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Pomyalov S, Minetti CA, Remeta DP, Bonala R, Johnson F, Zaitseva I, Iden C, Golebiewska U, Breslauer KJ, Shoham G, Sidorenko VS, Grollman AP. Structural and Mechanistic Insights into the Transport of Aristolochic Acids and their Active Metabolites by Human Serum Albumin. J Biol Chem 2024:107358. [PMID: 38782206 DOI: 10.1016/j.jbc.2024.107358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Aristolochic acids I and II (AA-I/II) are carcinogenic principles of Aristolochia plants, which have been employed in traditional medicinal practices and discovered as food contaminants. While the deleterious effects of AAs are broadly acknowledged, there is a dearth of information to define the mechanisms underlying their carcinogenicity. Following bioactivation in the liver, N-hydroxyaristolactam and N-sulfonyloxyaristolactam metabolites are transported via circulation and elicit carcinogenic effects by reacting with cellular DNA. In this study, we apply DNA adduct analysis, X-ray crystallography, isothermal titration calorimetry (ITC) and fluorescence quenching to investigate the role of human serum albumin (HSA) in modulating AA carcinogenicity. We find that HSA extends the half-life and reactivity of N-sulfonyloxyaristolactam-I with DNA, thereby protecting activated AAs from heterolysis. Applying novel pooled plasma HSA crystallization methods, we report high-resolution structures of myristic acid-enriched HSA (HSAMYR) and its AA complexes (HSAMYR/AA-I and HSAMYR/AA-II) at 1.9 Å resolution. Whereas AA-I is located within HSA subdomain IB, AA-II occupies subdomains IIA and IB. ITC binding profiles reveal two distinct AA sites in both complexes with association constants of 1.5 and 0.5 · 106 M-1 for HSA/AA-I versus 8.4 and 9.0 · 105 M-1 for HSA/AA-II. Fluorescence quenching of the HSA Trp214 suggests variable impacts of fatty acids on ligand binding affinities. Collectively, our structural and thermodynamic characterizations yield significant insights into AA binding, transport, toxicity, and potential allostery, critical determinants for elucidating the mechanistic roles of HSA in modulating AA carcinogenicity.
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Affiliation(s)
- Sergei Pomyalov
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem 91904 Israel
| | - Conceição A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854 USA
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854 USA.
| | - Radha Bonala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA
| | - Francis Johnson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA; Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 USA
| | - Irina Zaitseva
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA
| | - Charles Iden
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA
| | - Urszula Golebiewska
- Department of Physiology, Stony Brook University, Stony Brook, New York 11794 USA; Department of Biological Sciences, Queensborough Community College, Bayside, New York 11364 USA
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854 USA; Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08901 USA
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem 91904 Israel
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA
| | - Arthur P Grollman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794 USA
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Wu KY, Cheong IS, Lai JN, Hu CY, Hung KC, Chen YT, Chiu LT, Tsai HT, Jou YC, Tzai TS, Tsai YS. Risk of secondary primary malignancies in survivors of upper tract urothelial carcinoma: A nationwide population-based analysis. Cancer Epidemiol 2024; 89:102536. [PMID: 38281454 DOI: 10.1016/j.canep.2024.102536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND To investigate the cancer types and risk factors of secondary primary malignancy (SPM) in patients with upper tract urothelial carcinoma (UTUC) in Taiwan. METHODS Using National Health Insurance Research Dataset and catastrophic illness registry, we enrolled newly diagnosed UTUC patients from 2000 to 2013. Those without catastrophic illness registration were excluded from the study. The cancer types and hazard ratios (HRs) of subsequent SPMs were calculated according to the antecedent malignancy. We analyzed the risk factors for developing SPMs using multivariate Cox proportional hazard models. RESULTS A total of 9050 UTUC patients were registered and 2187 (24.2%) patients developed SPMs during the study period. As compared with primary UTUC, the relative risk ratios of SPM was 2.5 folds and 18% higher in those with antecedent non-UC malignancy and with bladder cancer history, respectively. Totally, 387 (37.8%) of 1022 UTUC patients with antecedent non-UC malignancy developed subsequent SPM after UTUC diagnosis. The antecedent and subsequent cancer types are similar and kidney cancer is most common, followed by hepatoma. Multivariate analysis showed that a history of antecedent non-UC malignancy is the most unfavorable factor for SPM development (HR, 2.50; 95% CI, 2.23-2.81), followed by liver disease, male gender, antecedent bladder cancer history, age ≥ 75 years, and chronic kidney disease. CONCLUSIONS Our study, conducted in Taiwan and involving 9050 UTUC patients, meticulously examined the types of SPM and the associated risk factors. Our research unearthed several pivotal discoveries: a preceding history of non-UC malignancies emerged as the single most influential factor contributing to the occurrence of subsequent cancers, followed by liver disease, male gender, antecedent bladder cancer history, age ≥75 years, and chronic kidney disease. Futhermore, kidney cancer emerged as the predominant subsequent malignancy, closely trailed by hepatoma..
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Affiliation(s)
- Kuan-Yu Wu
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Ian-Seng Cheong
- Department of Urology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi 600, Taiwan
| | - Jung-Nien Lai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 404, Taiwan; Department of Chinese Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Che-Yuan Hu
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Kuo-Chuan Hung
- Department of Anesthesiology, Chi Mei Medical Center, No.901, ChungHwa Road, Yung Kung Dist, Tainan 710, Taiwan; Department of Health and Nutrition, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
| | - Yi-Ting Chen
- Department of Anesthesiology, Chia-Yi Chang Gung Memorial Hospital, Chia-Yi 613, Taiwan
| | - Lu-Ting Chiu
- Management office for Health Data, China Medical University Hospital, Taichung 404, Taiwan
| | - Hsin-Tzu Tsai
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Yeong-Chin Jou
- Division of Urology, Department of Surgery, St Martin De Porres Hospital, Chia-Yi 600, Taiwan
| | - Tzong-Shin Tzai
- Department of Urology, An Nan Hospital, China Medical University, Tainan 709, Taiwan.
| | - Yuh-Shyan Tsai
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan.
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4
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Soares A, Bourlon MT, Wong A, Joshi A, Jardim D, Korbenfeld E, Karak FE, Orlandi F, Sze H, Ansari J, Zarba J, Mansour MA, Manneh R, Thirumulai R, Tsai YC, Morsi WA, Powles T. Management of Metastatic Urothelial Carcinoma in Emerging Markets (EM): An Expert Opinion. Clin Genitourin Cancer 2024; 22:467-475. [PMID: 38228413 DOI: 10.1016/j.clgc.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 01/18/2024]
Abstract
Urothelial carcinoma (UC) is the 10th most common cancer globally with an almost 4 times higher prevalence in men. The main risk factors for development of urothelial carcinoma are advanced age, smoking, arsenic contamination, exposure to carcinogens. Metastatic urothelial carcinoma (mUC) has overall poor prognosis with a 5-year overall survival rate of only < 5%. The standard of care comprises of platinum-based chemotherapy, but the responses are often not sustained. A working group was established with an objective to discuss the most recent clinical data on the genitourinary tumors of interest and comprised of experts across Latin America, Emerging Asia (except China, Japan, and South Korea), Africa, and the Middle East (known as Emerging Markets or EM). There is an evident disparity in terms of uneven mortality and incidence rate distribution among various regions. There is a lack and/or insufficient data on epidemiology, treatment, and outcomes in the EM. The lack of registries impacts the healthcare decisions and the lower incidence from the region might not be reflective of the true disease burden. The treatment outcomes of mUC can be improved by understanding the current disease burden and treatment approach of mUC and identifying the gaps and challenges associated with management. Hence, a literature review was developed to summarize the current disease burden and treatment approach of mUC across EM. The review also highlights the unmet needs for mUC management in EM and suggests a way forward to improve the current situation in order to better serve the patients.
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Affiliation(s)
- Andrey Soares
- Oncology and Hematology Center of Hospital Albert Einstein, Hospital Albert Einstein, Sao Paulo, Brazil.
| | - Maria T Bourlon
- Hemato-Oncology Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alvin Wong
- Sr Consultant, Department of Haematology Oncology National University Cancer Institute, Singapore
| | - Amit Joshi
- Professor, Medical Oncology, Tata Memorial Centre, HBNI, Mumbai, India
| | - Denis Jardim
- Oncology Department, Oncoclínicas Institute, São Paulo, Brazil
| | - Ernesto Korbenfeld
- Head of GU Tumors Unit, GU Tumors Unit, Hospital Británico de Buenos Aires, Buenos Aires, Argentina
| | - Fadi El Karak
- Hematology and Medical Oncology Service, University Medical Center Hôtel-Dieu De France Hospital, Faculty of Medicine, Saint Joseph University of Beirut, Lebanon
| | | | - Henry Sze
- Specialist in Clinical Oncology, Heal Oncology Centre, Hong Kong, China
| | - Jawaher Ansari
- Chief of Medical Oncology, Medical Oncology, Tawam Hospital, Al Ain, United Arab Emirates
| | - Jose Zarba
- Medical Oncologist, Centro Médico San Roque, Tucumán, Argentina
| | - Mubarak Al Mansour
- Adult Medical Oncology, Princess Noorah Oncology Center, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Ray Manneh
- edical Oncology, Sociedad de Oncología y Hematología del Cesar, Valledupar, Colombia
| | - Raja Thirumulai
- Senior Consultant, Medical Oncology, Apollo Specialty Hospital, Chennai, India
| | - Yu-Chieh Tsai
- Clinical Assistant Professor, Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Waleed Al Morsi
- GU & BSM Sr. Director Scientific Expert, Oncology Medical Affairs, Emerging Markets, Pfizer Ltd., Dubai, United Arab Emirates
| | - Thomas Powles
- Director of Barts Cancer Center, Professor of Urology Cancer, Barts Cancer Institute, London, United Kingdom
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5
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Linscott M, Ren JR, Gestl S, Gunther EJ. Different Oncogenes and Reproductive Histories Shape the Progression of Distinct Premalignant Clones in Multistage Mouse Breast Cancer Models. The American Journal of Pathology 2024:S0002-9440(24)00112-3. [PMID: 38537934 DOI: 10.1016/j.ajpath.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 04/10/2024]
Abstract
A remote carcinogen exposure can predispose to breast cancer onset decades later, suggesting carcinogen-induced mutations generate long-lived premalignant clones. How subsequent events influence the progression of specific premalignant clones remains poorly understood. Here, we generated multistage mouse models of mammary carcinogenesis by combining chemical carcinogen exposure [using 7,12-dimethylbenzanthracene (DMBA)] with transgenes that enable inducible expression of one of two clinically relevant mammary oncogenes: c-MYC (MYC) or PIK3CAH1047R (PIK). In prior work, DMBA exposure generated mammary clones bearing signature HrasQ61L mutations, which only progressed to mammary cancer after inducible Wnt1 oncogene expression. Here, after an identical DMBA exposure, MYC versus PIK drove cancer progression from mammary clones bearing mutations in distinct Ras family paralogs. For example, MYC drove cancer progression from either Kras- or Nras-mutant clones, whereas PIK transformed Kras-mutant clones only. These Ras mutation patterns were maintained whether oncogenic transgenes were induced within days of DMBA exposure or months later. Completing a full-term pregnancy (parity) failed to protect against either MYC- or PIK-driven tumor progression. Instead, a postpartum increase in mammary tumor predisposition was observed in the context of PIK-driven progression. However, parity decreased the overall prevalence of tumors bearing Krasmut, and the magnitude of this decrease depended on both the number and timing of pregnancies. These multistage models may be useful for elucidating biological features of premalignant mammary neoplasia.
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Affiliation(s)
- Maryknoll Linscott
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Jerry Ruizhe Ren
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Shelley Gestl
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Edward J Gunther
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania.
