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Zerrad C, Lkhider M, Bouqdayr M, Belkouchi A, Badre W, Tahiri M, Pineau P, Benjelloun S, Ezzikouri S. NOD1 and NOD2 genetic variants: Impact on hepatocellular carcinoma susceptibility and progression in Moroccan population. Gene 2024; 931:148847. [PMID: 39147112 DOI: 10.1016/j.gene.2024.148847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/25/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND Nucleotide-binding oligomerization domain 1 (NOD1) and NOD2 are involved in carcinogenic processes by recognizing bacterial cell wall components and triggering inflammation. This study explored the association between genetic variations in NOD1 and NOD2 and susceptibility to hepatocellular carcinoma (HCC) and its progression in a Moroccan population. METHODS Genotyping of NOD1 rs2075820 (C>T) and NOD2 rs718226 (A>G) was performed using the TaqMan allelic discrimination assay in 467 Moroccan individuals. The cohort included 156 patients with hepatocellular carcinoma (HCC), 155 patients with liver cirrhosis (LC) diagnosed with HBV, HCV, or MASLD, and 156 controls. RESULTS The NOD1 rs2075820 variant showed no association with HCC susceptibility or progression, which is consistent with in silico predictions. However, the NOD2 rs718226 G allele and GG genotype were more common in the HCC group compared to the cirrhosis and control groups. Individuals with the homozygous G variant had a 2-fold higher risk for HCC (ORad = 2.12; CI=1.01-4.44; Pad = 0.04). Those with the GG genotype also had an increased risk of HCC (GG vs. AG+AA ORad = 2.28; CI=1.15-4.54; Pad = 0.016). Furthermore, GG genotype carriers had a significantly higher risk of HCC progression (ORad = 2.58; CI=1.26-5.31; Pad = 0.031). Individuals with the rs718226 minor allele had a significantly elevated risk of progressing from LC to HCC (ORad = 1.50; CI=1.07-2.09; Pad = 0.016). Stratification analysis indicated that men had a higher risk of HCC progression compared to women (ORad = 4.63; CI=1.53-14.00 vs. ORad = 2.73; CI=1.05-7.09). CONCLUSION The NOD1 rs2075820 polymorphism does not appear to be a genetic risk factor for susceptibility to HCC. In contrast, the non-coding NOD2 rs718226 variant significantly increases HCC susceptibility and promotes liver cancer progression in the Moroccan population. Further studies involving larger cohorts are warranted to definitively confirm or refute the effects of NOD1 and NOD2 genetic variants on liver cancer susceptibility and progression.
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Affiliation(s)
- Chaimaa Zerrad
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco; Laboratoire de Virologie, Oncologie, Biosciences, Environnement et Énergies Nouvelles, Hassan II, Casablanca Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Mustapha Lkhider
- Laboratoire de Virologie, Oncologie, Biosciences, Environnement et Énergies Nouvelles, Hassan II, Casablanca Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Meryem Bouqdayr
- Virology Unit, Immunovirology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | | | - Wafaa Badre
- Service d'Hépato-Gastro-Entérologie, CHU Ibn Rochd, Casablanca, Morocco
| | - Mohamed Tahiri
- Service d'Hépato-Gastro-Entérologie, CHU Ibn Rochd, Casablanca, Morocco; Faculté de Médecine et de Pharmacie, Université Hassan II, Casablanca, Morocco
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
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Li Y, Zhang SW, Xie MY, Zhang T. PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer. Brief Bioinform 2023; 24:bbad291. [PMID: 37738403 DOI: 10.1093/bib/bbad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 09/24/2023] Open
Abstract
Identifying personalized cancer driver genes and further revealing their oncogenic mechanisms is critical for understanding the mechanisms of cell transformation and aiding clinical diagnosis. Almost all existing methods primarily focus on identifying driver genes at the cohort or individual level but fail to further uncover their underlying oncogenic mechanisms. To fill this gap, we present an interpretable framework, PhenoDriver, to identify personalized cancer driver genes, elucidate their roles in cancer development and uncover the association between driver genes and clinical phenotypic alterations. By analyzing 988 breast cancer patients, we demonstrate the outstanding performance of PhenoDriver in identifying breast cancer driver genes at the cohort level compared to other state-of-the-art methods. Otherwise, our PhenoDriver can also effectively identify driver genes with both recurrent and rare mutations in individual patients. We further explore and reveal the oncogenic mechanisms of some known and unknown breast cancer driver genes (e.g. TP53, MAP3K1, HTT, etc.) identified by PhenoDriver, and construct their subnetworks for regulating clinical abnormal phenotypes. Notably, most of our findings are consistent with existing biological knowledge. Based on the personalized driver profiles, we discover two existing and one unreported breast cancer subtypes and uncover their molecular mechanisms. These results intensify our understanding for breast cancer mechanisms, guide therapeutic decisions and assist in the development of targeted anticancer therapies.
