, Börcsök J, Xu C, Ye F, Tang W, Kang J, Yang L, Zhong J, Zhong T, Hu T, Yu R, Szallasi Z, Deng X, Li Q. Genetic Determinants of Somatic Selection of Mutational Processes in 3,566 Human Cancers. Cancer Res 2021; 81:4205-4217. [PMID: 34215622 PMCID: PMC9662923 DOI: 10.1158/0008-5472.can-21-0086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 01/07/2023]
Abstract
The somatic landscape of the cancer genome results from different mutational processes represented by distinct "mutational signatures." Although several mutagenic mechanisms are known to cause specific mutational signatures in cell lines, the variation of somatic mutational activities in patients, which is mostly attributed to somatic selection, is still poorly explained. Here, we introduce a quantitative trait, mutational propensity (MP), and describe an integrated method to infer genetic determinants of variations in the mutational processes in 3,566 cancers with specific underlying mechanisms. As a result, we report 2,314 candidate determinants with both significant germline and somatic effects on somatic selection of mutational processes, of which, 485 act via cancer gene expression and 1,427 act through the tumor-immune microenvironment. These data demonstrate that the genetic determinants of MPs provide complementary information to known cancer driver genes, clonal evolution, and clinical biomarkers. SIGNIFICANCE: The genetic determinants of the somatic mutational processes in cancer elucidate the biology underlying somatic selection and evolution of cancers and demonstrate complementary predictive power across cancer types.
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Affiliation(s)
- Jintao Guo
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ying Zhou
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Chaoqun Xu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Qinwei Chen
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | | | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Canqiang Xu
- XMU-Aginome Joint Lab, School of Informatics, Xiamen University, Xiamen, China
| | - Feng Ye
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Weiwei Tang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiapeng Kang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Lu Yang
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Teaching Hospital of Fujian Medical University, Xiamen, Fujian, China.,Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jiaxin Zhong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Taoling Zhong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Tianhui Hu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rongshan Yu
- XMU-Aginome Joint Lab, School of Informatics, Xiamen University, Xiamen, China
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Science, Xiamen University, Xiamen, China
| | - Qiyuan Li
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Department of hematology, School of Medicine, Xiamen University, Xiamen, China.,Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Corresponding Author: Qiyuan Li, School of Medicine, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China. Phone: 8659-2218-5175; E-mail:
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He Y, Shi M, Wu X, Ma J, Ng KTP, Xia Q, Zhu L, Fu PPC, Man K, Tsui SKW, Lin G. Mutational Signature Analysis Reveals Widespread Contribution of Pyrrolizidine Alkaloid Exposure to Human Liver Cancer. Hepatology 2021; 74:264-280. [PMID: 33462832 DOI: 10.1002/hep.31723] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/06/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Mutational signature analyses are an effective tool in identifying cancer etiology. Humans are frequently exposed to pyrrolizidine alkaloids (PAs), the most common carcinogenic phytotoxins widely distributed in herbal remedies and foods. However, due to the lack of human epidemiological data, PAs are classified as group II hepatocarcinogens by the World Health Organization. This study identified a PA mutational signature as the biomarker to investigate the association of PA exposure with human liver cancer. APPROACH AND RESULTS Pyrrole-protein adducts (PPAs), the PA exposure biomarker, were measured and found in 32% of surgically resected specimens from 34 patients with liver cancer in Hong Kong. Next, we delineated the mode of mutagenic and tumorigenic actions of retrorsine, a representative PA, in mice and human hepatocytes (HepaRG). Retrorsine induced DNA adduction, DNA damage, and activation of tumorigenic hepatic progenitor cells, which initiated hepatocarcinogenesis. PA mutational signature, as the unique molecular fingerprint of PA-induced mutation, was derived from exome mutations in retrorsine-exposed mice and HepaRG cells. Notably, PA mutational signature was validated in genomes of patients with PPA-positive liver cancer but not patients with PPA-negative liver cancer, confirming the specificity of this biomarker in revealing PA-associated liver cancers. Furthermore, we examined the established PA mutational signature in 1,513 liver cancer genomes and found that PA-associated liver cancers were potentially prevalent in Asia (Mainland China [48%], Hong Kong [44%], Japan [22%], South Korea [6%], Southeast Asia [25%]) but minor in Western countries (North America [3%] and Europe [5%]). CONCLUSIONS This study provides a clinical indication of PA-associated liver cancer. We discovered an unexpectedly extensive implication of PA exposure in patients with liver cancer, laying the scientific basis for precautionary approaches and prevention of PA-associated human liver cancers.