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6
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Yang G, Shahatiaili A, Bai S, Wang L, Jin D, Cao M, Su P, Liu Q, Tao K, Long Q, Shi Y, Xiao J, Tian F, Zhang L, Chen H, Su X. Mutational signature and prognosis in adenocarcinoma of the bladder. J Pathol 2024; 262:334-346. [PMID: 38180342 DOI: 10.1002/path.6239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 01/06/2024]
Abstract
Adenocarcinoma of the bladder is a rare urinary bladder carcinoma with limited therapy options due to lack of molecular characterization. Here, we aimed to reveal the mutational and transcriptomic landscapes of adenocarcinoma of the bladder and assess any relationship with prognosis. Between February 2015 and June 2021, a total of 23 patients with adenocarcinoma of the bladder were enrolled. These included 16 patients with primary bladder adenocarcinomas and seven patients with urachal adenocarcinoma. Whole exome sequencing (16 patients), whole genome sequencing (16 patients), bulk RNA sequencing (RNA-seq) (19 patients), and single-cell RNA-seq (5 patients) were conducted for the specimens. Correlation analysis, survival analysis, and t-tests were also performed. Prevalent T>A substitutions were observed among somatic mutations, and major trinucleotide contexts included 5'-CTC-3' and 5'-CTG-3'. This pattern was mainly contributed by COSMIC signature 22 related to chemical carcinogen exposure (probably aristolochic acid), which has not been reported in bladder adenocarcinoma. Moreover, genes with copy number changes were also enriched in the KEGG term 'chemical carcinogenesis'. Transcriptomic analysis suggested high immune cell infiltration and luminal-like features in the majority of samples. Interestingly, a small fraction of samples with an APOBEC-derived mutational signature exhibited a higher risk of disease progression compared with samples with only a chemical carcinogen-related signature, confirming the molecular and prognostic heterogeneity of bladder adenocarcinoma. This study presents mutational and transcriptomic landscapes of bladder adenocarcinoma, and indicates that a chemical carcinogen-related mutational signature may be related to a better prognosis compared with an APOBEC signature in adenocarcinoma of the bladder. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Guoliang Yang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Akezhouli Shahatiaili
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shihao Bai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Liyang Wang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Di Jin
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Ming Cao
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Peipei Su
- Innovative Program of Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Kun Tao
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Qi Long
- Joint School of Life Sciences, Guangzhou Medical University & Guangzhou Institutes of Biomedicine and Health-Chinese Academy of Sciences, Guangzhou, PR China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jing Xiao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Futong Tian
- Department of Design, Politecnico di Milano, Milan, Italy
| | - Lianhua Zhang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Haige Chen
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Xianbin Su
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
- eHealth Program of Shanghai Anti-doping Laboratory, Shanghai University of Sport, Shanghai, PR China
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7
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Zhu Y, Tang S, Yuan Q, Fu J, He J, Liu Z, Zhao X, Li Y, Zhao Y, Zhang Y, Zhang X, Zhang Y, Zhu Y, Wang W, Zheng B, Wu R, Wu T, Yang S, Qiu X, Shen S, Hu J, Chen L, Wang Y, Wang H, Gao D, Chen L. Integrated characterization of hepatobiliary tumor organoids provides a potential landscape of pharmacogenomic interactions. Cell Rep Med 2024; 5:101375. [PMID: 38278146 PMCID: PMC10897507 DOI: 10.1016/j.xcrm.2023.101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/20/2023] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
Despite considerable efforts to identify human liver cancer genomic alterations that might unveil druggable targets, the systematic translation of multiomics data remains challenging. Here, we report success in long-term culture of 64 patient-derived hepatobiliary tumor organoids (PDHOs) from a Chinese population. A divergent response to 265 metabolism- and epigenetics-related chemicals and 36 anti-cancer drugs is observed. Integration of the whole genome, transcriptome, chromatin accessibility profiles, and drug sensitivity results of 64 clinically relevant drugs defines over 32,000 genome-drug interactions. RUNX1 promoter mutation is associated with an increase in chromatin accessibility and a concomitant gene expression increase, promoting a cluster of drugs preferentially sensitive in hepatobiliary tumors. These results not only provide an annotated PDHO biobank of human liver cancer but also suggest a systematic approach for obtaining a comprehensive understanding of the gene-regulatory network of liver cancer, advancing the applications of potential personalized medicine.
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Affiliation(s)
- Yanjing Zhu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China
| | - Shijie Tang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuyue Yuan
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Fu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Juan He
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhuang Liu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Zhao
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yunguang Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yani Zhang
- Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyu Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yangqianwen Zhang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Yiqin Zhu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenwen Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bo Zheng
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Rui Wu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Tong Wu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Shuai Yang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinyao Qiu
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Siyun Shen
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Ji Hu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 330106, China; Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China; West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 330106, China.
| | - Hongyang Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China; Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai 200438, China.
| | - Dong Gao
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lei Chen
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai 200438, China.
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8
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. Cell Genom 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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9
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Liu M, Hong Y, Duan X, Zhou Q, Chen J, Liu S, Su J, Han L, Zhang J, Niu B. Unveiling the metal mutation nexus: Exploring the genomic impacts of heavy metal exposure in lung adenocarcinoma and colorectal cancer. J Hazard Mater 2024; 461:132590. [PMID: 37769449 DOI: 10.1016/j.jhazmat.2023.132590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023]
Abstract
Mutations that activate oncogenes and deactivate tumor suppressor genes are widely recognized as significant contributors to cancer development. We investigated relationships between heavy metal exposure and the frequencies and types of gene mutations in patients with lung adenocarcinoma (LUAD) and colorectal cancer (CRC). Plasma concentrations of arsenic (As), cadmium (Cd), chromium (Cr), mercury (Hg), and lead (Pb) were measured using inductively coupled plasma mass spectrometry (ICPMS), and next-generation sequencing (NGS) of 1123 cancer-related genes was performed using the tumor tissues. Through Bayesian kernel machine regression (BKMR) analysis, we found associations between the integrated concentrations of the heavy metals and the number of gene mutations, especially insertions/deletions (indels), and Pb, As, and Cd were found to be the most significant contributors to the increased mutation rates. We extracted previously established mutational signatures and observed that they exhibit significant correlations with metal exposure. Moreover, we detected substantial shifts in the mutational landscape when comparing groups with high and low metal exposures. Several frequently mutated genes displayed positive correlations with metal exposure, whereas EGFR indels showed a negative association with Cd exposure. These findings suggest that heavy metal exposure can impact genomic stability in cancer-related genes, underscoring the importance of heavy metal exposure in cancer development.
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Affiliation(s)
- Mengyuan Liu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; WillingMed Technology (Beijing) Co., Ltd, Beijing 100176, China; Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Yuting Hong
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaohong Duan
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Jing Chen
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Siyao Liu
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Junyan Su
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Li Han
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Jiali Zhang
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science, University of the Chinese Academy of Sciences, Beijing 100190, China.
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10
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Chung F, Zavadil J. New risk factors and molecular landscapes of hepatic angiosarcoma in the Taiwanese population †. J Pathol 2024; 262:1-3. [PMID: 37929656 DOI: 10.1002/path.6224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Hepatic angiosarcoma is a rare, highly aggressive malignancy of the liver. The tumorigenesis of hepatic angiosarcoma has been relatively understudied in terms of aetiology and molecular properties. A recent study published in The Journal of Pathology revealed a strong association between hepatic angiosarcoma incidence and chronic kidney disease, particularly in end-stage renal disease using population-based data from the National Health Insurance Research Database in Taiwan and an institutional cohort. The study also revealed enrichment in the mutational signature of aristolochic acid exposure and is the first reported observation of this mutational signature in human sarcomas. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Felicia Chung
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, Rhône-Alpes, France
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11
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Aplan P, Bertoli R, Chung YJ, Difilippantonio M, Wokasch A, Marasco M, Klimaszewski H, Garber S, Zhu Y, Walker R, Cao D, Doroshow J, Meltzer P. 5-Aza-4'-thio-2'-deoxycytidine induces C>G transversions in a specific trinucleotide context and leads to acute lymphoid leukemia. Res Sq 2023:rs.3.rs-3186246. [PMID: 38168433 PMCID: PMC10760231 DOI: 10.21203/rs.3.rs-3186246/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNA methyltransferase inhibitors (DNMTi), most commonly cytidine analogs, are compounds that are used clinically to decrease 5'-cytosine methylation, with the aim of re-expression of tumor suppressor genes. We used a murine pre-clinical model of myelodysplastic syndrome based on transplantation of cells expressing a NUP98::HOXD13 transgene to investigate 5-Aza-4'-thio-2'-deoxycytidine (Aza TdCyd or ATC), a thiol substituted DNMTi, as a potential therapy. We found that ATC treatment led to lymphoid leukemia in wild-type recipient cells; further study revealed that healthy mice treated with ATC also developed lymphoid leukemia. Whole exome sequencing revealed thousands of acquired mutations, almost all of which were C > G transversions in a previously unrecognized, specific 5'-NCG-3' context. These mutations involved dozens of genes well-known to be involved in human lymphoid leukemia, such as Notch1, Pten, Pax5, Trp53 , and Nf1 . Treatment of human cells in vitro showed thousands of acquired C > G transversions in a similar context. Deletion of Dck , the rate-limiting enzyme for the cytidine salvage pathway, eliminated C > G transversions. Taken together, these findings demonstrate that DNMTi can be potent mutagens in human and mouse cells, both in vitro and in vivo .
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12
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Abstract
PURPOSE OF REVIEW Urologic cancers result from the appearance of genomic alterations in the target organ due to the combination of genetic and environmental factors. Knowledge of the genomic markers involved in their etiology and mechanisms for their development continue to progress. This reviewed provides an update on recent genomic studies that have informed epidemiologic and clinical research in urology. RECENT FINDINGS Inherited variations are an established risk factor for urologic cancers with significant estimates of heritability for prostate, kidney, and bladder cancer. The roles of both rare germline variants, identified from family-based studies, and common variants, identified from genome-wide association studies, have provided important information about the genetic architecture for urologic cancers. Large-scale analyses of tumors have generated genomic, epigenomic, transcriptomic, and proteomic data that have also provided novel insights into etiology and mechanisms. These tumors characteristics, along with the associated tumor microenvironment, have attempted to provide more accurate risk stratification, prognosis of disease and therapeutic management. SUMMARY Genomic studies of inherited and acquired variation are changing the landscape of our understanding of the causes of urologic cancers and providing important translational insights for their management. Their use in epidemiologic and clinical studies is thus essential.
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Affiliation(s)
- Géraldine Cancel-Tassin
- Centre for Research on Prostatic Diseases (CeRePP), Paris, France
- GRC 5 Predictive Onco-Urology, Sorbonne University, Paris, France
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
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13
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Chang Y, Hsu W, Lee Y, Chiang C, Yang Y, You S, Chen Y, Lai T. Trends and sex-specific incidence of upper urinary tract cancer in Taiwan: A birth cohort study. Cancer Med 2023; 12:15350-15357. [PMID: 37392179 PMCID: PMC10417072 DOI: 10.1002/cam4.6084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Taiwan has one of the highest incidences of upper tract urothelial cancer (UTUC) worldwide, especially in women; however, no nationwide, long-term follow-up study has evaluated this. METHODS We investigated the incidence of UTUC in Taiwan using data from the national population-based Taiwan Cancer Registry database (1985-2019). We divided the birth cohort into nine 5-year age groups and calculated the age-specific incidence for these groups according to the corresponding birth years. RESULTS The average annual percent change in the incidence of renal pelvis cancer from 1985 to 2019 showed sex-specific differences, with 3.5% and 5.3% increases in the incidences in men and women, respectively. The age-specific incidence rate for renal pelvis cancer among women showed a gradual increase in the group with older women as well as an increase over time in each age group. The results of a birth cohort analysis revealed that younger cohorts had higher incidence rates of renal pelvis cancer than older cohorts did. CONCLUSION We demonstrated that the incidence of UTUC is unusually high among older Taiwanese women and that younger cohorts have a high risk of UTUC than older cohorts.
