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Klusek J, Lewitowicz P, Oblap R, Orlewska E, Witczak B, Marzec MT, Kozłowska-Geller M, Nawacki Ł, Wawszczak-Kasza M, Kocańda K, Jóźwik A, Głuszek S. NOS2 Polymorphism in Aspect of Left and Right-Sided Colorectal Cancer. J Clin Med 2024; 13:937. [PMID: 38398251 PMCID: PMC10888565 DOI: 10.3390/jcm13040937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Background: The NOS2 gene polymorphism rs2297518 is associated with an increased level of NO, which could contribute to colorectal cancer (CRC) development. We hypothesized that the potential influence of the NOS2 gene polymorphism on cancer development may vary between right-sided and left-sided colon cancers, and rectal cancers. The aim of this study was to determine the rs2297518 polymorphism influence on colorectal cancer development with regard to tumor localization. Methods: This case-control study included 199 patients with CRC and 120 controls. The qPCR endpoint genotyping was conducted using the TaqMan® genotyping assay. Results: This study revealed significant differences in tumor characteristic and in the minor alelle A frequency in the NOS2 genotype between colorectal cancers with different localizations. The mucinous adenocarcinoma was diagnosed significantly more often in right-sided cancers than in left-sided (30.6% vs. 10.9%, p = 0.009) and rectal cancers (30.6% vs. 7.1%, p = 0.0003). The minor allele A of the NOS2 genotype was observed more frequently in right-sided cancers than in left-sided cancers (44.9% vs. 23.1%, p = 0.0137) and more frequently in rectal cancers than in left-sided cancers (40.0% vs. 23.1%, p = 0.0285). Conclusions: In conclusion, the results support the hypothesis that the SNP rs2297518 of the NOS2 gene influences colorectal cancer development with regard to tumor localization.
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Affiliation(s)
- Justyna Klusek
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Piotr Lewitowicz
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Ruslan Oblap
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Ewa Orlewska
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Bartosz Witczak
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
- Holy Cross Mother and Newborn Provincional Centre, 25-371 Kielce, Poland
| | - Michał Tomasz Marzec
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Monika Kozłowska-Geller
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Łukasz Nawacki
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Monika Wawszczak-Kasza
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Kamila Kocańda
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
| | - Artur Jóźwik
- Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland;
| | - Stanisław Głuszek
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland; (P.L.); (R.O.); (E.O.); (B.W.); (M.K.-G.); (Ł.N.); (M.W.-K.); (K.K.); (S.G.)
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Jeremian R, Xie P, Fotovati M, Lefrançois P, Litvinov IV. Gene-Environment Analyses in a UK Biobank Skin Cancer Cohort Identifies Important SNPs in DNA Repair Genes That May Help Prognosticate Disease Risk. Cancer Epidemiol Biomarkers Prev 2023; 32:1599-1607. [PMID: 37642678 PMCID: PMC10840669 DOI: 10.1158/1055-9965.epi-23-0545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/12/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Despite well-established relationships between sun exposure and skin cancer pathogenesis/progression, specific gene-environment interactions in at-risk individuals remain poorly-understood. METHODS We leveraged a UK Biobank cohort of basal cell carcinoma (BCC, n = 17,221), cutaneous squamous cell carcinoma (cSCC, n = 2,331), melanoma in situ (M-is, n = 1,158), invasive melanoma (M-inv, n = 3,798), and healthy controls (n = 448,164) to quantify the synergistic involvement of genetic and environmental factors influencing disease risk. We surveyed 8,798 SNPs from 190 DNA repair genes, and 11 demographic/behavioral risk factors. RESULTS Clinical analysis identified darker skin (RR = 0.01-0.65) and hair (RR = 0.27-0.63) colors as protective factors. Eleven SNPs were significantly associated with BCC, three of which were also associated with M-inv. Gene-environment analysis yielded 201 SNP-environment interactions across 90 genes (FDR-adjusted q < 0.05). SNPs from the FANCA gene showed interactions with at least one clinical factor in all cancer groups, of which three (rs9926296, rs3743860, rs2376883) showed interaction with nearly every factor in BCC and M-inv. CONCLUSIONS We identified novel risk factors for keratinocyte carcinomas and melanoma, highlighted the prognostic value of several FANCA alleles among individuals with a history of sunlamp use and childhood sunburns, and demonstrated the importance of combining genetic and clinical data in disease risk stratification. IMPACT This study revealed genome-wide associations with important implications for understanding skin cancer risk in the context of the rapidly-evolving field of precision medicine. Major individual factors (including sex, hair and skin color, and sun protection use) were significant mediators for all skin cancers, interacting with >200 SNPs across four skin cancer types.