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Affiliation(s)
- Yisheng He
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mai Shi
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xu Wu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiang Ma
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Tak-Pan Ng
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Qingsu Xia
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR
| | - Lin Zhu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter Pi-Cheng Fu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR
| | - Kwan Man
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ge Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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Landi MT, Synnott NC, Rosenbaum J, Zhang T, Zhu B, Shi J, Zhao W, Kebede M, Sang J, Choi J, Mendoza L, Pacheco M, Hicks B, Caporaso NE, Abubakar M, Gordenin DA, Wedge DC, Alexandrov LB, Rothman N, Lan Q, Garcia-Closas M, Chanock SJ. Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers. Am J Epidemiol 2021; 190:962-976. [PMID: 33712835 DOI: 10.1093/aje/kwaa234] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Epidemiologic studies often rely on questionnaire data, exposure measurement tools, and/or biomarkers to identify risk factors and the underlying carcinogenic processes. An emerging and promising complementary approach to investigate cancer etiology is the study of somatic "mutational signatures" that endogenous and exogenous processes imprint on the cellular genome. These signatures can be identified from a complex web of somatic mutations thanks to advances in DNA sequencing technology and analytical algorithms. This approach is at the core of the Sherlock-Lung study (2018-ongoing), a retrospective case-only study of over 2,000 lung cancers in never-smokers (LCINS), using different patterns of mutations observed within LCINS tumors to trace back possible exposures or endogenous processes. Whole genome and transcriptome sequencing, genome-wide methylation, microbiome, and other analyses are integrated with data from histological and radiological imaging, lifestyle, demographic characteristics, environmental and occupational exposures, and medical records to classify LCINS into subtypes that could reveal distinct risk factors. To date, we have received samples and data from 1,370 LCINS cases from 17 study sites worldwide and whole-genome sequencing has been completed on 1,257 samples. Here, we present the Sherlock-Lung study design and analytical strategy, also illustrating some empirical challenges and the potential for this approach in future epidemiologic studies.
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34
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He Y, Zhu L, Ma J, Lin G. Metabolism-mediated cytotoxicity and genotoxicity of pyrrolizidine alkaloids. Arch Toxicol 2021; 95:1917-1942. [PMID: 34003343 DOI: 10.1007/s00204-021-03060-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Pyrrolizidine alkaloids (PAs) and PA N-oxides are common phytotoxins produced by over 6000 plant species. Humans are frequently exposed to PAs via ingestion of PA-containing herbal products or PA-contaminated foods. PAs require metabolic activation to form pyrrole-protein adducts and pyrrole-DNA adducts which lead to cytotoxicity and genotoxicity. Individual PAs differ in their metabolic activation patterns, which may cause significant difference in toxic potency of different PAs. This review discusses the current knowledge and recent advances of metabolic pathways of different PAs, especially the metabolic activation and metabolism-mediated cytotoxicity and genotoxicity, and the risk evaluation methods of PA exposure. In addition, this review provides perspectives of precision toxicity assessment strategies and biomarker development for the risk control and translational investigations of human intoxication by PAs.
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Affiliation(s)
- Yisheng He
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Lin Zhu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jiang Ma
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ge Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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35
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Díaz-Gay M, Alexandrov LB. Unraveling the genomic landscape of colorectal cancer through mutational signatures. Adv Cancer Res 2021; 151:385-424. [PMID: 34148618 DOI: 10.1016/bs.acr.2021.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer, along with most other cancer types, is driven by somatic mutations. Characteristic patterns of somatic mutations, known as mutational signatures, arise as a result of the activities of different mutational processes. Mutational signatures have diverse origins, including exogenous and endogenous sources. In the case of colorectal cancer, the analysis of mutational signatures has elucidated specific signatures for classically associated DNA repair deficiencies, namely mismatch repair (leading to microsatellite instability), base excision repair (due to MUTYH or NTHL1 mutations), and polymerase proofreading (due to POLE and POLD1 exonuclease domain mutations). Additional signatures also play a role in colorectal cancer, including those related to normal aging and those associated with gut microbiota, as well as a number of signatures with unknown etiologies. This chapter provides an overview of the current knowledge of mutational signatures, with a focus on colorectal cancer and on the recently reported signatures in physiologically normal and inflammatory bowel disease-affected somatic colon tissues.
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Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, United States; Department of Bioengineering, UC San Diego, La Jolla, CA, United States; Moores Cancer Center, UC San Diego, La Jolla, CA, United States.