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Affiliation(s)
- Yu‐Hsuan Chang
- School of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
| | - Wan‐Lun Hsu
- Data Science Center, College of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
- Master Program of Big Data Analysis in Biomedicine, College of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
| | - Yu‐Kwang Lee
- Department of Surgery, Division of General SurgeryNational Taiwan University HospitalTaipeiTaiwan
| | - Chun‐Ju Chiang
- Graduate Institute of Epidemiology and Preventive Medicine, College of Public HealthNational Taiwan UniversityTaipeiTaiwan
| | - Ya‐Wen Yang
- Graduate Institute of Epidemiology and Preventive Medicine, College of Public HealthNational Taiwan UniversityTaipeiTaiwan
| | - San‐Lin You
- School of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
- Data Science Center, College of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
| | - Yong‐Chen Chen
- Data Science Center, College of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
- Master Program of Big Data Analysis in Biomedicine, College of MedicineFu‐Jen Catholic UniversityNew Taipei CityTaiwan
| | - Tai‐Shuan Lai
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
- Department of Internal Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
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Huang SC, Chang IYF, Chang CJ, Liu H, Chen KH, Liu TT, Hsieh TY, Chuang HC, Chen CC, Lin IC, Ng KF, Huang HY, Chen TC. Association between hepatic angiosarcoma and end-stage renal disease: nationwide population-based evidence and enriched mutational signature of aristolochic acid exposure. J Pathol 2023; 260:165-176. [PMID: 36815532 DOI: 10.1002/path.6072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/31/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Hepatic angiosarcoma (HAS) is an aggressive mesenchymal malignancy that remains underexplored with respect to its etiology and mutational landscapes. To clarify the association between HAS and end-stage renal disease (ESRD), we used nationwide data of the National Health Insurance Research Database (NHIRD) in Taiwan, covering ~99% of the population, from 2001 to 2016. To investigate molecular signatures, we performed whole-exome sequencing (WES) in 27 surgical specimens, including nine ESRD-associated cases. The NHIRD analysis demonstrated that HAS ranked second among all angiosarcomas in Taiwan, with the incidence rates of HAS being 0.08, 2.49, and 5.71 per 100,000 person-years in the general population, chronic kidney disease (CKD), and ESRD patients, respectively. The standardized incidence ratios of HAS in CKD and ESRD patients were 29.99 and 68.77, respectively. In comparison with nonhepatic angiosarcoma, the multivariate regression analysis of our institutional cohort confirmed CKD/ESRD as an independent risk factor for HAS (odds ratio: 9.521, 95% confidence interval: 2.995-30.261, p < 0.001). WES identified a high tumor mutation burden (TMB; median: 8.66 variants per megabase) and dominant A:T-to-T:A transversion in HAS with frequent TP53 (81%) and ATRX (41%) mutations, KDR amplifications/gains (56%), and CDKN2A/B deletions (48%). Notably, ESRD-associated HAS had a significantly higher TMB (17.62 variants per megabase, p = 0.01) and enriched mutational signatures of aristolochic acid exposure (COSMIC SBS22, p < 0.001). In summary, a significant proportion of HAS in Taiwan is associated with ESRD and harbors a distinctive mutational signature, which concomitantly links nephrotoxicity and mutagenesis resulting from exposure to aristolochic acid or related compounds. A high TMB may support the eligibility for immunotherapy in treating ESRD-associated HAS. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Shih-Chiang Huang
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Chee-Jen Chang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Services Center for Health Information, Chang Gung University, Taoyuan, Taiwan
- Clinical Informatics and Medical Statistics Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Cardiology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kuang-Hua Chen
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ting-Ting Liu
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
- Department of Medical Laboratory Science, I-Shou University, Kaohsiung, Taiwan
| | - Tsan-Yu Hsieh
- Department of Anatomic Pathology, Keelung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Keelung, Taiwan
| | - Huei-Chieh Chuang
- Department of Anatomic Pathology, Chiayi Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Chiayi, Taiwan
| | - Chien-Cheng Chen
- Department of Radiology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - I-Chieh Lin
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kwai-Fong Ng
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Tse-Ching Chen
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
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Bašić D, Ignjatović I, Janković Veličković L, Veljković A. Molecular Characterization of Microrna Interference and Aristolochic Acid Intoxication Found in Upper Tract Urothelial Carcinoma in Patients with Balkan Endemic Nephropathy: A Systematic Review of the Current Literature. Balkan J Med Genet 2023; 25:105-111. [PMID: 37265966 PMCID: PMC10230835 DOI: 10.2478/bjmg-2022-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
The term "aristolochic acid nephropathy" (AAN) is used to include any form of toxic interstitial nephropathy that is caused either by ingestion of plants containing aristolochic acids (AA) or by the environmental contaminants in food such as in Balkan endemic nephropathy (BEN). Aristolochic acid (AA) intoxication is strongly associated with the development of upper tract urothelial carcinoma (UTUC); however, the underlying molecular mechanism remains to be defined. MicroRNAs (miRNA) regulate several biological processes, including cell proliferation, differentiation, and metabolism, acting as oncogenes or tumor suppressors. A unique miRNA expression profile suggested that miRNAs could function as regulators in UTUC developmental processes. This review aimed to summarize data available in the literature about underlying molecular mechanisms leading to the expression of miRNAs in AA-UTUC patients with BEN. Strong correlation in AA-UTUC has a distinctive gene alteration pattern, AL-DNA adducts, and a unique tumor protein (TP53) mutational spectrum AAG to TAG (A: T→T: A) transversion in codon 139 (Lys → Stop) of exon 5 activates the p53 tumor suppressor protein. Further, p53 protein is responsible not only for the expression of miRNAs but also acts as a target molecule for miRNAs and plays a crucial function in the AA-UTUC pathogenicity through activation of cyclin-dependent kinase (CyclinD1) and cyclin protein kinase 6(CDK6) to support cell cycle arrest. This study, proposed a molecular mechanism that represented a possible unique relationship between AA intoxication, miRNAs expression, and the progression of UTUC in patients with BEN.
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Affiliation(s)
- D Bašić
- Urology Clinic, University Clinical Center Niš, Faculty of Medicine, University of Niš, Niš, Serbia
| | - I Ignjatović
- Urology Clinic, University Clinical Center Niš, Faculty of Medicine, University of Niš, Niš, Serbia
| | - Lj Janković Veličković
- Center for Pathology, University Clinical Center Niš, Faculty of Medicine, University of Niš, Niš, Serbia
| | - A Veljković
- Department of Biochemistry, Faculty of Medicine, University of Niš, Niš, Serbia
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Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023; 15:cancers15071958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.
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Affiliation(s)
- Andrew Patterson
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Bin Tian
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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17
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Jhuang JR, Chiu PC, Hsieh TC, Chen CH, Pu YS, Lee WC. Latency period of aristolochic acid-induced upper urinary tract urothelial carcinoma. Front Public Health 2023; 11:1072864. [PMID: 36969664 PMCID: PMC10034135 DOI: 10.3389/fpubh.2023.1072864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
PurposeAristolochic acid (AA) is a carcinogen in upper urinary tract urothelial carcinoma (UTUC). This study investigated the latency period between AA exposure and UTUC development.Materials and methodsThis population-based cohort study was designed using record linkage of the National Health Insurance Research Database (NHIRD), Taiwan Cancer Registry Dataset, and cause-of-death data in Taiwan. Those aged 40–79 years were enrolled in this study. Patients who died or had renal insufficiency or UTUC before 2005 were excluded. The doses of AA exposure and rates of comorbidities between 2000 and 2005 were obtained. The Cox proportion hazard model was used to estimate the risk of UTUC between 2005 and 2016. In addition, the Cox model with time-varying coefficient of AA was used to measure the latency period of UTUC.ResultsOf the 752,232 participants enrolled from the NHIRD, 520,871 (68.29%), 210,447 (27.59%), and 31,415 (4.12%) were exposed to cumulative AA doses of 0–1 mg, 1–150 mg, and >150 mg, respectively. A total of 1,147 (0.15%) patients were diagnosed with UTUC between 2005 and 2016. The latency periods of UTUC in middle-aged (40–59 years old) men with cumulative AA doses of 1–150 mg and middle-aged women with cumulative AA doses of 1–150 mg and >150 mg were 8, 9, and 7 years, respectively. Among the aged (60–79 years) individuals, no time-varying effect was observed, and the latency period could not be measured.ConclusionA decreased risk of UTUC was observed after the ban on AA in Taiwan, especially in middle-aged women with moderate to high doses of AA exposure and men with moderate doses of AA exposure. The latency period of UTUC varies with age, the dose of AA exposure, and sex.
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Affiliation(s)
- Jing-Rong Jhuang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Taiwan Cancer Registry, Taipei, Taiwan
| | - Po-Chun Chiu
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tung-Che Hsieh
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
- *Correspondence: Chung-Hsin Chen ;
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chung Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Taiwan Cancer Registry, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
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18
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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Tomiyama E, Fujita K, Hashimoto M, Adomi S, Kawashima A, Minami T, Yoshimura K, Uemura H, Nonomura N. Comparison of molecular profiles of upper tract urothelial carcinoma vs. urinary bladder cancer in the era of targeted therapy: a narrative review. Transl Androl Urol 2022; 11:1747-1761. [PMID: 36632153 PMCID: PMC9827402 DOI: 10.21037/tau-22-457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022] Open
Abstract
Background and Objective Although upper tract urothelial carcinoma (UTUC) shares the histological appearance of urinary bladder cancer (UBC), molecular studies suggest that UTUC and UBC represent two distinct disease entities. However, treatment approaches for UTUC are virtually extrapolated from the evidence on UBC. As targeted drugs-immune-checkpoint inhibitors, fibroblast growth factor receptor inhibitors, and antibody-drug conjugates-target specific molecules, gaining more knowledge about the target-molecular profiles of each drug can help formulate optimal treatment strategies for UTUC. Methods This narrative review summarized the subgroup analyses of clinical trials of FDA-approved targeted drugs to explore the differential effects of each targeted drug when administered for UTUC compared to UBC. We focused on the differences in mutation frequency, RNA expression subtype, and therapeutic target protein expressions (specifically PD-L1, Nectin-4, and Trop-2) between UTUC and UBC and discussed their relationship with the efficacy of each targeted drug. Key Content and Findings A clinical trial of nivolumab in an adjuvant setting (CheckMate 274) implied that immune-checkpoint inhibitors might be less efficacious in UTUC than in UBC. Genomic and transcriptomic studies suggest that UTUC has a high frequency of FGFR3 mutations and predominantly shows the luminal papillary subtype, which is immunologically cold with low T-cell infiltration. These findings are consistent with a possible lower response rate to immunotherapy in UTUC than that in UBC. Clinical trials of enfortumab vedotin in a third-line setting (EV201 and EV301) implied that enfortumab vedotin might be less efficacious in UTUC than in UBC. Previous immunohistochemical analyses suggest that UTUC might have a slightly lower rate of Nectin-4 positivity than UBC, indicating that enfortumab vedotin was less efficacious in UTUC than in UBC. Conclusions Clinical differences in the effects of targeted drugs for UTUC and UBC may highlight the molecular differences between these diseases. The treatment strategy should be optimized based on further investigation of the molecular characteristics of UTUC.