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Affiliation(s)
- Yan Li
- School of Automation from Northwestern Polytechnical University, China
| | - Shao-Wu Zhang
- School of Automation from Northwestern Polytechnical University, China
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China
| | - Ming-Yu Xie
- School of Automation from Northwestern Polytechnical University, China
| | - Tong Zhang
- School of Automation from Northwestern Polytechnical University, China
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Zerrad C, Lkhider M, Belkouchi A, Tanouti IA, Badre W, Tahiri M, Ayassi S, Marchio A, Pineau P, Benjelloun S, Ezzikouri S. Association between TLR2, TLR4, and TLR5 genetic variants and the risk of hepatocellular carcinoma in Moroccan population. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:986-1003. [PMID: 37330637 DOI: 10.1080/15257770.2023.2225560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common human malignancy and the fourth most frequent cause of cancer-related deaths worldwide. Toll-like receptors (TLRs), are known to play a key role in hepatocarcinogenesis through induction of inflammation. We aimed to investigate the association between TLR2 rs3804099, TLR4 rs4986790, rs4986791, and rs11536889 and TLR5 rs5744174 and HCC risk in a total of 306 Moroccan subjects, including 152 HCC patient and 154 controls using a TaqMan allelic discrimination assay. Our result showed that the frequency of TLR4 rs11536889 C allele was higher in control group than in HCC patients (OR = 0.52, 95% CI = 0.30-0.88, p = 0.01). Moreover, under the dominant model, we observed that CG/CC genotypes were protective factors against HCC risk (OR = 0.51, 95% CI = 0.28-0.91, p = 0.02). However, no significant differences were found in the allele and genotype frequencies of TLR4 rs4986790 and rs4986791, between HCC patients and controls. Similarly, genotypic frequencies of TLR2 and TLR5 polymorphisms did not differ significantly between HCC patients and controls. However, TLR4 haplotype analysis revealed that ACC haplotype may be protective of HCC risk in patients with HCC (OR = 0.53, 95% CI = 0.31-0.92, p = 0.02). In conclusion, our result suggest that TLR4 rs11536889 polymorphism and ACC haplotype may decrease risk of hepatocellular carcinoma in Moroccan population.
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Affiliation(s)
- Chaimaa Zerrad
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratory of Virology, Oncology, Biosciences, Environment and New Energies, University Hassan II Casablanca Faculty des Sciences Techniques, Mohammedia, Morocco
| | - Mustapha Lkhider
- Laboratory of Virology, Oncology, Biosciences, Environment and New Energies, University Hassan II Casablanca Faculty des Sciences Techniques, Mohammedia, Morocco
| | | | - Ikram-Allah Tanouti
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Wafaa Badre
- CHU Ibn Rochd, Médecine B, Casablanca, Morocco
| | - Mohamed Tahiri
- CHU Ibn Rochd, Médecine B, Casablanca, Morocco
- Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Sarra Ayassi
- Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Agnès Marchio
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Huang ZL, Zhang PB, Zhang JT, Li F, Li TT, Huang XY. Comprehensive Genomic Profiling Identifies FAT1 as a Negative Regulator of EMT, CTCs, and Metastasis of Hepatocellular Carcinoma. J Hepatocell Carcinoma 2023; 10:369-382. [PMID: 36915393 PMCID: PMC10007982 DOI: 10.2147/jhc.s398573] [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: 11/28/2022] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Background FAT atypical cadherin 1 (FAT1) acts as a tumor suppressor or oncogene, which regulates cell adherence, proliferation, motility, and actin kinetics. FAT1 gene expression is closely related to hepatocarcinogenesis; however, the function and mechanism of FAT1 in hepatocellular carcinoma (HCC) remain unclear. Methods Here, we screened for the FAT1, which is intimately linked to the development and progression of HCC, both in circulating tumor cells (CTCs) and tumor tissues using next generation sequencing (NGS). Immunohistochemical staining was performed to detect FAT1 protein expression. To determine the impact of FAT1 on epithelial-mesenchymal transition (EMT), migration and invasion of HCC, an in vitro transwell assay and Western blot were performed. Moreover, Gene Set Enrichment Analysis was carried out to discover the underlying mechanism. Finally, animal experiments were conducted to confirm the effects of FAT1 on HCC metastasis and tumorigenicity. Results Our results showed that FAT1 expression was decreased in HCC tissues, while in vitro and in vivo, the FAT1 knockdown facilitated invasion, cell motility, colony formation, and proliferation. FAT1 knockdown also resulted in decreased expression of E-cadherin and markedly elevated expression of N-cadherin, vimentin, and snail. We also confirmed our hypothesis from the analysis of group differences in the CTC phenotype and lung metastasis in nude mice. Conclusion Our findings illustrated that FAT1 played a negative regulatory role in the HCC EMT and metastasis, providing further evidence for the role played by FAT1 in the formation and progression of HCC.