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36
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Tomar R, Minko IG, Kellum AH, Voehler MW, Stone MP, McCullough AK, Lloyd RS. DNA Sequence Modulates the Efficiency of NEIL1-Catalyzed Excision of the Aflatoxin B 1-Induced Formamidopyrimidine Guanine Adduct. Chem Res Toxicol 2021; 34:901-911. [PMID: 33595290 DOI: 10.1021/acs.chemrestox.0c00517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dietary exposure to aflatoxins is a significant risk factor in the development of hepatocellular carcinomas. Following bioactivation by microsomal P450s, the reaction of aflatoxin B1 (AFB1) with guanine (Gua) in DNA leads to the formation of stable, imidazole ring-opened 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adducts. In contrast to most base modifications that result in destabilization of the DNA duplex, the AFB1-FapyGua adduct increases the thermal stability of DNA via 5'-interface intercalation and base-stacking interactions. Although it was anticipated that this stabilization might make these lesions difficult to repair relative to helix distorting modifications, prior studies have shown that both the nucleotide and base excision repair pathways participate in the removal of the AFB1-FapyGua adduct. Specifically for base excision repair, we previously showed that the DNA glycosylase NEIL1 excises AFB1-FapyGua and catalyzes strand scission in both synthetic oligodeoxynucleotides and liver DNA of exposed mice. Since it is anticipated that error-prone replication bypass of unrepaired AFB1-FapyGua adducts contributes to cellular transformation and carcinogenesis, the structural and thermodynamic parameters that modulate the efficiencies of these repair pathways are of considerable interest. We hypothesized that the DNA sequence context in which the AFB1-FapyGua adduct is formed might modulate duplex stability and consequently alter the efficiencies of NEIL1-initiated repair. To address this hypothesis, site-specific AFB1-FapyGua adducts were synthesized in three sequence contexts, with the 5' neighbor nucleotide being varied. DNA structural stability analyses were conducted using UV absorbance- and NMR-based melting experiments. These data revealed differentials in thermal stabilities associated with the 5'-neighbor base pair. Single turnover kinetic analyses using the NEIL1 glycosylase demonstrated corresponding sequence-dependent differences in the repair of this adduct, such that there was an inverse correlation between the stabilization of the duplex and the efficiency of NEIL1-mediated catalysis.
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Affiliation(s)
- Rachana Tomar
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Andrew H Kellum
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Markus W Voehler
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Michael P Stone
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B, Box 351822, Nashville, Tennessee 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States.,Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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Otsubo Y, Matsumura S, Ikeda N, Morita O. Hawk-Seq™ differentiates between various mutations in Salmonella typhimurium TA100 strain caused by exposure to Ames test-positive mutagens. Mutagenesis 2021; 36:245-254. [PMID: 33590004 PMCID: PMC8262380 DOI: 10.1093/mutage/geab006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/03/2021] [Indexed: 11/27/2022] Open
Abstract
A precise understanding of differences in genomic mutations according to the mutagenic mechanisms detected in mutagenicity data is required to evaluate the carcinogenicity of environmental mutagens. Recently, we developed a highly accurate genome sequencing method, ‘Hawk-Seq™’, that enables the detection of mutagen-induced genome-wide mutations. However, its applicability to detect various mutagens and identify differences in mutational profiles is not well understood. Thus, we evaluated DNA samples from Salmonella typhimurium TA100 exposed to 11 mutagens, including alkylating agents, aldehydes, an aromatic nitro compound, epoxides, aromatic amines and polycyclic aromatic hydrocarbons (PAHs). We extensively analysed mutagen-induced mutational profiles and studied their association with the mechanisms of mutagens. Hawk-Seq™ sensitively detected mutations induced by all 11 mutagens, including one that increased the number of revertants by approximately 2-fold in the Ames test. Although the sensitivity for less water-soluble mutagens was relatively low, we increased the sensitivity to obtain high-resolution spectra by modifying the exposure protocol. Moreover, two epoxides indicated similar 6- or 96-dimensional mutational patterns; likewise, three SN1-type alkylating agents indicated similar mutational patterns, suggesting that the mutational patterns are compound category specific. Meanwhile, an SN2 type alkylating agent exhibited unique mutational patterns compared to those of the SN1 type alkylating agents. Although the mutational patterns induced by aldehydes, the aromatic nitro compound, aromatic amines and PAHs did not differ substantially from each other, the maximum total base substitution frequencies (MTSFs) were similar among mutagens in the same structural groups. Furthermore, the MTSF was found to be associated with the carcinogenic potency of some direct-acting mutagens. These results indicate that our method can generate high-resolution mutational profiles to identify characteristic features of each mutagen. The detailed mutational data obtained by Hawk-Seq™ can provide useful information regarding mutagenic mechanisms and help identify its association with the carcinogenicity of mutagens without requiring carcinogenicity data.