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Affiliation(s)
- Richie Jeremian
- Faculty of Medicine and Health Sciences, McGill University
- Department of Medicine, Division of Dermatology, Research Institute of the McGill University Health Centre (RI-MUHC) Montreal, Quebec
| | - Pingxing Xie
- Faculty of Medicine and Health Sciences, McGill University
- Department of Medicine, Division of Dermatology, Research Institute of the McGill University Health Centre (RI-MUHC) Montreal, Quebec
| | - Misha Fotovati
- Faculty of Medicine and Health Sciences, McGill University
- Department of Medicine, Division of Dermatology, Lady Davis Institute (LDI), Jewish General Hospital, Montreal, Quebec
| | - Philippe Lefrançois
- Faculty of Medicine and Health Sciences, McGill University
- Department of Medicine, Division of Dermatology, Lady Davis Institute (LDI), Jewish General Hospital, Montreal, Quebec
| | - Ivan V. Litvinov
- Faculty of Medicine and Health Sciences, McGill University
- Department of Medicine, Division of Dermatology, Research Institute of the McGill University Health Centre (RI-MUHC) Montreal, Quebec
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Huang L, Xu W, Yan D, Shi X, Zhang S, Chen M, Dai L. Identification of a RAD51B enhancer variant for susceptibility and progression to glioma. Cancer Cell Int 2023; 23:246. [PMID: 37858068 PMCID: PMC10585866 DOI: 10.1186/s12935-023-03100-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND RAD51B plays a significant role in homologous recombination-mediated repair of DNA double-strand breaks. Many enhancer variants are involved in cancer development and progression. However, the significance of enhancer variants of RAD51B in glioma susceptibility and progression remains unclear. METHODS A case-control study consisting of 1056 individuals was conducted to evaluate the associations of enhancer variants of RAD51B with glioma susceptibility and progression. Sequenom MassARRAY technology was used for genotyping. The function of enhancer variants was explored by biochemical assays. RESULTS A significantly decreased risk of glioma was associated with rs6573816 GC genotype compared with rs6573816 GG genotype (OR = 0.66, 95% CI 0.45-0.97; P = 0.034). Multivariable Cox regression revealed that rs6573816 was significantly associated with glioma progression in a sex-dependent manner. Worse PFS was found in the male patients with high grade glioma carrying rs6573816 GC or CC genotype (HR = 2.28, 95% CI 1.14-4.57; P = 0.020). The rs6573816 C allele repressed enhancer activity by affecting transcription factor POU2F1 binding, which resulted in lower expression of RAD51B. Remarkably attenuated expression of RAD51B was observed following POU2F1 knockdown. Consistently, positive correlation between the expression of POU2F1 and RAD51B was found in lymphoblastic cells and glioma tissues. CONCLUSIONS These results indicate that an enhancer variant of RAD51B rs6573816 influences enhancer activity by changing a POU2F1 binding site and confers susceptibility and progression to glioma.
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Affiliation(s)
- Liming Huang
- Department of Oncology, The Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, #602 Bayiqizhong Road, Fuzhou, 350004, China.
| | - Wenshen Xu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Danfang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xi Shi
- Department of Medical Oncology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Shu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Meiqin Chen
- Department of Oncology, The Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, #602 Bayiqizhong Road, Fuzhou, 350004, China
| | - Lian Dai
- Department of Medicine, The Third Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, #363 Guobin Road, Fuzhou, 350108, China.
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Tabatabaei ES, Mazloomnejad R, Rejali L, Forouzesh F, Naderi-Noukabadi F, Khanabadi B, Salehi Z, Nazemalhosseini-Mojarad E. Integrated bioinformatics and wet-lab analysis revealed cell adhesion prominent genes CDC42, TAGLN and GSN as prognostic biomarkers in colonic-polyp lesions. Sci Rep 2023; 13:10307. [PMID: 37365287 DOI: 10.1038/s41598-023-37501-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023] Open
Abstract
Colorectal cancers are derived from intestinal polyps. Normally, alterations in cell adhesion genes expression cause deviation from the normal cell cycle, leading to cancer development, progression, and invasion. The present study aimed to investigate the elusive expression pattern of CDC42, TAGLN, and GSN genes in patients with high and low-risk polyp samples, and also colorectal cancer patients and their adjacent normal tissues. In upcoming study, 40 biopsy samples from Taleghani Hospital (Tehran, Iran) were collected, consisting of 20 colon polyps and 20 paired adjacent normal tissues. The expression of the nominated genes CDC42, TAGLN, and GSN was analyzed using quantitative polymerase chain reaction (Q-PCR) and relative quantification was determined using the 2-ΔΔCt method. ROC curve analysis was performed to compare high-risk and low-risk polyps for the investigated genes. The expression of adhesion molecule genes was also evaluated using TCGA data and the correlation between adhesion molecule gene expression and immunophenotype was analyzed. The role of mi-RNAs and lncRNAs in overexpression of adhesion molecule genes was studied. Lastly, GO and KEGG were performed to identify pathways related to adhesion molecule genes expression in healthy, normal adjacent, and COAD tissues. The results showed that the expression patterns of these genes were significantly elevated in high-risk adenomas compared to low-risk polyps and normal tissues and were associated with various clinicopathological characteristics. The estimated AUC for CDC42, TAGLN, and GSN were 0.87, 0.77, and 0.80, respectively. The study also analyzed COAD cancer patient data and found that the selected gene expression in cancer patients was significantly reduced compared to high-risk polyps and healthy tissues. Survival analysis showed that while the expression level of the GSN gene had no significant relationship with survival rate, the expression of CDC42 and TAGLN genes did have a meaningful relationship, but with opposite effects, suggesting the potential use of these genes as diagnostic or prognostic markers for colorectal cancer. The present study's findings suggest that the expression pattern of CDC42, TAGLN, and GSN genes was significantly increased during the transformation of normal tissue to polyp lesions, indicating their potential as prognostic biomarkers for colorectal polyp development. Further results provide valuable insights into the potential use of these genes as diagnostic or prognostic markers for colorectal cancer. However, further studies are necessary to validate these findings in larger cohorts and to explore the underlying mechanisms of these genes in the development and progression of colorectal cancer.