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Affiliation(s)
- Eisuke Tomiyama
- Department of Urology, Osaka University Graduate School of Medicine, Yamadaoka, Suita, Osaka, Japan
| | - Kazutoshi Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Yamadaoka, Suita, Osaka, Japan;,Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Mamoru Hashimoto
- Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Shogo Adomi
- Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Atsunari Kawashima
- Department of Urology, Osaka University Graduate School of Medicine, Yamadaoka, Suita, Osaka, Japan
| | - Takafumi Minami
- Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Kazuhiro Yoshimura
- Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kindai University Faculty of Medicine, Ohno-Higashi, Osaka-Sayama, Osaka, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Yamadaoka, Suita, Osaka, Japan
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Lin CT, Su PJ, Huang SY, Wu CC, Wang HJ, Cheng YT, Luo HL, Chen CH, Liu TT, Huang CC, Su YL. First-line Immune Checkpoint Inhibitor Versus Immune Checkpoint Inhibitor With Chemotherapy for Cisplatin-ineligible Metastatic Urothelial Carcinoma: Evidence From a Real-world, Multicenter Analysis. J Immunother 2022; 45:407-414. [PMID: 36121316 PMCID: PMC9528941 DOI: 10.1097/cji.0000000000000441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022]
Abstract
Immune checkpoint inhibitors (ICIs) are widely used for first-line cisplatin-ineligible patients with metastatic urothelial carcinoma (mUC). However, whether to use ICIs as monotherapy or in combination with chemotherapy is still uncertain. We retrospectively analyzed cisplatin-ineligible patients with mUC who underwent first-line ICI monotherapy or ICI plus chemotherapy at 2 medical centers in Taiwan from 2016 to 2021. We calculated the objective response rate, progression-free survival, and overall survival (OS) using the Kaplan-Meier method and Cox regression model for multivariable analysis. In total, 130 patients were enrolled and categorized into 2 groups: an ICI monotherapy group [immunotherapy (IO), n=101] and an ICI plus noncisplatin chemotherapy group [immunotherapy and chemotherapy (IC), n=29]. The median OS of patients in the IO and IC groups was 19.5 and 9.7 months ( P =0.33). Among patients with high programmed cell death ligand-1-expressing tumors, the median OS was significantly prolonged in the IO group compared with the IC group (not reached vs. 6.3 mo, P =0.02). First-line ICI monotherapy demonstrated robust antitumor activity in cisplatin-ineligible patients with mUC. Combining noncisplatin chemotherapy with ICI did not improve clinical outcomes.
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Affiliation(s)
- Chang-Ting Lin
- Division of Hematology Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | - Po-Jung Su
- Division of Hematology Oncology, Chang Gung Memorial Hospital at Linkou and Chang Gung University, College of Medicine, Taoyuan
| | - Shih-Yu Huang
- Division of Hematology Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | - Chia-Che Wu
- Division of Hematology Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | | | | | | | | | | | - Chun-Chieh Huang
- Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine
| | - Yu-Li Su
- Division of Hematology Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
- Clinical Trial Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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Das S, Thakur S, Korenjak M, Sidorenko VS, Chung FFL, Zavadil J. Aristolochic acid-associated cancers: a public health risk in need of global action. Nat Rev Cancer 2022; 22:576-591. [PMID: 35854147 DOI: 10.1038/s41568-022-00494-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
Aristolochic acids (AAs) are a group of naturally occurring compounds present in many plant species of the Aristolochiaceae family. Exposure to AA is a significant risk factor for severe nephropathy, and urological and hepatobiliary cancers (among others) that are often recurrent and characterized by the prominent mutational fingerprint of AA. However, herbal medicinal products that contain AA continue to be manufactured and marketed worldwide with inadequate regulation, and possible environmental exposure routes receive little attention. As the trade of food and dietary supplements becomes increasingly globalized, we propose that further inaction on curtailing AA exposure will have far-reaching negative effects on the disease trends of AA-associated cancers. Our Review aims to systematically present the historical and current evidence for the mutagenicity and carcinogenicity of AA, and the effect of removing sources of AA exposure on cancer incidence trends. We discuss the persisting challenges of assessing the scale of AA-related carcinogenicity, and the obstacles that must be overcome in curbing AA exposure and preventing associated cancers. Overall, this Review aims to strengthen the case for the implementation of prevention measures against AA's multifaceted, detrimental and potentially fully preventable effects on human cancer development.
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Affiliation(s)
- Samrat Das
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
| | - Shefali Thakur
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael Korenjak
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Malaysia.
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer WHO, Lyon, France.
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22
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Zhu J, Ai Q, Cheng Q, Shen D, Dong Z, Li J, Shen D, Wang W, Zhang X, Li H. Mutational signature and clonal relatedness of recurrent urothelial carcinomas with aristolochic acid. Front Oncol 2022; 12:990023. [PMID: 36185218 PMCID: PMC9516318 DOI: 10.3389/fonc.2022.990023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Urothelial carcinomas (UCs) are malignant tumors that arise from the lower and upper urinary tract and are characterized by multiple recurrences. Aristolochic acid (AA) is a potent nephrotoxin and human carcinogen associated with UC. East Asian populations with a high UC prevalence have an unusual genome-wide AA-induced mutational pattern. To address the genomic differences and clonal relatedness between primary and recurrent tumors in the UCs with AA pattern, we investigated the genomic differences and tumor microenvironment (TME) of AA and non-AA UCs. 17 UC patients were recruited, with nine documented AA exposure. Eleven of them showed recurrence. After-surgery tissues of primary and paired recurrent tumors were collected. Capture-based targeted deep sequencing was performed using a commercial panel consisting of 520 cancer-related genes. Tumor-infiltrating lymphocytes (TILs) were identified with an immunofluorescence-based microenvironment analysis panel (MAP). Hierarchical clustering based on the COSMIC signatures confirmed two significant subtypes: AA Sig and non-AA Sig. AA Sig was associated with AA-containing herbal drug intake, recurrence, and higher tumor mutation burden (TMB). The clonal architecture of UCs revealed three types of clonal evolution patterns. Non-AA Sig cohort showed shared clonal origin of primary and recurrent tumors. AA Sig showed heterogeneity and had multiple independent origins. Recurrent tumors as second primary tumors in AA Sig showed immunoreactive TME, indicating a better response with immune checkpoint inhibitor therapy. The AA mutational signature and unique immune profiles are helpful molecular markers to distinguish AA exposure from other carcinogens. These results also provide new insights into the origin of recurrent UCs that could affect treatment strategies.
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Affiliation(s)
- Jie Zhu
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Qing Ai
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Qiang Cheng
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Dan Shen
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Zhouhuan Dong
- Department of Pathology, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jie Li
- Department of Pathology, The First Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Donglai Shen
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Wei Wang
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xu Zhang
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Hongzhao Li, ; Xu Zhang,
| | - Hongzhao Li
- Senior Department of Urology, The Third Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Hongzhao Li, ; Xu Zhang,
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23
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Lin PC, Tsai YS, Yeh YM, Shen MR. Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care. Biomolecules 2022; 12:biom12081133. [PMID: 36009026 PMCID: PMC9405970 DOI: 10.3390/biom12081133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
To provide precision medicine for better cancer care, researchers must work on clinical patient data, such as electronic medical records, physiological measurements, biochemistry, computerized tomography scans, digital pathology, and the genetic landscape of cancer tissue. To interpret big biodata in cancer genomics, an operational flow based on artificial intelligence (AI) models and medical management platforms with high-performance computing must be set up for precision cancer genomics in clinical practice. To work in the fast-evolving fields of patient care, clinical diagnostics, and therapeutic services, clinicians must understand the fundamentals of the AI tool approach. Therefore, the present article covers the following four themes: (i) computational prediction of pathogenic variants of cancer susceptibility genes; (ii) AI model for mutational analysis; (iii) single-cell genomics and computational biology; (iv) text mining for identifying gene targets in cancer; and (v) the NVIDIA graphics processing units, DRAGEN field programmable gate arrays systems and AI medical cloud platforms in clinical next-generation sequencing laboratories. Based on AI medical platforms and visualization, large amounts of clinical biodata can be rapidly copied and understood using an AI pipeline. The use of innovative AI technologies can deliver more accurate and rapid cancer therapy targets.
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Affiliation(s)
- Peng-Chan Lin
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Yi-Shan Tsai
- Department of Medical Imaging, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Yu-Min Yeh
- Department of Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Meng-Ru Shen
- Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Department of Pharmacology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: ; Tel.: +886-6-235-3535
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24
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Dickman KG, Chen CH, Grollman AP, Pu YS. Aristolochic acid-containing Chinese herbal medicine and upper urinary tract urothelial carcinoma in Taiwan: a narrative review. World J Urol 2022; 41:899-907. [PMID: 35867141 DOI: 10.1007/s00345-022-04100-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE The high incidence of upper urinary tract urothelial carcinoma (UTUC) in Taiwan is largely due to exposure to aristolochic acid (AA), a principal component of Aristolochia-based herbal medicines. Here we systematically review the molecular epidemiology, clinical presentation and biomarkers associated with AA-induced UTUC. METHODS This is a narrative review. Medline, Embase, and Web of Science were searched from inception to December 31, 2021. Studies evaluating the association, detection, and clinical characteristics of AA and UTUC were included. RESULTS A nationwide database revealed 39% of the Taiwanese population had been exposed to AA-containing herbs between 1997 and 2003. Epidemiological reports revealed AA posed a significantly higher hazard for renal failure and UTUC in herbalists and the general population who ingested AA-containing herbs. The presence of aristolactam-DNA adducts and a distinctive signature mutation, A:T to T:A transversions, located predominantly on the non-transcribed DNA strand, with a strong preference for deoxyadenosine in a consensus sequence (CAG), was observed in many UTUC patients. Clinically, AA-related UTUC patients were characterized by a younger age, female gender, impaired renal function and recurrence of contralateral UTUC. To date, there are no preventive measures, except prophylactic nephrectomy, for subjects at risk of AA nephropathy or AA-related UTUC. CONCLUSION AA exposure via Aristolochia-based herbal medicines is a problem throughout Taiwan, resulting in a high incidence of UTUC. Aristolactam-DNA adducts and a distinctive signature mutation, A:T to T:A transversions, can be used as biomarkers to identify AA-related UTUC. AA-related UTUC is associated with a high recurrence rate of contralateral UTUC.
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Affiliation(s)
- Kathleen G Dickman
- Departments of Pharmacological Sciences and Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei, 100, Taiwan, ROC.
| | - Arthur P Grollman
- Departments of Pharmacological Sciences and Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Yeong-Shiau Pu
- Department of Urology, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei, 100, Taiwan, ROC
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25
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Abstract
2,6-Diaminopurine (Z) is a naturally occurring adenine (A) analog that bacteriophages employ in place of A in their genetic alphabet. Recent discoveries of biogenesis pathways of Z in bacteriophages have stimulated substantial research interest in this DNA modification. Here, we systematically examined the effects of Z on the efficiency and fidelity of DNA transcription. Our results showed that Z exhibited no mutagenic yet substantial inhibitory effects on transcription mediated by purified T7 RNA polymerase and by human RNA polymerase II in HeLa nuclear extracts and in human cells. A structurally related adenine analog, 2-aminopurine (2AP), strongly blocked T7 RNA polymerase but did not impede human RNA polymerase II in vitro or in human cells, where no mutant transcript could be detected. The lack of mutagenic consequence and the presence of a strong blockage effect of Z on transcription suggest a role of Z in transcriptional regulation. Z is also subjected to removal by transcription-coupled nucleotide-excision repair (TC-NER), but not global-genome NER in human cells. Our findings provide new insight into the effects of Z on transcription and its potential biological functions.
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Affiliation(s)
| | | | - Jiyeong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Hyun Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | | | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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26
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Pich O, Bailey C, Watkins TBK, Zaccaria S, Jamal-Hanjani M, Swanton C. The translational challenges of precision oncology. Cancer Cell 2022; 40:458-478. [PMID: 35487215 DOI: 10.1016/j.ccell.2022.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
The translational challenges in the field of precision oncology are in part related to the biological complexity and diversity of this disease. Technological advances in genomics have facilitated large sequencing efforts and discoveries that have further supported this notion. In this review, we reflect on the impact of these discoveries on our understanding of several concepts: cancer initiation, cancer prevention, early detection, adjuvant therapy and minimal residual disease monitoring, cancer drug resistance, and cancer evolution in metastasis. We discuss key areas of focus for improving cancer outcomes, from biological insights to clinical application, and suggest where the development of these technologies will lead us. Finally, we discuss practical challenges to the wider adoption of molecular profiling in the clinic and the need for robust translational infrastructure.