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Affiliation(s)
- Yuki Otsubo
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Shoji Matsumura
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Naohiro Ikeda
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa 210-0821, Japan
| | - Osamu Morita
- R&D Safety Science Research, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi 321-3497, Japan
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Lou J, Yang Y, Gu Q, Price BA, Qiu Y, Fedoriw Y, Desai S, Mose LE, Chen B, Tateishi S, Parker JS, Vaziri C, Wu D. Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo. NAR Cancer 2021; 3:zcaa037. [PMID: 33447826 PMCID: PMC7787264 DOI: 10.1093/narcan/zcaa037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/01/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
The E3 ubiquitin ligase Rad18 promotes a damage-tolerant and error-prone mode of DNA replication termed trans-lesion synthesis that is pathologically activated in cancer. However, the impact of vertebrate Rad18 on cancer genomes is not known. To determine how Rad18 affects mutagenesis in vivo, we have developed and implemented a novel computational pipeline to analyze genomes of carcinogen (7, 12-Dimethylbenz[a]anthracene, DMBA)-induced skin tumors from Rad18+/+ and Rad18- / - mice. We show that Rad18 mediates specific mutational signatures characterized by high levels of A(T)>T(A) single nucleotide variations (SNVs). In Rad18- /- tumors, an alternative mutation pattern arises, which is characterized by increased numbers of deletions >4 bp. Comparison with annotated human mutational signatures shows that COSMIC signature 22 predominates in Rad18+/+ tumors whereas Rad18- / - tumors are characterized by increased contribution of COSMIC signature 3 (a hallmark of BRCA-mutant tumors). Analysis of The Cancer Genome Atlas shows that RAD18 expression is strongly associated with high SNV burdens, suggesting RAD18 also promotes mutagenesis in human cancers. Taken together, our results show Rad18 promotes mutagenesis in vivo, modulates DNA repair pathway choice in neoplastic cells, and mediates specific mutational signatures that are present in human tumors.
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Affiliation(s)
- Jitong Lou
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina at Chapel Hill, 385 S. Columbia Street, Chapel Hill, NC 27599, USA
| | - Brandon A Price
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Yuheng Qiu
- Department of Statistics, Purdue University, 250 N. University St, West Lafayette, IN 47907, USA
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Siddhi Desai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Brian Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Satoshi Tateishi
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto 860-0811, Japan
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
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39
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Totsuka Y, Watanabe M, Lin Y. New horizons of DNA adductome for exploring environmental causes of cancer. Cancer Sci 2021; 112:7-15. [PMID: 32978845 PMCID: PMC7780056 DOI: 10.1111/cas.14666] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/08/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Chemical carcinogenesis is focused on the formation of DNA adducts, a form of DNA damage caused by covalent binding of a chemical moiety to DNA. The detection of carcinogen-DNA adducts in human tissues, along with demonstration of mutagenicity/carcinogenicity in experimental systems, and validation of adducts as biomarkers of environmental exposure and indicators of cancer risk in molecular epidemiological studies suggests a pivotal role of DNA adducts in cancer development. However, accurate measurement of DNA adducts in varied biological samples is challenging. Advances in mass spectrometry have prompted the development of DNA adductome analysis, an emerging method that simultaneously screens for multiple DNA adducts and provides relevant structural information. In this review, we summarize the basic principle and applications of DNA adductome analysis that would contribute to the elucidation of the environmental causes of cancer. Based on parallel developments in several fields, including next-generation sequencing, we describe a new approach used to explore cancer etiology, which integrates analyses of DNA adductome data and mutational signatures derived from whole-genome/exome sequencing.
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Affiliation(s)
- Yukari Totsuka
- Department of Cancer Model DevelopmentNational Cancer Center Research InstituteTokyoJapan
| | | | - Yingsong Lin
- Department of Public HealthAichi Medical University School of MedicineNagakuteJapan
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40
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Hölzl-Armstrong L, Moody S, Kucab JE, Zwart EP, Bellamri M, Luijten M, Turesky RJ, Stratton MR, Arlt VM, Phillips DH. Mutagenicity of 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) in human TP53 knock-in (Hupki) mouse embryo fibroblasts. Food Chem Toxicol 2020; 147:111855. [PMID: 33189884 DOI: 10.1016/j.fct.2020.111855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/03/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a possible human carcinogen formed in cooked fish and meat. PhIP is bioactivated by cytochrome P450 enzymes to form 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP), a genotoxic metabolite that reacts with DNA leading to the mutation-prone DNA adduct N-(deoxyguanosin-8-yl)-PhIP (dG-C8-PhIP). Here, we studied N-OH-PhIP-induced whole genome mutagenesis in human TP53 knock-in (Hupki) mouse embryo fibroblasts (HUFs) immortalised and subjected to whole genome sequencing (WGS). In addition, mutagenicity of N-OH-PhIP in TP53 and the lacZ reporter gene were assessed. TP53 mutant frequency in HUF cultures treated with N-OH-PhIP (2.5 μM for 24 h, n = 90) was 10% while no TP53 mutations were found in untreated controls (DMSO for 24 h, n = 6). All N-OH-PhIP-induced TP53 mutations occurred at G:C base pairs with G > T/C > A transversions accounting for 58% of them. TP53 mutations characteristic of those induced by N-OH-PhIP have been found in human tumours including breast and colorectal, which are cancer types that have been associated with PhIP exposure. LacZ mutant frequency increased 25-fold at 5 μM N-OH-PHIP and up to ~350 dG-C8-PhIP adducts/108 nucleosides were detected by ultra-performance liquid chromatography-electrospray ionisation multistage scan mass spectrometry (UPLC-ESI-MS3) at this concentration. In addition, a WGS mutational signature defined by G > T/C > A transversions was present in N-OH-PhIP-treated immortalised clones, which showed similarity to COSMIC SBS4, 18 and 29 signatures found in human tumours.