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Affiliation(s)
- Elmira Sadat Tabatabaei
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
| | - Radman Mazloomnejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O. Box 19857-17413, Tehran, Iran
| | - Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O. Box 19857-17413, Tehran, Iran
| | - Flora Forouzesh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
| | - Fatemeh Naderi-Noukabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O. Box 19857-17413, Tehran, Iran
| | - Binazir Khanabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O. Box 19857-17413, Tehran, Iran
| | - Zahra Salehi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O. Box 19857-17413, Tehran, Iran.
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, P.O. Box 19857-17413, Tehran, Iran.
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Vodicka P, Vodenkova S, Horak J, Opattova A, Tomasova K, Vymetalkova V, Stetina R, Hemminki K, Vodickova L. An investigation of DNA damage and DNA repair in chemical carcinogenesis triggered by small-molecule xenobiotics and in cancer: Thirty years with the comet assay. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 885:503564. [PMID: 36669813 DOI: 10.1016/j.mrgentox.2022.503564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In the present review we addressed the determination of DNA damage induced by small-molecule carcinogens, considered their persistence in DNA and mutagenicity in in vitro and in vivo systems over a period of 30 years. The review spans from the investigation of the role of DNA damage in the cascade of chemical carcinogenesis. In the nineties, this concept evolved into the biomonitoring studies comprising multiple biomarkers that not only reflected DNA/chromosomal damage, but also the potential of the organism for biotransformation/elimination of various xenobiotics. Since first years of the new millennium, dynamic system of DNA repair and host susceptibility factors started to appear in studies and a considerable knowledge has been accumulated on carcinogens and their role in carcinogenesis. It was understood that the final biological links bridging the arising DNA damage and cancer onset remain to be elucidated. In further years the community of scientists learnt that cancer is a multifactorial disease evolving over several decades of individual´s life. Moreover, DNA damage and DNA repair are inseparable players also in treatment of malignant diseases, but affect substantially other processes, such as degeneration. Functional monitoring of DNA repair pathways and DNA damage response may cast some light on above aspects. Very little is currently known about the relationship between telomere homeostasis and DNA damage formation and repair. DNA damage/repair in genomic and mitochondrial DNA and crosstalk between these two entities emerge as a new interesting topic.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Rudolf Stetina
- Department of Research and Development, University Hospital Hradec Kralove, 500 03 Hradec Kralove, Czech Republic
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 691 20 Heidelberg, Germany
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic.