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Affiliation(s)
- Zi-Li Huang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China.,Department of Radiology, Xuhui District Central Hospital of Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Ping-Bao Zhang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China.,Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jun-Tao Zhang
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Feng Li
- School of Materials of Science and Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ting-Ting Li
- Department of Infectious Disease, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Xiu-Yan Huang
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
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Skhoun H, Khattab M, Belkhayat A, Takki Chebihi Z, Bakri Y, Dakka N, El Baghdadi J. Association of TP53 gene polymorphisms with the risk of acute lymphoblastic leukemia in Moroccan children. Mol Biol Rep 2022; 49:8291-8300. [PMID: 35705773 DOI: 10.1007/s11033-022-07643-3] [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: 12/03/2021] [Accepted: 05/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND TP53 gene plays a pivotal role in maintaining genetic stability and prevention of malignancies. Alterations of this gene are implicated in more than half of human cancers. To the best of our knowledge, this study is the first to explore TP53 polymorphisms in Moroccan childhood acute lymphoblastic leukemia (ALL). METHODS AND RESULTS DNA samples of 45 ALL children were obtained from peripheral blood. A total of 333 healthy Moroccans were used as controls. Polymerase chain reaction and Sanger sequencing were performed to analyze TP53 hotspot exons in cases. We identified a significant protective effect of the TP53-Arg variant at rs1042522 [OR 0.4593 (0.249-0.8472), p = 0.0127] and the Pro/Arg genotype [OR 0.0350 (0.0047-0.2583), p = 0.0010]. Additionally, we found a novel association between the C-allele of Arg213Arg 1800372 [OR 2.7736 (1.3821-5.5664), p = 0.0041] and the risk of childhood ALL. Importantly, TC/CC genotypes of this polymorphism were revealed to enhance the risk of ALL among females [OR 9.0 (3.1555-25.6693), p < 0.0001]. Arg213Arg was also noticed to be associated with the hemoglobin count of patients at diagnosis by linear regression (p = 0.0318). The analysis of penetrance showed a significant association of the CG/GG genotypes at rs1042522 and TC/CC genotypes at rs1800372 to childhood ALL via dominant model [OR 0.2090 (0.09074-0.4814), p = 0.0002 and OR 3.4205 (1.6084-7.2742), p = 0.0014 for rs1042522 and rs1800372 respectively]. No association was found between TP53 polymorphisms and patients survival. CONCLUSION Altogether, our findings indicated that TP53 polymorphisms are significantly involved in the genetic susceptibility to childhood ALL in Morocco.