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Affiliation(s)
- Lisa Hölzl-Armstrong
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jill E Kucab
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Edwin P Zwart
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, the Netherlands
| | - Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, USA
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720 BA, the Netherlands
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK.
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
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41
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Genome Profiling for Aflatoxin B 1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B 1-Associated DNA Damage. G3-GENES GENOMES GENETICS 2020; 10:3929-3947. [PMID: 32994210 PMCID: PMC7642924 DOI: 10.1534/g3.120.401723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to the mycotoxin aflatoxin B1 (AFB1) strongly correlates with hepatocellular carcinoma (HCC). P450 enzymes convert AFB1 into a highly reactive epoxide that forms unstable 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N 7-Gua) DNA adducts, which convert to stable mutagenic AFB1 formamidopyrimidine (FAPY) DNA adducts. In CYP1A2-expressing budding yeast, AFB1 is a weak mutagen but a potent recombinagen. However, few genes have been identified that confer AFB1 resistance. Here, we profiled the yeast genome for AFB1 resistance. We introduced the human CYP1A2 into ∼90% of the diploid deletion library, and pooled samples from CYP1A2-expressing libraries and the original library were exposed to 50 μM AFB1 for 20 hs. By using next generation sequencing (NGS) to count molecular barcodes, we initially identified 86 genes from the CYP1A2-expressing libraries, of which 79 were confirmed to confer AFB1 resistance. While functionally diverse genes, including those that function in proteolysis, actin reorganization, and tRNA modification, were identified, those that function in postreplication DNA repair and encode proteins that bind to DNA damage were over-represented, compared to the yeast genome, at large. DNA metabolism genes also included those functioning in checkpoint recovery and replication fork maintenance, emphasizing the potency of the mycotoxin to trigger replication stress. Among genes involved in postreplication repair, we observed that CSM2, a member of the CSM2 (SHU) complex, functioned in AFB1-associated sister chromatid recombination while suppressing AFB1-associated mutations. These studies thus broaden the number of AFB1 resistance genes and have elucidated a mechanism of error-free bypass of AFB1-associated DNA adducts.
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42
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Parallelized Latent Dirichlet Allocation Provides a Novel Interpretability of Mutation Signatures in Cancer Genomes. Genes (Basel) 2020; 11:genes11101127. [PMID: 32992754 PMCID: PMC7600398 DOI: 10.3390/genes11101127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Mutation signatures are defined as the distribution of specific mutations such as activity of AID/APOBEC family proteins. Previous studies have reported numerous signatures, using matrix factorization methods for mutation catalogs. Different mutation signatures are active in different tumor types; hence, signature activity varies greatly among tumor types and becomes sparse. Because of this, many previous methods require dividing mutation catalogs for each tumor type. Here, we propose parallelized latent Dirichlet allocation (PLDA), a novel Bayesian model to simultaneously predict mutation signatures with all mutation catalogs. PLDA is an extended model of latent Dirichlet allocation (LDA), which is one of the methods used for signature prediction. It has parallelized hyperparameters of Dirichlet distributions for LDA, and they represent the sparsity of signature activities for each tumor type, thus facilitating simultaneous analyses. First, we conducted a simulation experiment to compare PLDA with previous methods (including SigProfiler and SignatureAnalyzer) using artificial data and confirmed that PLDA could predict signature structures as accurately as previous methods without searching for the optimal hyperparameters. Next, we applied PLDA to PCAWG (Pan-Cancer Analysis of Whole Genomes) mutation catalogs and obtained a signature set different from the one predicted by SigProfiler. Further, we have shown that the mutation spectrum represented by the predicted signature with PLDA provides a novel interpretability through post-analyses.
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43
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Hu X, Xu Z, De S. Characteristics of mutational signatures of unknown etiology. NAR Cancer 2020; 2:zcaa026. [PMID: 33015626 PMCID: PMC7520824 DOI: 10.1093/narcan/zcaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/01/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Although not all somatic mutations are cancer drivers, their mutational signatures, i.e. the patterns of genomic alterations at a genome-wide scale, provide insights into past exposure to mutagens, DNA damage and repair processes. Computational deconvolution of somatic mutation patterns and expert curation pan-cancer studies have identified a number of mutational signatures associated with point mutations, dinucleotide substitutions, insertions and deletions, and rearrangements, and have established etiologies for a subset of these signatures. However, the mechanisms underlying nearly one-third of all mutational signatures are not yet understood. The signatures with established etiology and those with hitherto unknown origin appear to have some differences in strand bias, GC content and nucleotide context diversity. It is possible that some of the hitherto ‘unknown’ signatures predominantly occur outside gene regions. While nucleotide contexts might be adequate to establish etiologies of some mutational signatures, in other cases additional features, such as broader (epi)genomic contexts, including chromatin, replication timing, processivity and local mutational patterns, may help fully understand the underlying DNA damage and repair processes. Nonetheless, remarkable progress in characterization of mutational signatures has provided fundamental insights into the biology of cancer, informed disease etiology and opened up new opportunities for cancer prevention, risk management, and therapeutic decision making.