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Affiliation(s)
- Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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27
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Guo W, Shi Z, Zeng T, He Y, Cai Z, Zhang J. Metabolic study of aristolochic acid I-exposed mice liver by atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry imaging and machine learning. Talanta 2022; 241:123261. [DOI: 10.1016/j.talanta.2022.123261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/19/2022] [Accepted: 01/22/2022] [Indexed: 10/19/2022]
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28
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Mani DR, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA. Cancer proteogenomics: current impact and future prospects. Nat Rev Cancer 2022; 22:298-313. [PMID: 35236940 DOI: 10.1038/s41568-022-00446-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.
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Affiliation(s)
- D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
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29
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Chen CJ, Chiu WC, Tseng YH, Lin CM, Yang HY, Yang YH, Chen PC. Aristolochic acid and the risk of cancers in patients with type 2 diabetes: Nationwide population-based cohort study. Phytomedicine 2022; 99:154023. [PMID: 35276591 DOI: 10.1016/j.phymed.2022.154023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/12/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Both aristolochic acid (AA) exposure and diabetic can increase risk of certain cancers,whetherAAexposureincreases cancer risk in diabetic patientsisunknown. The purpose of this study was to investigate the association between the use of Chinese herbal products containing AA and the risk of cancer in diabetic patients. METHODS A cohort study was conducted using the National Health Insurance Research Database in Taiwan. Patients older than 18 years who were diagnosed with diabetes between 1997 and 2010 were enrolled in our cohort. The use of Chinese herbal products containing AA was recorded from the beginning of 1997 until the ban of herbs containing AA in November 2003. Patients were individually tracked to identify cancer incidence between 1997 and 2013. Only patients who visited traditional Chinese medicine clinics between 1997 and 1 year before the end of follow-up were included in the cohort to ensure comparability. Cox proportional hazards regression was used to calculate the hazard ratio for the association between the use of Chinese herbal products containing AA and the occurrence of cancer. RESULTS Among the 430 377 male and 431 956 female patients with diabetes enrolled in our cohort, 37 554 and 31 535 cancer diagnoses were recorded during the study period, respectively. The use of AA-containing herbal products was associated with a significantly higher risk of liver, colorectum, kidney, bladder, prostate, pelvis, and ureter cancer in a dose-dependent manner. An increased risk of extrahepatic bile duct cancer in women was also associated with AA exposure at doses of more than 500 mg. CONCLUSIONS Association between AA exposure and the risk of some cancers were found in this study. AA exposure might increase risk of kidney,bladder,pelvis, ureter,liver,colorectum,andprostatecancer in all patientsandextrahepatic bile duct cancerin women.
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Affiliation(s)
- Chi-Jen Chen
- Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan
| | - Wei-Che Chiu
- Department of Psychiatry, Cathay General Hospital, Taipei, Taiwan; School of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
| | - Yao-Hsien Tseng
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Division of Geriatrics, Puli Branch, Taichung Veterans General Hospital, Nantou, Taiwan
| | - Chien-Mu Lin
- Department of Nuclear Medicine (C.-M.L.), Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiao-Yu Yang
- Institute of Environmental and Occupational Health Sciences, National Taiwan University College of Public Health, Taipei, Taiwan; Department of Public Health, National Taiwan University College of Public Health, Taipei, Taiwan
| | - Yao-Hsu Yang
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Chiayi County, Taiwan; Health Informatics and Epidemiology Laboratory, Chang Gung Memorial Hospital, Chiayi County, Taiwan; School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Pau-Chung Chen
- Institute of Environmental and Occupational Health Sciences, National Taiwan University College of Public Health, Taipei, Taiwan; Department of Public Health, National Taiwan University College of Public Health, Taipei, Taiwan; Department of Environmental and Occupational Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan.
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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Lai HY, Wu LC, Kong PH, Tsai HH, Chen YT, Cheng YT, Luo HL, Li CF. High Level of Aristolochic Acid Detected With a Unique Genomic Landscape Predicts Early UTUC Onset After Renal Transplantation in Taiwan. Front Oncol 2022; 11:828314. [PMID: 35071023 PMCID: PMC8770835 DOI: 10.3389/fonc.2021.828314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Background The unusual high dialysis prevalence and upper urinary tract urothelial carcinoma (UTUC) incidence in Taiwan may attribute to aristolochic acid (AA), which is nephrotoxic and carcinogenic, exposure. AA can cause a unique mutagenic pattern showing A:T to T:A transversions (mutational Signature 22) analyzed by whole exome sequencing (WES). However, a fast and cost-effective tool is still lacking for clinical practice. To address this issue, we developed an efficient and quantitative platform for the quantitation of AA and tried to link AA detection with clinical outcomes and decipher the genomic landscape of UTUC in Taiwan. Patients and Methods We recruited 61 patients with de novo onset of UTUC after kidney transplantation who underwent radical nephroureterectomy. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform was developed for the quantitation of AA. Pearson’s chi-square test, Kaplan–Meier method, and Cox proportional hazard model were utilized to assess the correlations among AA detection, clinicopathological characteristics, and clinical outcomes. Seven tumors and seven paired normal tissues were sequenced using WES (approximately 800x sequencing depth) and analyzed by bioinformatic tool. Results We found that high level of 7-(deoxyadenosin-N6-yl)aristolactam I (dA-AL-I) detected in paired normal tissues was significantly correlated with fast UTUC initiation times after renal transplantation (p = 0.035) and with no use of sirolimus (p = 0.046). Using WES analysis, we further observed that all tumor samples were featured by Signature 22 mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC)-associated gene mutations, p53 mutations, no fibroblast growth factor receptor 3 (FGFR3) mutation, and high tumor mutation burden (TMB). Especially, mammalian target of rapamycin (mTOR) activation predominated in dA-AL-I-detected samples compared with those without dA-AL-I detection and might be associated with UTUC initiation through cell proliferation and suppression of UTUC progression via autophagy inhibition. Conclusion Accordingly, dA-AL-I detection can provide more direct evidence to AA exposure and serve as a more specific predictive and prognostic biomarker for patients with de novo onset of UTUC after kidney transplantation.
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Affiliation(s)
- Hong-Yue Lai
- Center for Precision Medicine, Chi Mei Medical Center, Tainan, Taiwan.,Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
| | - Li-Ching Wu
- Center for Precision Medicine, Chi Mei Medical Center, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Po-Hsin Kong
- Center for Precision Medicine, Chi Mei Medical Center, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsin-Hwa Tsai
- Center for Precision Medicine, Chi Mei Medical Center, Tainan, Taiwan.,Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
| | - Yen-Ta Chen
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yuan-Tso Cheng
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hao-Lun Luo
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Feng Li
- Center for Precision Medicine, Chi Mei Medical Center, Tainan, Taiwan.,Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan.,Department of Clinical Pathology, Chi Mei Medical Center, Tainan, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan.,Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Pathology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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32
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Lim AH, Chan JY, Yu MC, Wu TH, Hong JH, Ng CCY, Low ZJ, Liu W, Vikneswari R, Sung PC, Fan WL, Teh BT, Hsieh SY. Rare Occurrence of Aristolochic Acid Mutational Signatures in Oro-Gastrointestinal Tract Cancers. Cancers (Basel) 2022; 14:cancers14030576. [PMID: 35158844 PMCID: PMC8833562 DOI: 10.3390/cancers14030576] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Aristolochic acids (AAs) are potent mutagens commonly found in herbal plant-based remedies widely used throughout Asian countries. PATIENTS AND METHODS To understand whether AA is involved in the tumorigenesis of the oro-gastrointestinal tract, we used whole-exome sequencing to profile 54 cases of four distinct types of oro-gastrointestinal tract cancer (OGITC) from Taiwan. RESULTS A diverse landscape of mutational signatures including those from DNA mismatch repair and reactive oxygen species was observed. APOBEC mutational signatures were observed in 60% of oral squamous cell carcinomas. Only one sample harbored AA mutational signatures, contradictory to prior reports of cancers from Taiwan. The metabolism of AA in the liver and urinary tract, transient exposure time, and high cell turnover rates at OGITC sites may explain our findings. CONCLUSION AA signatures in OGITCs are rare and unlikely to be a major contributing factor in oro-gastrointestinal tract tumorigenesis.
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Affiliation(s)
- Abner Herbert Lim
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Ming-Chin Yu
- Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan; (M.-C.Y.); (T.-H.W.)
- Department of Surgery, New Taipei Municipal Tucheng Hospital, New Taipei City 236, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Tsung-Han Wu
- Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan; (M.-C.Y.); (T.-H.W.)
| | - Jing Han Hong
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Cedric Chuan Young Ng
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Zhen Jie Low
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
| | - Wei Liu
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Rajasegaran Vikneswari
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Pin-Cheng Sung
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan;
| | - Wen-Lang Fan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan;
| | - Bin Tean Teh
- Cheng Kin Ku Herbal Biodiversity & Medicine Program, SingHealth Duke-NUS Institute of Biodiversity Medicine, Singapore 169610, Singapore; (A.H.L.); (J.H.H.); (C.C.Y.N.); (Z.J.L.); (W.L.)
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore 169610, Singapore; (J.Y.C.); (R.V.)
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence: (B.T.T.); or (S.-Y.H.); Tel.: +65-6436-8000 (B.T.T.); +886-975368031 (S.-Y.H.)
| | - Sen-Yung Hsieh
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan;
- Correspondence: (B.T.T.); or (S.-Y.H.); Tel.: +65-6436-8000 (B.T.T.); +886-975368031 (S.-Y.H.)
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Karanović S, Ardin M, Tang Z, Tomić K, Villar S, Renard C, Venturini E, Lorch AH, Lee DS, Stipančić Ž, Slade N, Vuković Brinar I, Dittrich D, Karlović K, Borovečki F, Dickman KG, Olivier M, Grollman AP, Jelaković B, Zavadil J. Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure. Int J Cancer 2022; 150:374-386. [PMID: 34569060 PMCID: PMC8627473 DOI: 10.1002/ijc.33827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/25/2021] [Accepted: 08/31/2021] [Indexed: 12/23/2022]
Abstract
Recurrent upper tract urothelial carcinomas (UTUCs) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). Here we delineated the molecular programs underlying UTUC tumorigenesis in patients from endemic aristolochic acid nephropathy (AAN) regions in Southern Europe. We applied an integrative multiomics analysis of UTUCs, corresponding unaffected tissues and of patient urines. Quantitative microRNA (miRNA) and messenger ribonucleic acid (mRNA) expression profiling, immunohistochemical analysis by tissue microarrays and exome and transcriptome sequencing were performed in UTUC and nontumor tissues. Urinary miRNAs of cases undergoing surgery were profiled before and after tumor resection. Ribonucleic acid (RNA) and protein levels were analyzed using appropriate statistical tests and trend assessment. Dedicated bioinformatic tools were used for analysis of pathways, mutational signatures and result visualization. The results delineate UTUC-specific miRNA:mRNA networks comprising 89 miRNAs associated with 1,862 target mRNAs, involving deregulation of cell cycle, deoxyribonucleic acid (DNA) damage response, DNA repair, bladder cancer, oncogenes, tumor suppressors, chromatin structure regulators and developmental signaling pathways. Key UTUC-specific transcripts were confirmed at the protein level. Exome and transcriptome sequencing of UTUCs revealed AA-specific mutational signature SBS22, with 68% to 76% AA-specific, deleterious mutations propagated at the transcript level, a possible basis for neoantigen formation and immunotherapy targeting. We next identified a signature of UTUC-specific miRNAs consistently more abundant in the patients' urine prior to tumor resection, thereby defining biomarkers of tumor presence. The complex gene regulation programs of AAN-associated UTUC tumors involve regulatory miRNAs prospectively applicable to noninvasive urine-based screening of AAN patients for cancer presence and recurrence.