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Singh S, Singh N, Sharma S. Genetic polymorphisms in the mismatch repair pathway (MMR) genes contribute to hematological and gastrointestinal toxicity in North Indian lung cancer patients treated with platinum-based chemotherapy. J Biochem Mol Toxicol 2022; 36:e23183. [PMID: 35924411 DOI: 10.1002/jbt.23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 07/21/2022] [Indexed: 11/12/2022]
Abstract
The present study investigated the relationship between MLH1, MSH2, MSH3, and MSH6 polymorphisms and toxicity due to platinum-based doublet chemotherapy for North Indian lung cancer patients. Polymerase chain reaction-restriction fragment length polymorphism technique was used to assess the polymorphism. For MSH2 IVS1 + 9G > C polymorphism variant type genotype reported a 1.4-fold increased risk of anemia (AOR = 1.4; 95% CI = 0.98-1.99; p = 0.04) and decreased risk of developing gastrointestinal toxicity (diarrhea) (AOR = 0.53; 95% CI = 0.28-1.01; p = 0.04). Further, we also reported a 10-fold increased risk of developing severe grade anorexia in combined genotype (GC + CC) (AOR = 9.18; 95% CI = 0.98-86.1; p = 0.05). For MSH2 T > C/-6 polymorphism, variant type reported a 3-fold and 2-fold increased risk of developing severe grade leukopenia (AOR = 3.37; 95% CI = 1.44-7.88; p = 0.005) and neutropenia respectively (AOR = 2.23; 95% CI = 1.07-4.66; p = 0.03). For MSH3 G > A polymorphism, heterozygous (GA) and combined genotype (GA + AA) reported a 7-fold and 6-fold increased risk of developing anemia (AOR = 7.23; 95% CI = 1.51-34.6; p = 0.01, AOR = 6.39; 95% CI = 1.53-26.6; p = 0.01). Our results suggest that polymorphisms in DNA mismatch repair genes are associated with hematological, and gastrointestinal toxicities and might be considered a predictor for pretreatment evaluation in lung cancer patients.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, Punjab, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Sharma S, Singh S, Singh N, Baranwal M. Association of MLH1-93G>A polymorphisms toward lung cancer susceptibility and its association with clinical outcome in North Indian patients treated with platinum-based chemotherapy. J Cancer Res Ther 2022; 19:S0. [PMID: 37147951 DOI: 10.4103/jcrt.jcrt_465_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Lung cancer is one of the most prevalent and main causes of malignancy-related deaths worldwide, especially in developed countries. Epidemiological studies have demonstrated that individuals having alterations in a particular gene may have a high risk of developing certain types of cancer. Materials and Methods In the present study, 500 Indian lung cancer patients and 500 healthy controls were enrolled. Polymerase chain reaction-restriction fragment length polymorphism method was used to identify the genotype of enrolled individuals and MedCalc statistical package was used for carrying out statistical analysis. Results In this study, we found a reduced risk of developing adenocarcinoma in patients harboring variant (P = 0.0007) and combined type genotype (P = 0.008), whereas an increased risk for small-cell lung carcinoma (SCLC) development for those subject harboring GA genotypes (P = 0.03) was also observed. Further, heterozygous type and combined type genotype of heavy smokers for MLH1 polymorphism reported a 2-fold (P = 0.001) and 1.8-fold increased risk toward lung cancer development, respectively (P = 0.007). In case of females, the subjects harboring a variant allele have a significantly reduced risk for lung cancer development (P = 0.0001). For MLH1 polymorphism, reduced risk of developing tumor to T3 or T4 stage was observed (P = 0.04). Moreover, this is the first study reporting overall survival (OS) association for north Indian lung cancer patients with platinum-based doublet chemotherapy; for docetaxel, a three-fold increase in hazard ratio and corresponding low median standard survival time (8.4 months) for mutant and combined type genotype (P = 0.04) was observed. Conclusions These results suggest that MLH1-93G>A polymorphism is involved in modulating the risk toward lung cancer. Our study also concluded a negative association of OS in patients undergoing carboplatin/cisplatin and docetaxel chemotherapy.
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Boni J, Idani A, Roca C, Feliubadaló L, Tomiak E, Weber E, Foulkes WD, Orthwein A, El Haffaf Z, Lazaro C, Rivera B. A decade of RAD51C and RAD51D germline variants in cancer. Hum Mutat 2021; 43:285-298. [PMID: 34923718 DOI: 10.1002/humu.24319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/12/2022]
Abstract
Defects in DNA repair genes have been extensively associated with cancer susceptibility. Germline pathogenic variants (GPV) in genes involved in homologous recombination repair pathways predispose to cancers arising mainly in the breast and ovary, but also other tissues. The RAD51 paralogs RAD51C and RAD51D were included in this group 10 years ago when germline variants were associated with non-BRCA1/2 familial ovarian cancer. Here, we have reviewed the landscape of RAD51C and RAD51D germline variants in cancer reported in the literature during the last decade, integrating this list with variants identified by in-house patient screening. A comprehensive catalog of 341 variants that have been classified applying ACMG/AMP criteria has been generated pinpointing the existence of recurrent variants in both genes. Recurrent variants have been extensively discussed compiling data on population frequencies and functional characterization if available, highlighting variants that have not been fully characterized yet to properly establish their pathogenicity. Finally, we have complemented this data with relevant information regarding the conservation of mutated residues among RAD51 paralogs and modeling of putative hotspot areas, which contributes to generating an exhaustive update on these two cancer predisposition genes.