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Affiliation(s)
- Xiaoju Hu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Zhuxuan Xu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
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44
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Hölzl-Armstrong L, Kucab JE, Moody S, Zwart EP, Loutkotová L, Duffy V, Luijten M, Gamboa da Costa G, Stratton MR, Phillips DH, Arlt VM. Mutagenicity of acrylamide and glycidamide in human TP53 knock-in (Hupki) mouse embryo fibroblasts. Arch Toxicol 2020; 94:4173-4196. [PMID: 32886187 PMCID: PMC7655573 DOI: 10.1007/s00204-020-02878-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/12/2020] [Indexed: 11/30/2022]
Abstract
Acrylamide is a suspected human carcinogen formed during high-temperature cooking of starch-rich foods. It is metabolised by cytochrome P450 2E1 to its reactive metabolite glycidamide, which forms pre-mutagenic DNA adducts. Using the human TP53 knock-in (Hupki) mouse embryo fibroblasts (HUFs) immortalisation assay (HIMA), acrylamide- and glycidamide-induced mutagenesis was studied in the tumour suppressor gene TP53. Selected immortalised HUF clones were also subjected to next-generation sequencing to determine mutations across the whole genome. The TP53-mutant frequency after glycidamide exposure (1.1 mM for 24 h, n = 198) was 9% compared with 0% in cultures treated with acrylamide [1.5 (n = 24) or 3 mM (n = 6) for 48 h] and untreated vehicle (water) controls (n = 36). Most glycidamide-induced mutations occurred at adenines with A > T/T > A and A > G/T > C mutations being the most common types. Mutations induced by glycidamide occurred at specific TP53 codons that have also been found to be mutated in human tumours (i.e., breast, ovary, colorectal, and lung) previously associated with acrylamide exposure. The spectrum of TP53 mutations was further reflected by the mutations detected by whole-genome sequencing (WGS) and a distinct WGS mutational signature was found in HUF clones treated with glycidamide that was again characterised by A > G/T > C and A > T/T > A mutations. The WGS mutational signature showed similarities with COSMIC mutational signatures SBS3 and 25 previously found in human tumours (e.g., breast and ovary), while the adenine component was similar to COSMIC SBS4 found mostly in smokers’ lung cancer. In contrast, in acrylamide-treated HUF clones, only culture-related background WGS mutational signatures were observed. In summary, the results of the present study suggest that glycidamide may be involved in the development of breast, ovarian, and lung cancer.
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Affiliation(s)
- Lisa Hölzl-Armstrong
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Jill E Kucab
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Edwin P Zwart
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, The Netherlands
| | - Lucie Loutkotová
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.,Covance Inc., Salt Lake City, Utah, 84124, USA
| | - Veronica Duffy
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3720, The Netherlands
| | - Gonçalo Gamboa da Costa
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, UK. .,Toxicology Department, GAB Consulting GmbH, 69126, Heidelberg, Germany.
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45
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Beal MA, Meier MJ, LeBlanc DP, Maurice C, O'Brien JM, Yauk CL, Marchetti F. Chemically induced mutations in a MutaMouse reporter gene inform mechanisms underlying human cancer mutational signatures. Commun Biol 2020; 3:438. [PMID: 32796912 PMCID: PMC7429849 DOI: 10.1038/s42003-020-01174-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Transgenic rodent (TGR) models use bacterial reporter genes to quantify in vivo mutagenesis. Pairing TGR assays with next-generation sequencing (NGS) enables comprehensive mutation pattern analysis to inform mutational mechanisms. We used this approach to identify 2751 independent lacZ mutations in the bone marrow of MutaMouse animals exposed to four chemical mutagens: benzo[a]pyrene, N-ethyl-N-nitrosourea, procarbazine, and triethylenemelamine. We also collected published data for 706 lacZ mutations from eight additional environmental mutagens. We report that lacZ gene sequencing generates chemical-specific mutation signatures observed in human cancers with established environmental causes. For example, the mutation signature of benzo[a]pyrene, a carcinogen present in tobacco smoke, matched the signature associated with tobacco-induced lung cancers. Our results suggest that the analysis of chemically induced mutations in the lacZ gene shortly after exposure provides an effective approach to characterize human-relevant mechanisms of carcinogenesis and propose novel environmental causes of mutation signatures observed in human cancers.