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Affiliation(s)
- Sandra Karanović
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center ZagrebSchool of Medicine, University of ZagrebZagrebCroatia
| | - Maude Ardin
- Epigenomics and Mechanisms BranchInternational Agency for Research on Cancer, WHOLyonFrance
| | - Zuojian Tang
- Institute for Systems GeneticsNew York University Langone Medical CenterNew YorkNew YorkUSA
- Present address:
Boehringer Ingelheim Pharmaceuticals, Inc.RidgefieldCTUSA
| | - Karla Tomić
- Department of PathologyGeneral Hospital Dr. Josip BenčevićSlavonski BrodCroatia
- Present address:
Department of PathologyÅlesund Hospital, Møre and Romsdal Health TrustÅlesundNorway
| | - Stephanie Villar
- Epigenomics and Mechanisms BranchInternational Agency for Research on Cancer, WHOLyonFrance
| | - Claire Renard
- Epigenomics and Mechanisms BranchInternational Agency for Research on Cancer, WHOLyonFrance
| | - Elisa Venturini
- Office for Collaborative ScienceNew York University Langone Medical CenterNew YorkNew YorkUSA
- Present address:
Natera, Inc.San CarlosCAUSA
| | - Adam H. Lorch
- Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Daniel S. Lee
- Office for Collaborative ScienceNew York University Langone Medical CenterNew YorkNew YorkUSA
| | - Želimir Stipančić
- Department for Dialysis OdžakCounty Hospital OrašjeOdžakBosnia and Herzegovina
| | - Neda Slade
- Division of Molecular MedicineInstitute Ruđer BoškovićZagrebCroatia
| | - Ivana Vuković Brinar
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center ZagrebSchool of Medicine, University of ZagrebZagrebCroatia
| | - Damir Dittrich
- Department of UrologyGeneral Hospital Dr. Josip BenčevićSlavonski BrodCroatia
| | - Krešimir Karlović
- Department of UrologyGeneral Hospital Dr. Josip BenčevićSlavonski BrodCroatia
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical ResearchUniversity Hospital Center Zagreb, School of Medicine, University of ZagrebZagrebCroatia
| | - Kathleen G. Dickman
- Department of MedicineStony Brook UniversityStony BrookNew YorkUSA
- Department of Medicine/NephrologyStony Brook UniversityStony BrookNew YorkUSA
| | - Magali Olivier
- Epigenomics and Mechanisms BranchInternational Agency for Research on Cancer, WHOLyonFrance
| | | | - Bojan Jelaković
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center ZagrebSchool of Medicine, University of ZagrebZagrebCroatia
| | - Jiri Zavadil
- Epigenomics and Mechanisms BranchInternational Agency for Research on Cancer, WHOLyonFrance
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Ibrahim IH, Abd El-Aziz HG, Amer NNL, Abd El-Sameea HS. Mutational pattern of PIK3CA exon 20 in circulating DNA in breast cancer. Saudi J Biol Sci 2022; 29:2828-2835. [PMID: 35531214 PMCID: PMC9073026 DOI: 10.1016/j.sjbs.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is one of the most common cancers with diverse mutations, etiology and causes. Mutational signature of the driver genes could allow for better understanding disease etiology and progression. This study aims to assess PIK3CA Exon 20 somatic mutational signature in relation to potential underlying etiology. Circulating DNA of 71 Egyptian BC patients was isolated, amplified for PIK3CA Exon 20, and sequenced. Mutational signature was determined according to COSMIC v2 signature. Public BC dataset was analysed to assess PIK3CA mutations effect on the transcriptomic profile. Somatic mutations of PIK3CA exon 20 were found in 66.2% of the study cohort. Nucleotide substitution patterns were similar to general nucleotide substitution patterns in BC. Signature 3 and 9 were the most common signatures in the studied BC patients. Signature of Aristolochic acid exposure was found in some cases. The most common nucleotide substitution was T > A transversion, but substitutions T > G and T > C were correlated to each other and to the total mutation number. PIK3CA mutations were found to disrupt several pathways including RAC1, PDGF, Wnt, and integrin signalling. PIK3CA exon 20 mutational signatures in Egyptian BC patients could suggest a disease etiology involving homologous recombination deficiency (HRD) and polymerase eta (Pol η). Nucleotide substitution patterns could indicate the role of exposure to oxidative stress and some carcinogens such as 4-aminobiphenyl and Aristolochic acid.
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Kang M, Na HY, Ahn S, Kim JW, Lee S, Ahn S, Lee JH, Youk J, Kim HT, Kim KJ, Suh KJ, Lee JS, Kim SH, Kim JW, Kim YJ, Lee KW, Yoon YS, Kim JH, Chung JH, Han HS, Lee JS. Gallbladder adenocarcinomas undergo subclonal diversification and selection from precancerous lesions to metastatic tumors. eLife 2022; 11:78636. [PMID: 36476508 PMCID: PMC9771369 DOI: 10.7554/elife.78636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
We aimed to elucidate the evolutionary trajectories of gallbladder adenocarcinoma (GBAC) using multi-regional and longitudinal tumor samples. Using whole-exome sequencing data, we constructed phylogenetic trees in each patient and analyzed mutational signatures. A total of 11 patients including 2 rapid autopsy cases were enrolled. The most frequently altered gene in primary tumors was ERBB2 and TP53 (54.5%), followed by FBXW7 (27.3%). Most mutations in frequently altered genes in primary tumors were detectable in concurrent precancerous lesions (biliary intraepithelial neoplasia [BilIN]), but a substantial proportion was subclonal. Subclonal diversity was common in BilIN (n=4). However, among subclones in BilIN, a certain subclone commonly shrank in concurrent primary tumors. In addition, selected subclones underwent linear and branching evolution, maintaining subclonal diversity. Combined analysis with metastatic tumors (n=11) identified branching evolution in nine patients (81.8%). Of these, eight patients (88.9%) had a total of 11 subclones expanded at least sevenfold during metastasis. These subclones harbored putative metastasis-driving mutations in cancer-related genes such as SMAD4, ROBO1, and DICER1. In mutational signature analysis, six mutational signatures were identified: 1, 3, 7, 13, 22, and 24 (cosine similarity >0.9). Signatures 1 (age) and 13 (APOBEC) decreased during metastasis while signatures 22 (aristolochic acid) and 24 (aflatoxin) were relatively highlighted. Subclonal diversity arose early in precancerous lesions and clonal selection was a common event during malignant transformation in GBAC. However, selected cancer clones continued to evolve and thus maintained subclonal diversity in metastatic tumors.
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Affiliation(s)
- Minsu Kang
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Hee Young Na
- Department of Pathology, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Soomin Ahn
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of MedicineSeoulRepublic of Korea
| | - Ji-Won Kim
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea,Genealogy IncSeoulRepublic of Korea
| | - Sejoon Lee
- Center for Precision Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Soyeon Ahn
- Medical Research Collaboration Center, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Ju Hyun Lee
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jeonghwan Youk
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Haesook T Kim
- Department of Data Science, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Kui-Jin Kim
- Biomedical Research Institute, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Koung Jin Suh
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jun Suh Lee
- Department of Surgery, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Se Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jin Won Kim
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Yu Jung Kim
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Keun-Wook Lee
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Yoo-Seok Yoon
- Department of Surgery, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jin-Haeng Chung
- Department of Pathology, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Ho-Seong Han
- Department of Surgery, Seoul National University Bundang HospitalSeongnamRepublic of Korea
| | - Jong Seok Lee
- Department of Internal Medicine, Seoul National University Bundang HospitalSeongnamRepublic of Korea
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Liu S, Xian Z, Zhao Y, Wang L, Tian J, Pan C, Han J, Zhang Y, Li C, Yi Y, Liu C, Wang D, Meng J, Qin S, Wang F, Liang A. Quantitative Determination and Toxicity Evaluation of Aristolochic Acid Analogues in Asarum heterotropoides F. Schmidt (Xixin) and Traditional Chinese Patent Medicines. Front Pharmacol 2021; 12:761593. [PMID: 34899315 PMCID: PMC8662950 DOI: 10.3389/fphar.2021.761593] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022] Open
Abstract
Asarum (Xixin), which contains analogues of aristolochic acid (AA), is the only species of the genus Aristolochia included in the Chinese Pharmacopoeia 2020. However, the contents and nephrotoxic effects of AA analogs in Asarum (Xixin) and its formulations have not been clarified. An automatic, effective solid phase extraction process and UPLC-MS/MS method were established for the pretreatment and quantitative detection of AA analogues in commercially available traditional Chinese patent medicines. The cytotoxicity and DNA damage induced by five analogues of AA were evaluated by CCK8 using human kidney cells (HK-2) and comet assays. HPLC was used to detect the analogues of AA in Asarum heterotropoides F. Schmidt (Xixin). The results showed that the contents of AA I, AA II, and AA IIIa were below the detection limit, while AA IVa and AL I presented relatively high contents of Asarum heterotropoides F. Schmidt (Xixin), within the range of 66.50–121.03 μg/g and 19.73–43.75 μg/g, respectively. The levels of AA analogues were in the nanogram-per-gram level in the main traditional Chinese patent medicines. AA I and AL I exhibited relatively high cytotoxicity at 48 h in CCK8 assays, while AA II, AA IIIa, and AA IVa showed weak cytotoxicity even at 800–1,000 μM. AA I induced significant pathological alterations and direct DNA damage at 40 mg/kg and 20 mg/kg, respectively. No distinct nephrotoxicity or hepatotoxicity was observed in mice treated with AA II, AA IIIa, AA IVa, or AL I at 40 mg/kg in this study. Consumption of Asarum heterotropoides F. Schmidt (Xixin) with controlled doses and periods is relatively safe as the contents of AA analogues in Asarum heterotropoides F. Schmidt (Xixin) and its formulations were far below those causing acute toxicity in this study. But, the long-term toxicity of Asarum heterotropoides F. Schmidt (Xixin) still needs further study.
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Affiliation(s)
- Suyan Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhong Xian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yong Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lianmei Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingzhuo Tian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chen Pan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiayin Han
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yushi Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunying Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yan Yi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chenyue Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dunfang Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shasha Qin
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fang Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Aihua Liang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, State Key Laboratory of Innovative Natural Medicine and TCM Injections, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Mealey NE, O’Sullivan DE, Peters CE, Heng DYC, Brenner DR. Mutational signatures among young-onset testicular cancers. BMC Med Genomics 2021; 14:280. [PMID: 34819066 PMCID: PMC8611954 DOI: 10.1186/s12920-021-01121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Incidence of testicular cancer is highest among young adults and has been increasing dramatically for men born since 1945. This study aimed to elucidate the factors driving this trend by investigating differences in mutational signatures by age of onset. METHODS We retrieved somatic variant and clinical data pertaining to 135 testicular tumors from The Cancer Genome Atlas. We compared mutational load, prevalence of specific mutated genes, mutation types, and mutational signatures between age of onset groups (< 30 years, 30-39 years, ≥ 40 years) after adjusting for subtype. A recursively partitioned mixture model was utilized to characterize combinations of signatures among the young-onset cases. RESULTS Mutational load was significantly higher among older-onset tumors (p < 0.05). There were no highly prevalent driver mutations among young-onset tumors. Mutated genes and types of nucleotide mutations were not significantly different by age group (p > 0.05). Signatures 1, 8 and 29 were more common among young-onset tumors, while signatures 11 and 16 had higher prevalence among older-onset tumors (p < 0.05). Among young-onset tumors, clustering of signatures resulted in four distinct tumor classes. CONCLUSIONS Signature contributions differ by age with signatures 1, 8 and 29 were more common among younger-onset tumors. While these signatures are connected with endogenous deamination of 5-methylcytosine, late replication errors and chewing tobacco, respectively, additional research is needed to further elucidate the etiology of young-onset testicular cancer. Large studies of mutational signatures among young-onset patients are required to understand epidemiologic trends as well as inform targeted prevention and treatment strategies.