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Affiliation(s)
- Jacopo Boni
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Aida Idani
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Carla Roca
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Tomiak
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Evan Weber
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Quebec, Montreal, Canada
| | - William D Foulkes
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Quebec, Montreal, Canada.,Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
| | - Alexandre Orthwein
- Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
| | - Zaki El Haffaf
- Division of Genetics, Department of Medicine, Research Center, Centre Hospitalier de l'Université de Montréal (CRCHUM), Quebec, Montreal, Canada
| | - Conxi Lazaro
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
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Patterns and grades of presentation of colon cancer in Northern Saudi Arabia. PRZEGLAD GASTROENTEROLOGICZNY 2021; 16:235-239. [PMID: 34584586 PMCID: PMC8456767 DOI: 10.5114/pg.2021.104168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/30/2021] [Indexed: 11/17/2022]
Abstract
Introduction The primary concern related to colon cancer in Saudi Arabia is the presentation of many patients with advanced disease stages. Aim To determine the patterns and grades of colon cancer presentation in Northern Saudi Arabia. Material and methods Retrieved data and tissue blocks related to 50 colorectal patients from King Khalid Hospital, Hai'l province, Northern Saudi Arabia were used. The sample represented all available colorectal specimens (full coverage of cancer cases within 10 years). The retrieved data included a full histopathology report, gender, and age. All tissues were retrieved in the form of formalin-fixed paraffin wax processed blocks. The tissues were found to be obtained in the form of colonoscopy or/and biopsy. Results The diagnosed colon cancers included conventional adenocarcinoma 36 (72%), mucinous adenocarcinoma 4 (8%), carcinoma-in-situ 4 (8%), and invasive adenocarcinoma 6 (12%). Moderately differentiated and poorly differentiated stages were confirmed in 46 (92%) and 4 (8%), respectively. Conclusions Conventional adenocarcinoma is the most common presenting colon cancer at and relatively younger age. Mucinous adenocarcinoma is frequently presented in female patients of a somewhat more youthful generation. Most patients are diagnosed with moderately differentiated adenocarcinoma, followed by poorly differentiated adenocarcinoma. The findings necessitate the urgent intervention of national policies for early detection by implementing sustainable screening programs.
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10
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Apoptosis Induced by Ziziphora tenuior Essential Oil in Human Colorectal Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5522964. [PMID: 34337019 PMCID: PMC8324347 DOI: 10.1155/2021/5522964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/06/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
Ziziphora (Cacotti in Persian) belongs to the Lamiaceae family (mint group) and is vastly found in Iran and Asia. This traditional medicinal plant is normally used as analgesic and for treatment of particular gastrointestinal diseases. Since colorectal cancer is one of the most common causes of death in the world and the second leading cause of cancer death among adults, there is a pressing need to inhibit this malignancy by using methods with minimal side effects. One of these methods is the use of natural resources such as medical plants. This study is aimed at investigating the expression of apoptosis-related genes in the adjacent culture of colorectal cancer epithelial cells (HT-29) with Ziziphora essential oil (ZEO). The essential oil was extracted from Ziziphora leaves, and its compounds were determined and then added to the HT-29 culture medium at different concentrations. After 24 hours, the HT-29 cells were harvested from the medium and cytotoxicity was analyzed by MTT assay. After MTT assay and determination of the percentage of apoptosis by flow cytometry, RNA extraction was performed and the expression levels of Bax, Bcl-2, caspase 3 (C3), and caspase 9 (C9) were analyzed using newly designed primers by reverse transcription (RT) qPCR method and GeniX6 software. Also, specific antibodies were used for western blot analyses of those molecules. GC analysis revealed 42 different compounds in the ZEO, including pulegone (26.65%), menthone (5.74%), thymol (5.51%), and menthol (1.02%). MTT assay showed that the concentration of 200 μg/ml of ZEO had the highest HT-29 cell death during 24 hours. After incubation with the concentration of 50 μg/ml of ZEO for 24 and 48 hours, caspase 3 and 9 gene expressions in the treated group increased compared to those in the control group (P < 0.001), while the Bcl-2 expression decreased. The results showed that having anticancer compounds, ZEO can increase C3 and C9 and decrease Bcl-2 expressions, causing apoptosis in HT-29 cells in vitro. This can lead to the use of ZEO as a factor for colorectal cancer treatment.