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Affiliation(s)
- Marc A Beal
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
- Existing Substances Risk Assessment Bureau, Health Canada, Ottawa, ON, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Danielle P LeBlanc
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Clotilde Maurice
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
- Existing Substances Risk Assessment Bureau, Health Canada, Ottawa, ON, Canada
| | - Jason M O'Brien
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, ON, K1A 0H3, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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46
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Boot A, Ng AWT, Chong FT, Ho SC, Yu W, Tan DSW, Iyer NG, Rozen SG. Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types. Genome Res 2020; 30:803-813. [PMID: 32661091 PMCID: PMC7370881 DOI: 10.1101/gr.255620.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 06/04/2020] [Indexed: 12/24/2022]
Abstract
Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who presented with oral bacterial infections showed novel mutational signatures. One of these novel signatures, SBS_AnT, is characterized by a preponderance of thymine mutations, strong transcriptional strand bias, and enrichment for adenines in the 4 bp 5′ of mutation sites. The mutational signature described in this manuscript was shown to be caused by colibactin, a bacterial mutagen produced by E. coli carrying the pks-island. Examination of publicly available sequencing data revealed SBS_AnT in 25 tumors from several mucosal tissue types, expanding the list of tissues in which this mutational signature is observed.
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Affiliation(s)
- Arnoud Boot
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore
| | - Alvin W T Ng
- Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 117456, Singapore
| | - Fui Teen Chong
- Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - Szu-Chi Ho
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Willie Yu
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore
| | - Daniel S W Tan
- Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - N Gopalakrishna Iyer
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - Steven G Rozen
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 117456, Singapore
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47
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Claeys L, Romano C, De Ruyck K, Wilson H, Fervers B, Korenjak M, Zavadil J, Gunter MJ, De Saeger S, De Boevre M, Huybrechts I. Mycotoxin exposure and human cancer risk: A systematic review of epidemiological studies. Compr Rev Food Sci Food Saf 2020; 19:1449-1464. [PMID: 33337079 DOI: 10.1111/1541-4337.12567] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/13/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023]
Abstract
In recent years, there has been an increasing interest in investigating the carcinogenicity of mycotoxins in humans. This systematic review aims to provide an overview of data linking exposure to different mycotoxins with human cancer risk. Publications (2019 and earlier) of case-control or longitudinal cohort studies were identified in PubMed and EMBASE. These articles were then screened by independent reviewers and their quality was assessed according to the Newcastle-Ottawa scale. Animal, cross-sectional, and molecular studies satisfied criteria for exclusion. In total, 14 articles were included: 13 case-control studies and 1 longitudinal cohort study. Included articles focused on associations of mycotoxin exposure with primary liver, breast, and cervical cancer. Overall, a positive association between the consumption of aflatoxin-contaminated foods and primary liver cancer risk was verified. Two case-control studies in Africa investigated the relationship between zearalenone and its metabolites and breast cancer risk, though conflicting results were reported. Two case-control studies investigated the association between hepatocellular carcinoma and fumonisin B1 exposure, but no significant associations were observed. This systematic review incorporates several clear observations of dose-dependent associations between aflatoxins and liver cancer risk, in keeping with IARC Monograph conclusions. Only few human epidemiological studies investigated the associations between mycotoxin exposures and cancer risk. To close this gap, more in-depth research is needed to unravel evidence for other common mycotoxins, such as deoxynivalenol and ochratoxin A. The link between mycotoxin exposures and cancer risk has mainly been established in experimental studies, and needs to be confirmed in human epidemiological studies to support the evidence-based public health strategies.
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Affiliation(s)
- Liesel Claeys
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
- CRIG, Cancer Research Institute Ghent, Ghent, Belgium
| | - Chiara Romano
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Karl De Ruyck
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent, Belgium
| | - Hayley Wilson
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Beatrice Fervers
- Department of Cancer and Environment, Centre Léon Bérnard, UA08 INSERM Radiation, Defense, Health and Environment, Lyon, France
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Marc J Gunter
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent, Belgium
| | - Marthe De Boevre
- Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent, Belgium
| | - Inge Huybrechts
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
- CRIG, Cancer Research Institute Ghent, Ghent, Belgium
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Shrestha R, Nabavi N, Volik S, Anderson S, Haegert A, McConeghy B, Sar F, Brahmbhatt S, Bell R, Le Bihan S, Wang Y, Collins C, Churg A. Well-Differentiated Papillary Mesothelioma of the Peritoneum Is Genetically Distinct from Malignant Mesothelioma. Cancers (Basel) 2020; 12:cancers12061568. [PMID: 32545767 PMCID: PMC7352777 DOI: 10.3390/cancers12061568] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Well-differentiated papillary mesothelioma (WDPM) is an uncommon mesothelial proliferation that is most commonly encountered as an incidental finding in the peritoneal cavity. There is controversy in the literature about whether WDPM is a neoplasm or a reactive process and, if neoplastic, whether it is a variant or precursor of epithelial malignant mesothelioma or is a different entity. Using whole exome sequencing of five WDPMs of the peritoneum, we have identified distinct mutations in EHD1, ATM, FBXO10, SH2D2A, CDH5, MAGED1, and TP73 shared by WDPM cases but not reported in malignant mesotheliomas. Furthermore, we show that WDPM is strongly enriched with C > A transversion substitution mutations, a pattern that is also not found in malignant mesotheliomas. The WDPMs lacked the alterations involving BAP1, SETD2, NF2, CDKN2A/B, LASTS1/2, PBRM1, and SMARCC1 that are frequently found in malignant mesotheliomas. We conclude that WDPMs are neoplasms that are genetically distinct from malignant mesotheliomas and, based on observed mutations, do not appear to be precursors of malignant mesotheliomas.