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Affiliation(s)
- Nicole E. Mealey
- Department of Oncology, Cumming School of Medicine, University of Calgary, Room 382B, Heritage Medical Research Building, 3310 Hospital Drive NW, Calgary, AB T2N 4N1 Canada
| | - Dylan E. O’Sullivan
- Department of Oncology, Cumming School of Medicine, University of Calgary, Room 382B, Heritage Medical Research Building, 3310 Hospital Drive NW, Calgary, AB T2N 4N1 Canada
| | - Cheryl E. Peters
- Department of Oncology, Cumming School of Medicine, University of Calgary, Room 382B, Heritage Medical Research Building, 3310 Hospital Drive NW, Calgary, AB T2N 4N1 Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
- Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, CancerControl Alberta, Calgary, AB Canada
- CAREX Canada, Simon Fraser University, Vancouver, BC Canada
| | - Daniel Y. C. Heng
- Department of Oncology, Cumming School of Medicine, University of Calgary, Room 382B, Heritage Medical Research Building, 3310 Hospital Drive NW, Calgary, AB T2N 4N1 Canada
- Department of Internal Medicine, Medical Oncology, Alberta Health Services, Calgary, AB Canada
| | - Darren R. Brenner
- Department of Oncology, Cumming School of Medicine, University of Calgary, Room 382B, Heritage Medical Research Building, 3310 Hospital Drive NW, Calgary, AB T2N 4N1 Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
- Department of Cancer Epidemiology and Prevention Research, Alberta Health Services, CancerControl Alberta, Calgary, AB Canada
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38
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Freire TS, Mori MP, Miranda JNFA, Muta LYM, Machado FT, Moreno NC, Souza-Pinto NC. Increased H2O2 levels and p53 stabilization lead to mitochondrial dysfunction in XPC-deficient cells. Carcinogenesis 2021; 42:1380-1389. [PMID: 34447990 DOI: 10.1093/carcin/bgab079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/07/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
XPC deficiency is associated with mitochondrial dysfunction, increased mitochondrial H2O2 production and sensitivity to the Complex III inhibitor antimycin A (AA), through a yet unclear mechanism. We found an imbalanced expression of several proteins that participate in important mitochondrial function and increased expression and phosphorylation of the tumor suppressor p53 in Xeroderma pigmentosum complementation group C (XP-C) (XPC-null) cells compared with an isogenic line corrected in locus with wild-type XPC (XPC-wt). Interestingly, inhibition of p53 nuclear import reversed the overexpression of mitochondrial proteins, whereas AA treatment increased p53 expression more strongly in the XP-C cells. However, inhibition of p53 substantially increased XP-C cellular sensitivity to AA treatment, suggesting that p53 is a critical factor mediating the cellular response to mitochondrial stress. On the other hand, treatment with the antioxidant N-acetylcysteine increased glutathione concentration and decreased basal H2O2 production, p53 levels and sensitivity to AA treatment in the XPC-null back to the levels found in XPC-wt cells. Thus, the results suggest a critical role for mitochondrially generated H2O2 in the regulation of p53 expression, which in turn modulates XP-C sensitivity to agents that cause mitochondrial stress.
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Affiliation(s)
- T S Freire
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - M P Mori
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - J N F A Miranda
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - L Y M Muta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - F T Machado
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - N C Moreno
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
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39
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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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Bárta F, Dedíková A, Bebová M, Dušková Š, Mráz J, Schmeiser HH, Arlt VM, Hodek P, Stiborová M. Co-Exposure to Aristolochic Acids I and II Increases DNA Adduct Formation Responsible for Aristolochic Acid I-Mediated Carcinogenicity in Rats. Int J Mol Sci 2021; 22:ijms221910479. [PMID: 34638820 PMCID: PMC8509051 DOI: 10.3390/ijms221910479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
The plant extract aristolochic acid (AA), containing aristolochic acids I (AAI) and II (AAII) as major components, causes aristolochic acid nephropathy (AAN) and Balkan endemic nephropathy (BEN), unique renal diseases associated with upper urothelial cancer. Recently (Chemical Research in Toxicology 33(11), 2804–2818, 2020), we showed that the in vivo metabolism of AAI and AAII in Wistar rats is influenced by their co-exposure (i.e., AAI/AAII mixture). Using the same rat model, we investigated how exposure to the AAI/AAII mixture can influence AAI and AAII DNA adduct formation (i.e., AA-mediated genotoxicity). Using 32P-postlabelling, we found that AA-DNA adduct formation was increased in the livers and kidneys of rats treated with AAI/AAII mixture compared to rats treated with AAI or AAII alone. Measuring the activity of enzymes involved in AA metabolism, we showed that enhanced AA-DNA adduct formation might be caused partially by both decreased AAI detoxification as a result of hepatic CYP2C11 inhibition during treatment with AAI/AAII mixture and by hepatic or renal NQO1 induction, the key enzyme predominantly activating AA to DNA adducts. Moreover, our results indicate that AAII might act as an inhibitor of AAI detoxification in vivo. Consequently, higher amounts of AAI might remain in liver and kidney tissues, which can be reductively activated, resulting in enhanced AAI DNA adduct formation. Collectively, these results indicate that AAII present in the plant extract AA enhances the genotoxic properties of AAI (i.e., AAI DNA adduct formation). As patients suffering from AAN and BEN are always exposed to the plant extract (i.e., AAI/AAII mixture), our findings are crucial to better understanding host factors critical for AAN- and BEN-associated urothelial malignancy.
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Affiliation(s)
- František Bárta
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic; (F.B.); (A.D.); (M.B.); (P.H.); (M.S.)
| | - Alena Dedíková
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic; (F.B.); (A.D.); (M.B.); (P.H.); (M.S.)
| | - Michaela Bebová
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic; (F.B.); (A.D.); (M.B.); (P.H.); (M.S.)
| | - Šárka Dušková
- Centre of Occupational Health, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic; (Š.D.); (J.M.)
| | - Jaroslav Mráz
- Centre of Occupational Health, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic; (Š.D.); (J.M.)
| | - Heinz H. Schmeiser
- Division of Radiopharmaceutical Chemistry, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Volker M. Arlt
- Department of Analytical, Environmental and Forensic Sciences Division, King’s College London, 150 Stamford Street, London SE1 9NH, UK
- Toxicology Department, GAB Consulting GmbH, Heinrich-Fuchs-Str. 96, 69126 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-432018-0
| | - Petr Hodek
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic; (F.B.); (A.D.); (M.B.); (P.H.); (M.S.)
| | - Marie Stiborová
- Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, 128 40 Prague 2, Czech Republic; (F.B.); (A.D.); (M.B.); (P.H.); (M.S.)
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Guan B, Liang Y, Lu H, Xu Z, Shi Y, Li J, Kong W, Tian C, Tan Y, Gong Y, Liu J, Fang D, Shen Q, He S, Shakeel M, Zhang Z, He Q, Li X, Ci W, Zhou L. Copy Number Signatures and Clinical Outcomes in Upper Tract Urothelial Carcinoma. Front Cell Dev Biol 2021; 9:713499. [PMID: 34513842 PMCID: PMC8427613 DOI: 10.3389/fcell.2021.713499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/02/2021] [Indexed: 11/15/2022] Open
Abstract
Tumor staging of upper tract urothelial carcinomas (UTUCs) is relatively difficult to assert accurately before surgery. Here, we used copy number (CN) signatures as a tool to explore their clinical significance of molecular stratification in UTUC. CN signatures were extracted by non-negative matrix factorization from the whole-genome sequencing (WGS) data of 90 Chinese UTUC primary tumor samples. A validation UTUC cohort (n = 56) and a cohort from urinary cell-free DNA (cfDNA) of urothelial cancer patients (n = 94) and matched primary tumors were also examined. Survival analyses were measured using the Kaplan–Meier, and Cox regression was used for multivariate analysis. Here, we identified six CN signatures (Sig1–6). Patients with a high contribution of Sig6 (Sig6high) were associated with higher microsatellite instability level and papillary architecture and had a favorable outcome. Patients with a low weighted genome integrity index were associated with positive lymph node and showed the worst outcome. Sig6high was identified to be an independently prognostic factor. The predictive significance of CN signature was identified by a validation UTUC cohort. CN signatures retained great concordance between primary tumor and urinary cfDNA. In conclusion, our results reveal that CN signature assessment for risk stratification is feasible and provides a basis for clinical studies that evaluate therapeutic interventions and prognosis.
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Affiliation(s)
- Bao Guan
- Department of Urology, Peking University First Hospital, Beijing, China.,Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Yuan Liang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Huan Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengzheng Xu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yue Shi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Juan Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenwen Kong
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuanyu Tian
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yezhen Tan
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Jin Liu
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Dong Fang
- Department of Urology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Qi Shen
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Muhammad Shakeel
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Jamil-ur-Rahman Center for Genome Research, PCMD, ICCBS, University of Karachi, Karachi, Pakistan
| | - Zhongyuan Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Qun He
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
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Xu T, Chen W, Zhou J, Dai J, Li Y, Zhao Y. Computational Analysis of Naturally Occurring Aristolochic Acid Analogues and Their Biological Sources. Biomolecules 2021; 11:1344. [PMID: 34572557 PMCID: PMC8471445 DOI: 10.3390/biom11091344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Aristolochic acids are known for nephrotoxicity, and implicated in multiple cancer types such as hepatocellular carcinomas demonstrated by recent studies. Natural products that are analogues to aristolochic acids have been constantly isolated from organisms; a larger chemical space of these compounds and a wider coverage of biological sources should be determined in consideration of the potential hazard of aristolochic acid analogues and the wide distribution of their biological sources in the nature. Therefore, we carried out an in silico research of naturally occurring aristolochic acid analogues and their biological sources, as a supplement to existing studies. The result shows a chemical space of 238 naturally occurring aristolochic acid analogues that are present in 175 species of biological sources including 44 traditional medicines. With the computational estimation for toxicity and the implication in hazard assessment of a biological source with the presence of aristolochic acid analogues, we propose that additional awareness should be raised to the public for avoidance of toxic species, especially those that are used as herbal medicines and easily accessible.
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Affiliation(s)
- Tingjun Xu
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China; (W.C.); (J.Z.); (J.D.); (Y.L.); (Y.Z.)
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Thouvenin J, Martínez Chanzá N, Alhalabi O, Lang H, Tannir NM, Barthélémy P, Malouf GG. Efficacy of Immune Checkpoint Inhibitors in Upper Tract Urothelial Carcinomas: Current Knowledge and Future Directions. Cancers (Basel) 2021; 13:4341. [PMID: 34503152 DOI: 10.3390/cancers13174341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Upper tract urothelial carcinoma (UTUC) represents a rare and aggressive malignancy arising from the renal pelvis or ureter. It can develop sporadically or have a hereditary origin, such as Lynch syndrome, caused by DNA mismatch repair deficiency, leading to microsatellite instability phenotype. According to molecular characterization studies, UTUC presents different mutational profiles as compared to urinary bladder urothelial carcinomas. In particular, it has been reported that UTUC harbored a higher level of FGFR3 alterations associated with a T-cell depleted immune microenvironment. The therapeutic landscape in urothelial carcinoma is rapidly evolving, with immune checkpoint inhibitors forming part of the standard of care. A greater understanding of the molecular alterations and immune microenvironment leads to the development of new treatment combinations and targeted therapy. This review summarizes the available evidence concerning the use of immune checkpoint inhibitors and the biological rationale underlying their use in high-grade UTUC.