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11
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Cumova A, Vymetalkova V, Opattova A, Bouskova V, Pardini B, Kopeckova K, Kozevnikovova R, Lickova K, Ambrus M, Vodickova L, Naccarati A, Soucek P, Vodicka P. Genetic variations in 3´UTRs of SMUG1 and NEIL2 genes modulate breast cancer risk, survival and therapy response. Mutagenesis 2021; 36:269-279. [PMID: 34097065 DOI: 10.1093/mutage/geab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/06/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancer (BC) is the most frequent malignancy in women accounting for approximately 2 million new cases worldwide annually. Several genetic, epigenetic and environmental factors are known to be involved in BC development and progression, including alterations in post-transcriptional gene regulation mediated by microRNAs (miRNAs). Single nucleotide polymorphisms (SNPs) located in miRNA binding sites (miRSNPs) in 3'-untranslated (UTR) regions of target genes may affect miRNA-binding affinity and consequently modulate gene expression. We have previously reported a significant association of miRSNPs in the SMUG1 and NEIL2 genes with overall survival in colorectal cancer patients. SMUG1 and NEIL2 are DNA glycosylases involved in base excision DNA repair (BER). Assuming that certain genetic traits are common for solid tumours, we have investigated wherever variations in SMUG1 and NEIL2 genes display an association with BC risk, prognosis, and therapy response in a group of 673 BC patients and 675 healthy female controls. Patients with TC genotype of NEIL2 rs6997097 and receiving only hormonal therapy displayed markedly shorter overall survival (OS) (HR=4.15, 95% CI=1.7-10.16, P= 0.002) and disease-free survival (DFS) (HR=2.56, 95% CI=1.5-5.7, P= 0.02). Our results suggest that regulation of base excision repair glycosylases operated by miRNAs may modulate the prognosis of hormonally treated BC.
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Affiliation(s)
- Andrea Cumova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Alena Opattova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Bouskova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Katerina Kopeckova
- Department of Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Katerina Lickova
- Radiotherapy and Oncology Department, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Miloslav Ambrus
- Radiotherapy and Oncology Department, Third Faculty of Medicine, Charles University and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Alessio Naccarati
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,IIGM Italian Institute for Genomic Medicine, Candiolo, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Pavel Soucek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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12
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Försti A, Hemminki K. DNA repair gene polymorphisms and chromosomal aberrations in healthy, nonsmoking population. DNA Repair (Amst) 2021; 101:103079. [PMID: 33676360 DOI: 10.1016/j.dnarep.2021.103079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Nonspecific structural chromosomal aberrations (CAs) can be found at around 1% of circulating lymphocytes from healthy individuals but the frequency may be higher after exposure to carcinogenic chemicals or radiation. The frequency of CAs has been measured in occupational monitoring and an increased frequency of CAs has also been associated with cancer risk. Alterations in DNA damage repair and telomere maintenance are thought to contribute to the formation of CAs, which include chromosome type of aberrations and chromatid type of aberrations. In the present study, we used the result of our published genome-wide association studies to extract data on 153 DNA repair genes from 866 nonsmoking persons who had no known occupational exposure to genotoxic substances. Considering an arbitrary cut-off level of P< 5 × 10-3, single nucleotide polymorphisms (SNPs) tagging 22 DNA repair genes were significantly associated with CAs and they remained significant at P < 0.05 when adjustment for multiple comparisons was done by the Binomial Sequential Goodness of Fit test. Nucleotide excision repair pathway genes showed most associations with 6 genes. Among the associated genes were several in which mutations manifest CA phenotype, including Fanconi anemia, WRN, BLM and genes that are important in maintaining genome stability, as well as PARP2 and mismatch repair genes. RPA2 and RPA3 may participate in telomere maintenance through the synthesis of the C strand of telomeres. Errors in NHEJ1 function may lead to translocations. The present results show associations with some genes with known CA phenotype and suggest other pathways with mechanistic rationale for the formation of CAs in healthy nonsmoking population.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 6910 Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Soňa Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Malá Hora 4D, 03601 Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
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Yuan H, Ji J, Shi M, Shi Y, Liu J, Wu J, Yang C, Xi W, Li Q, Zhu W, Li J, Gong X, Zhang J. Characteristics of Pan-Cancer Patients With Ultrahigh Tumor Mutation Burden. Front Oncol 2021; 11:682017. [PMID: 33968789 PMCID: PMC8100597 DOI: 10.3389/fonc.2021.682017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/06/2021] [Indexed: 12/31/2022] Open
Abstract
Background Tumor mutation burden has been proven to be a good predictor for the efficacy of immunotherapy, especially in patients with hypermutation. However, most research focused on the analysis of hypermutation in individual tumors, and there is a lack of integrated research on the hypermutation across different cancers. This study aimed to characterize hypermutated patients to distinguish between these patients and non-hypermutated patients. Methods A total of 5,980 tumor samples involving 23 types of solid tumors from the in-house database were included in the study. Based on the cutoff value of tumor mutation burden (TMB), all samples were divided into hypermutated or non-hypermutated groups. Microsatellite instability status, PD-L1 expression and other mutation-related indicators were analyzed. Results Among the 5,980 tumor samples, 1,164 were selected as samples with hypermutation. Compared with the non-hypermutated group, a significant increase in the mutation rates of DNA mismatch repair genes and polymerase genes was detected in the hypermutated group, and there was an overlap between high TMB and high microsatellite instability or high PD-L1. In addition, we found that EGFR, KRAS and PIK3CA had a high frequency of both single nucleotide variation and copy number variation mutations. These identified mutant genes were enriched in the oncogenic signaling pathway and the DNA damage repair pathway. At the same time, the somatic cell characteristics and distribution of the two groups were significantly different. Conclusions This study identified genetic and phenotypic characteristics of hypermutated tumors and demonstrated that DNA damage repair is critically involved in hypermutation.