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Affiliation(s)
- Raunak Shrestha
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA94143, USA
| | - Noushin Nabavi
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Stanislav Volik
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Shawn Anderson
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Anne Haegert
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Brian McConeghy
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Funda Sar
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Sonal Brahmbhatt
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Robert Bell
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Stephane Le Bihan
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Department of Experimental Therapeutics, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Vancouver, BC V6H 3ZH, Canada; (R.S.); (N.N.); (S.V.); (S.A.); (A.H.); (B.M.); (F.S.); (S.B.); (R.B.); (S.L.B.); (Y.W.)
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Correspondence: (C.C.); (A.C.)
| | - Andrew Churg
- Department of Pathology, Vancouver General Hospital, Vancouver, BC V5Z 1M9, Canada
- Correspondence: (C.C.); (A.C.)
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Liebal UW, Phan ANT, Sudhakar M, Raman K, Blank LM. Machine Learning Applications for Mass Spectrometry-Based Metabolomics. Metabolites 2020; 10:E243. [PMID: 32545768 PMCID: PMC7345470 DOI: 10.3390/metabo10060243] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
The metabolome of an organism depends on environmental factors and intracellular regulation and provides information about the physiological conditions. Metabolomics helps to understand disease progression in clinical settings or estimate metabolite overproduction for metabolic engineering. The most popular analytical metabolomics platform is mass spectrometry (MS). However, MS metabolome data analysis is complicated, since metabolites interact nonlinearly, and the data structures themselves are complex. Machine learning methods have become immensely popular for statistical analysis due to the inherent nonlinear data representation and the ability to process large and heterogeneous data rapidly. In this review, we address recent developments in using machine learning for processing MS spectra and show how machine learning generates new biological insights. In particular, supervised machine learning has great potential in metabolomics research because of the ability to supply quantitative predictions. We review here commonly used tools, such as random forest, support vector machines, artificial neural networks, and genetic algorithms. During processing steps, the supervised machine learning methods help peak picking, normalization, and missing data imputation. For knowledge-driven analysis, machine learning contributes to biomarker detection, classification and regression, biochemical pathway identification, and carbon flux determination. Of important relevance is the combination of different omics data to identify the contributions of the various regulatory levels. Our overview of the recent publications also highlights that data quality determines analysis quality, but also adds to the challenge of choosing the right model for the data. Machine learning methods applied to MS-based metabolomics ease data analysis and can support clinical decisions, guide metabolic engineering, and stimulate fundamental biological discoveries.
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Affiliation(s)
- Ulf W. Liebal
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
| | - An N. T. Phan
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
| | - Malvika Sudhakar
- Department of Biotechnology, Bhupat and Juoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India; (M.S.); (K.R.)
- Initiative for Biological Systems Engineering, IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Juoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India; (M.S.); (K.R.)
- Initiative for Biological Systems Engineering, IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lars M. Blank
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
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50
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Wei R, Li P, He F, Wei G, Zhou Z, Su Z, Ni T. Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers. Brief Bioinform 2020; 22:5841903. [PMID: 32480415 DOI: 10.1093/bib/bbaa066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Alcohol consumption is a critical risk factor for multiple types of cancer. A genome can be attacked and acquire numerous somatic mutations in the environment of alcohol exposure. Mutational signature has the capacity illustrating the complex somatic mutation patterns in cancer genome. Recent studies have discovered distinct mutational signatures associating with alcohol consumption in liver and esophageal cancers. However, their prevalence among diverse cancers, impact of genetic background and origin of alcohol-induced mutational signatures remain unclear. By a comprehensive bioinformatics analysis on somatic mutations from patients of four cancer types with drinking information, we identified nine mutational signatures (signatures B-J), among which signature J (similar to COSMIC signature 16) was distinctive to alcohol drinking. Signature J was associated with HNSC, ESCA and LIHC but not PAAD. Interestingly, patients with mutated allele rs1229984 in ADH1B had lower level of signature J while mutated allele rs671 in ALDH2 exhibited higher signature J abundance, suggesting acetaldehyde is one cause of signature J. Intriguingly, somatic mutations of three potential cancer driver genes (TP53, CUL3 and NSD1) were found the critical contributors for increased mutational load of signature J in alcohol consumption patients. Furthermore, signature J was enriched with early accumulated clonal mutations compared to mutations derived from late tumor growth. This study systematically characterized alcohol-related mutational signature and indicated mechanistic insights into the prevalence, origin and gene-environment interaction regarding the risk oncogenic mutations associated with alcohol intake.
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