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Bellamri M, Brandt K, Brown CV, Wu MT, Turesky RJ. Cytotoxicity and genotoxicity of the carcinogen aristolochic acid I (AA-I) in human bladder RT4 cells. Arch Toxicol 2021; 95:2189-2199. [PMID: 33938965 DOI: 10.1007/s00204-021-03059-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022]
Abstract
Aristolochic acid (AA-I) induces upper urothelial tract cancer (UUTC) and bladder cancer (BC) in humans. AA-I forms the 7-(2'-deoxyadenosin-N6-yl)aristolactam I (dA-AL-I) adduct, which induces multiple A:T-to-T:A transversion mutations in TP53 of AA-I exposed UTUC patients. This mutation is rarely reported in TP53 of other transitional cell carcinomas and thus recognized as an AA-I mutational signature. A:T-to-T:A transversion mutations were recently detected in bladder tumors of patients in Asia with known AA-I-exposure, implying that AA-I contributes to BC. Mechanistic studies on AA-I genotoxicity have not been reported in human bladder. In this study, we examined AA-I DNA adduct formation and mechanisms of toxicity in the human RT4 bladder cell line. The biological potencies of AA-I were compared to 4-aminobiphenyl, a recognized human bladder carcinogen, and several structurally related carcinogenic heterocyclic aromatic amines (HAA), which are present in urine of smokers and omnivores. AA-I (0.05-10 µM) induced a concentration- and time-dependent cytotoxicity. AA-I (100 nM) DNA adduct formation occurred at over a thousand higher levels than the principal DNA adducts formed with 4-ABP or HAAs (1 µM). dA-AL-I adduct formation was detected down to a 1 nM concentration. Studies with selective chemical inhibitors provided evidence that NQO1 is the major enzyme involved in AA-I bio-activation in RT4 cells, whereas CYP1A1, another enzyme implicated in AA-I toxicity, had a lesser role in bio-activation or detoxification of AA-I. AA-I DNA damage also induced genotoxic stress leading to p53-dependent apoptosis. These biochemical data support the human mutation data and a role for AA-I in BC.
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Affiliation(s)
- Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA
| | - Kyle Brandt
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA
| | - Christina V Brown
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA
| | - Ming-Tsang Wu
- Department of Environmental and Occupational Medicine, Kaohsiung Medical University, CS Building, 100 Shih-Chuan 1st Road, Kaohsiung, Taiwan
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, MN, 55455, USA.
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Cao L, Liu H, Xie W, Jiao S, Wu X, Yuan K, Zhou X, Yang M, Guan Y, Cai H, Lai Z, Chen J, Zhou H. Real-time monitoring of aristolochic acid I reduction process using surface-enhanced Raman Spectroscopy with DFT simulation. Biosens Bioelectron 2021; 179:113061. [DOI: 10.1016/j.bios.2021.113061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
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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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Kang YC, Chen MH, Lin CY, Lin CY, Chen YT. Aristolochic acid-associated urinary tract cancers: an updated meta-analysis of risk and oncologic outcomes after surgery and systematic review of molecular alterations observed in human studies. Ther Adv Drug Saf 2021; 12:2042098621997727. [PMID: 33815744 PMCID: PMC7989132 DOI: 10.1177/2042098621997727] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/03/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The risk of primary aristolochic acid (AA)-associated urothelial carcinoma (AA-UC) has been summarized by a 2013-published meta-analysis. Given that additional evidence has been continuously reported by original studies, an updated meta-analysis is needed. Meanwhile, to complete the whole picture, a systematic review of molecular alterations observed in AA-urinary tract cancers (AA-UTC) was also performed. METHODS We searched PubMed, Embase and four Chinese databases up to October 2020. Observational studies comparing risk or oncologic outcomes of UTC between patients with and without AA exposure were eligible for systematic review and meta-analysis. Studies investigating molecular alterations in AA-UTC using human tissue samples were eligible for systematic review. RESULTS In total, 38 and 20 studies were included in the systematic review and meta-analysis, respectively. Exposure to AA led to an overall increased risks of primary UTC [UC and renal cell carcinoma (RCC)] (OR 6.085, 95% CI 3.045-12.160) and postoperatively recurrent UC (RR 1.831, 95% CI 1.528-2.194). Subgroup analysis of postoperative primary AA-upper tract UC (AA-UTUC) showed increased risks of bladder recurrence (adjusted RR 1.949, 95% CI 1.462-2.597) and contralateral UTUC recurrence (crude RR 3.760, 95% CI 2.225-6.353), worse overall survival (adjusted HR 2.025, 95% CI 1.432-2.865) and worse disease-specific survival (adjusted HR 3.061, 95% CI 1.190-7.872), but no effect on cancer-specific survival (adjusted HR 0.772, 95% CI 0.269-2.215). High mutation load with AA mutational signature presenting largely in the putative driver genes was observed in AA-UTUC. In contrast, AA mutational signature is rarely found in the mutated RCC driver genes and the mutation load in AA-RCC is low. Therefore, AA has different roles in the genesis of UTUC and RCC. CONCLUSIONS Implementing effective strategies to completely protect people from exposure to AA is urgently needed. Additionally, more effort should be made in identifying the precise carcinogenic mechanisms of AA to determine the future treatment strategies. PLAIN LANGUAGE SUMMARY Risk, recurrence and survival outcomes after surgery and molecular changes possibly involved in the genesis of aristolochic acid-associated urinary tract cancers Background: The association between aristolochic acid (AA) and primary urothelial carcinoma (UC) has been summarized by a 2013-published meta-analysis. Given that additional evidence has been reported in the past 7 years, an updated meta-analysis is needed. Meanwhile, to complete the whole picture, a systematic review of molecular changes possibly involved in AA-mediated urinary tract carcinogenesis was also performed. Methods: We searched PubMed, Embase and four Chinese databases for human studies up to October 2020. Studies comparing the risk of urinary tract cancer (UTC) between patients with and without AA exposure and studies investigating the molecular changes in AA-associated UTC (AA-UTC) using human tissue samples were eligible for inclusion. Thirty-eight studies were finally included. Results: The results showed that exposure to AA was associated with a 6-fold increased risk of primary UTC (UC and renal cell carcinoma, RCC) and a 1.8-fold increased risk of postoperatively recurrent UC. After studies reporting primary AA-upper tract UC (AA-UTUC) were analyzed, a 1.9-fold increased risk of bladder recurrence and a 3.8-fold increased risk of contralateral UTUC recurrence was observed. Additionally, exposure to AA worsened the postoperative survival of patients with UTUC by a 2-fold increased risk of overall death and a 3-fold increased risk of death from other diseases and recurrences. However, there was no effect on death due to cancer. Lastly, AA seemed to play different roles in the etiology of UTUC and RCC based on the observations of different mutation loads and different distributions of AA-induced mutations in AA-UTUC and AA-RCC samples. Conclusions: Implementing effective strategies to completely protect people from exposure to AA is urgently needed. Moreover, more effort should be made in identifying the precise carcinogenic mechanisms of AA-UTC to determine the future treatment strategies.
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Affiliation(s)
- Yu-Chan Kang
- Department of Pharmacy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | - Ming-Hong Chen
- Department of Pharmacy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | - Chung-Ying Lin
- Institute of Allied Health Sciences, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan
| | - Chih-Yun Lin
- Biostatistics Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung
| | - Yen-Ta Chen
- Division of Urology, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, College of Medicine, Kaohsiung, No.123, Ta-Pei Road, Niao-Sung District, Kaohsiung City 83301
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De Lorenzis E, Albo G, Longo F, Bebi C, Boeri L, Montanari E. Current Knowledge on Genomic Profiling of Upper Tract Urothelial Carcinoma. Genes (Basel) 2021; 12:genes12030333. [PMID: 33668859 PMCID: PMC7996334 DOI: 10.3390/genes12030333] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Recent research in next-generation sequencing characterized the genomic landscape of urothelial cancer. However, the majority of the studies focused on bladder cancer (BC). Upper urinary tract urothelial carcinomas (UTUC) and BC share some histological characteristics, but, considering the differences in terms of embryologic precursors, epidemiology, genetics, medical and surgical management and response to therapy, UTUC and BC should be considered as two distinct diseases. Our objective is to analyze through a literature search the latest updates and the current knowledge about the genomics of UTUC. We also evaluate genetic differences between BC and UTUC and the potential implications for systemic therapy. Molecular subtyping and variant histology and their correlation with response to chemotherapy were also explored. In summary, the most frequent genomic variations in UTUC included FGFR3, chromatin remodeling genes, TP53/MDM2 and other tumor suppressors/oncogenes. The genomics of UTUC, integrated with clinical data, could drive the selection of patients who could benefit from targeted therapy or off-label treatment. Routine implementation of tumor genomic characterization in UTUC patients should therefore be contemplated and evaluated prospectively.
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Affiliation(s)
- Elisa De Lorenzis
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Correspondence: ; Tel.: +39-02-55034546; Fax: +39-02-50320584
| | - Giancarlo Albo
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Fabrizio Longo
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
| | - Carolina Bebi
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
- University of Milan, 20122 Milan, Italy
| | - Luca Boeri
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
- University of Milan, 20122 Milan, Italy
| | - Emanuele Montanari
- Urology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (G.A.); (F.L.); (C.B.); (L.B.); (E.M.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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Afsari B, Kuo A, Zhang Y, Li L, Lahouel K, Danilova L, Favorov A, Rosenquist TA, Grollman AP, Kinzler KW, Cope L, Vogelstein B, Tomasetti C. Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer. eLife 2021; 10:61082. [PMID: 33491650 PMCID: PMC7872524 DOI: 10.7554/elife.61082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Determining the etiologic basis of the mutations that are responsible for cancer is one of the fundamental challenges in modern cancer research. Different mutational processes induce different types of DNA mutations, providing 'mutational signatures' that have led to key insights into cancer etiology. The most widely used signatures for assessing genomic data are based on unsupervised patterns that are then retrospectively correlated with certain features of cancer. We show here that supervised machine-learning techniques can identify signatures, called SuperSigs, that are more predictive than those currently available. Surprisingly, we found that aging yields different SuperSigs in different tissues, and the same is true for environmental exposures. We were able to discover SuperSigs associated with obesity, the most important lifestyle factor contributing to cancer in Western populations.
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Affiliation(s)
- Bahman Afsari
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - YiFan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Lu Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Kamel Lahouel
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | - Alexander Favorov
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | | | - Arthur P Grollman
- State University of New York at Stony Brook, Stony Brook, United States
| | - Ken W Kinzler
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Leslie Cope
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Bert Vogelstein
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
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Baiken Y, Kanayeva D, Taipakova S, Groisman R, Ishchenko AA, Begimbetova D, Matkarimov B, Saparbaev M. Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs. Front Cell Dev Biol 2021; 8:617884. [PMID: 33553154 PMCID: PMC7862338 DOI: 10.3389/fcell.2020.617884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/17/2020] [Indexed: 01/22/2023] Open
Abstract
Chemical alterations in DNA induced by genotoxic factors can have a complex nature such as bulky DNA adducts, interstrand DNA cross-links (ICLs), and clustered DNA lesions (including double-strand breaks, DSB). Complex DNA damage (CDD) has a complex character/structure as compared to singular lesions like randomly distributed abasic sites, deaminated, alkylated, and oxidized DNA bases. CDD is thought to be critical since they are more challenging to repair than singular lesions. Although CDD naturally constitutes a relatively minor fraction of the overall DNA damage induced by free radicals, DNA cross-linking agents, and ionizing radiation, if left unrepaired, these lesions cause a number of serious consequences, such as gross chromosomal rearrangements and genome instability. If not tightly controlled, the repair of ICLs and clustered bi-stranded oxidized bases via DNA excision repair will either inhibit initial steps of repair or produce persistent chromosomal breaks and consequently be lethal for the cells. Biochemical and genetic evidences indicate that the removal of CDD requires concurrent involvement of a number of distinct DNA repair pathways including poly(ADP-ribose) polymerase (PARP)-mediated DNA strand break repair, base excision repair (BER), nucleotide incision repair (NIR), global genome and transcription coupled nucleotide excision repair (GG-NER and TC-NER, respectively), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ), and translesion DNA synthesis (TLS) pathways. In this review, we describe the role of DNA glycosylase-mediated BER pathway in the removal of complex DNA lesions.
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Affiliation(s)
- Yeldar Baiken
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Damira Kanayeva
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Regina Groisman
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Alexander A Ishchenko
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Dinara Begimbetova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Bakhyt Matkarimov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
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