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Affiliation(s)
- Hong Yuan
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Ji
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Liu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junwei Wu
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Yang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqi Xi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingyuan Li
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Wei Zhu
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Jingjie Li
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Xiaoli Gong
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China
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14
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Song H, Ding N, Li S, Liao J, Xie A, Yu Y, Zhang C, Ni C. Identification of Hub Genes Associated With Hepatocellular Carcinoma Using Robust Rank Aggregation Combined With Weighted Gene Co-expression Network Analysis. Front Genet 2020; 11:895. [PMID: 33133125 PMCID: PMC7561391 DOI: 10.3389/fgene.2020.00895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background Bioinformatics provides a valuable tool to explore the molecular mechanisms underlying pathogenesis of hepatocellular carcinoma (HCC). To improve prognosis of patients, identification of robust biomarkers associated with the pathogenic pathways of HCC remains an urgent research priority. Methods We employed the Robust Rank Aggregation method to integrate nine qualified HCC datasets from the Gene Expression Omnibus. A robust set of differentially expressed genes (DEGs) between tumor and normal tissue samples were screened. Weighted gene co-expression network analysis was applied to cluster DEGs and the key modules related to clinical traits identified. Based on network topology analysis, novel risk genes derived from key modules were mined and biological verification performed. The potential functions of these risk genes were further explored with the aid of miRNA–mRNA regulatory networks. Finally, the prognostic ability of these genes was assessed by constructing a clinical prediction model. Results Two key modules showed significant association with clinical traits. In combination with protein–protein interaction analysis, 29 hub genes were identified. Among these genes, 19 from one module showed a pattern of upregulation in HCC and were associated with the tumor node metastasis stage, and 10 from the other module displayed the opposite trend. Survival analyses indicated that all these genes were significantly related to patient prognosis. Based on the miRNA-mRNA regulatory network, 29 genes strongly linked to tumor activity were identified. Notably, five of the novel risk genes, ABAT, DAO, PCK2, SLC27A2, and HAO1, have rarely been reported in previous studies. Gene set enrichment analysis for each gene revealed regulatory roles in proliferation and prognosis of HCC. Least absolute shrinkage and selection operator regression analysis further validated DAO, PCK2, and HAO1 as prognostic factors in an external HCC dataset. Conclusion Analysis of multiple datasets combined with global network information presents a successful approach to uncover the complex biological mechanisms of HCC. More importantly, this novel integrated strategy facilitates identification of risk hub genes as candidate biomarkers for HCC, which could effectively guide clinical treatments.
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Affiliation(s)
- Hao Song
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Intervention Therapy, The Fourth Medical Center of PLA General Hospital, Beijing, China
| | - Na Ding
- Department of Computational Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shang Li
- Department of Computational Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianlong Liao
- Department of Computational Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Aimin Xie
- Department of Computational Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Youtao Yu
- Department of Intervention Therapy, The Fourth Medical Center of PLA General Hospital, Beijing, China
| | - Chunlong Zhang
- Department of Computational Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Caifang Ni
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, China
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15
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DNA Mismatch Repair Gene Variants in Sporadic Solid Cancers. Int J Mol Sci 2020; 21:ijms21155561. [PMID: 32756484 PMCID: PMC7432688 DOI: 10.3390/ijms21155561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
The phenotypic effects of single nucleotide polymorphisms (SNPs) in the development of sporadic solid cancers are still scarce. The aim of this review was to summarise and analyse published data on the associations between SNPs in mismatch repair genes and various cancers. The mismatch repair system plays a unique role in the control of the genetic integrity and it is often inactivated (germline and somatic mutations and hypermethylation) in cancer patients. Here, we focused on germline variants in mismatch repair genes and found the outcomes rather controversial: some SNPs are sometimes ascribed as protective, while other studies reported their pathological effects. Regarding the complexity of cancer as one disease, we attempted to ascertain if particular polymorphisms exert the effect in the same direction in the development and treatment of different malignancies, although it is still not straightforward to conclude whether polymorphisms always play a clear positive role or a negative one. Most recent and robust genome-wide studies suggest that risk of cancer is modulated by variants in mismatch repair genes, for example in colorectal cancer. Our study shows that rs1800734 in MLH1 or rs2303428 in MSH2 may influence the development of different malignancies. The lack of functional studies on many DNA mismatch repair SNPs as well as their interactions are not explored yet. Notably, the concerted action of more variants in one individual may be protective or harmful. Further, complex interactions of DNA mismatch repair variations with both the environment and microenvironment in the cancer pathogenesis will deserve further attention.
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16
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Vymetalkova V, Rosa F, Susova S, Bendova P, Levy M, Buchler T, Kral J, Bartu L, Vodickova L, Hughes DJ, Soucek P, Naccarati A, Kumar R, Vodicka P, Pardini B. Expression quantitative trait loci in ABC transporters are associated with survival in 5-FU treated colorectal cancer patients. Mutagenesis 2020; 35:273-281. [DOI: 10.1093/mutage/gez050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Abstract
The chemotherapeutic efficacy in colorectal cancer (CRC) is limited due to the inter-individual variability in drug response and the development of tumour resistance. ATP-binding cassette (ABC) transporters are crucial in the development of resistance by the efflux of anticancer agents from cancer cells. In this study, we identified 14 single nucleotide polymorphisms (SNPs) in 11 ABC transporter genes acting as an expression of quantitative trait loci (eQTLs), i.e. whose variation influence the expression of many downstream genes. These SNPs were genotyped in a case–control study comprising 1098 cases and 1442 healthy controls and analysed in relation to CRC development risk and patient survival. Considering a strict correction for multiple tests, we did not observe any significant association between SNPs and CRC risk. The rs3819720 polymorphism in the ABCB3/TAP2 gene was statistically significantly associated with shorter overall survival (OS) in the codominant, and dominant models [GA vs. GG, hazard ratio (HR) = 1.48; P = 0.002; AA vs. GG, HR = 1.70; P = 0.004 and GA + AA vs. GG, HR = 1.52; P = 0.0006]. Additionally, GA carriers of the same SNP displayed worse OS after receiving 5-FU based chemotherapy. The variant allele of rs3819720 polymorphism statistically significantly affected the expression of 36 downstream genes. Screening for eQTL polymorphisms in relevant genes such as ABC transporters that can regulate the expression of several other genes may help to identify the genetic background involved in the individual response to the treatment of CRC patients.
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Affiliation(s)
- Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Fabio Rosa
- IIGM Italian Institute for Genomic Medicine, Turin, Italy
| | - Simona Susova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Petra Bendova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Jan Kral
- Institute for Clinical and Experimental Medicine, IKEM, Prague, Czech Republic
| | - Linda Bartu
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - David J Hughes
- Cancer Biology and Therapeutics Group, UCD Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Pavel Soucek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- IIGM Italian Institute for Genomic Medicine, Turin, Italy
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology
- Division of Functional Genome Analysis, German Cancer Research Centre, Heidelberg, Germany
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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17
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Oxidative Damage in Sporadic Colorectal Cancer: Molecular Mapping of Base Excision Repair Glycosylases in Colorectal Cancer Patients. Int J Mol Sci 2020; 21:ijms21072473. [PMID: 32252452 PMCID: PMC7177219 DOI: 10.3390/ijms21072473] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress with subsequent premutagenic oxidative DNA damage has been implicated in colorectal carcinogenesis. The repair of oxidative DNA damage is initiated by lesion-specific DNA glycosylases (hOGG1, NTH1, MUTYH). The direct evidence of the role of oxidative DNA damage and its repair is proven by hereditary syndromes (MUTYH-associated polyposis, NTHL1-associated tumor syndrome), where germline mutations cause loss-of-function in glycosylases of base excision repair, thus enabling the accumulation of oxidative DNA damage and leading to the adenoma-colorectal cancer transition. Unrepaired oxidative DNA damage often results in G:C>T:A mutations in tumor suppressor genes and proto-oncogenes and widespread occurrence of chromosomal copy-neutral loss of heterozygosity. However, the situation is more complicated in complex and heterogeneous disease, such as sporadic colorectal cancer. Here we summarized our current knowledge of the role of oxidative DNA damage and its repair on the onset, prognosis and treatment of sporadic colorectal cancer. Molecular and histological tumor heterogeneity was considered. Our study has also suggested an additional important source of oxidative DNA damage due to intestinal dysbiosis. The roles of base excision repair glycosylases (hOGG1, MUTYH) in tumor and adjacent mucosa tissues of colorectal cancer patients, particularly in the interplay with other factors (especially microenvironment), deserve further attention. Base excision repair characteristics determined in colorectal cancer tissues reflect, rather, a disease prognosis. Finally, we discuss the role of DNA repair in the treatment of colon cancer, since acquired or inherited defects in DNA repair pathways can be effectively used in therapy.
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