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Affiliation(s)
- Hanaa Skhoun
- Genetics Unit, Military Hospital Mohammed V, Rabat, Morocco.,Laboratory of Human Pathologies Biology and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohammed Khattab
- Pediatric Hematology and Oncology Center, Children's Hospital, Rabat, Morocco
| | | | | | - Youssef Bakri
- Laboratory of Human Pathologies Biology and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Nadia Dakka
- Laboratory of Human Pathologies Biology and Genomic Center of Human Pathologies, Department of Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Crudele A, Dato S, Re OL, Maugeri A, Sanna P, Giallongo S, Oben J, Panera N, De Rango F, Mosca A, Rose G, Passarino G, Alisi A, Vinciguerra M. Pediatric Non-Alcoholic Fatty Liver Disease Is Affected by Genetic Variants Involved in Lifespan/Healthspan. J Pediatr Gastroenterol Nutr 2021; 73:161-168. [PMID: 33720087 DOI: 10.1097/mpg.0000000000003123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Non-alcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease in both adults and children. Along with obesity and metabolic syndrome, genetic predisposition influences the progression of NAFLD. Here, we investigated the effect of lifespan/healthspan-related single nucleotide polymorphisms (SNPs) on metabolically associated fatty liver disease in children. METHODS We evaluated the impact of 10 SNPs involved in both human liver/metabolic diseases and healthspan (interleukin-6 [IL-6] rs1800795, antisense non coding RNA in the INK4 locus (ANRIL) rs1556516, SH2B3/ATXN2 rs7137828, FURIN rs17514846, TP53 rs1042522, APOC3 rs2542052, KL rs9536314, KL rs9527025, SIRT6 rs107251, FOXO3 rs2802292) on NAFLD-related metabolic and liver features in 177 pediatric patients with biopsy-proven NAFLD, by comparing them to 146 healthy controls. We then applied a multidimensional reduction (MDR) case-control analysis of SNP-SNP interactions, to identify the joint effect of analyzed SNPs in predicting NAFLD and associated features. RESULTS Discrete SNPs were significantly associated with individual metabolic NAFLD features, but none of them significantly associated with NAFLD diagnosis. By testing potential synergies using the MDR approach, the best combination to diagnose NAFLD (P = 0.0011) resulted in the one encompassing IL-6 rs1800795 and ANRIL rs1556516. Consistently, the risk combinations suggested by SNP-SNP analysis strongly associated with a higher level of fasting plasma blood glucose level (P = 0.024). CONCLUSION In conclusion, here we demonstrated a synergic interaction between IL-6 rs1800795 and ANRIL rs1556516 in the diagnosis of NAFLD, and NAFLD-associated hyperglycemia in children. Larger studies are required to confirm our findings and to elucidate mechanisms by which the genetic interaction between these two genes influences healthspan in pediatric NAFLD.
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Affiliation(s)
- Annalisa Crudele
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Oriana Lo Re
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Andrea Maugeri
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
| | - Paola Sanna
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Sebastiano Giallongo
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Jude Oben
- Institute for Liver and Digestive Health, Division of Medicine, University College London (UCL), London, United Kingdom
| | - Nadia Panera
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Antonella Mosca
- Research Unit of Hepato-Gastroenterology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppina Rose
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Manlio Vinciguerra
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
- Institute for Liver and Digestive Health, Division of Medicine, University College London (UCL), London, United Kingdom
- ERA Chair in Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
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7
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Zhang H, Zhang Z, Liu X, Duan H, Xiang T, He Q, Su Z, Wu H, Liang Z. DNA Methylation Haplotype Block Markers Efficiently Discriminate Follicular Thyroid Carcinoma from Follicular Adenoma. J Clin Endocrinol Metab 2021; 106:1011-1021. [PMID: 33394038 PMCID: PMC7993581 DOI: 10.1210/clinem/dgaa950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Indexed: 12/19/2022]
Abstract
CONTEXT Follicular thyroid carcinoma (FTC) is the second most common type of thyroid carcinoma and must be pathologically distinguished from benign follicular adenoma (FA). Additionally, the clinical assessment of thyroid tumors with uncertain malignant potential (TT-UMP) demands effective indicators. OBJECTIVE We aimed to identify discriminating DNA methylation markers between FA and FTC. METHODS DNA methylation patterns were investigated in 33 FTC and 33 FA samples using reduced representation bisulfite sequencing and methylation haplotype block-based analysis. A prediction model was constructed and validated in an independent cohort of 13 FTC and 13 FA samples. Moreover, 36 TT-UMP samples were assessed using this model. RESULTS A total of 70 DNA methylation markers, approximately half of which were located within promoters, were identified to be significantly different between the FTC and FA samples. All the Gene Ontology terms enriched among the marker-associated genes were related to "DNA binding," implying that the inactivation of DNA binding played a role in FTC development. A random forest model with an area under the curve of 0.994 was constructed using those markers for discriminating FTC from FA in the validation cohort. When the TT-UMP samples were scored using this model, those with fewer driver mutations also exhibited lower scores. CONCLUSION An FTC-predicting model was constructed using DNA methylation markers, which distinguished between FA and FTC tissues with a high degree of accuracy. This model can also be used to help determine the potential of malignancy in TT-UMP.
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Affiliation(s)
- Hui Zhang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | | | - Xiaoding Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | | | - Qiye He
- Singlera Genomics Inc. Shanghai, China
| | - Zhixi Su
- Singlera Genomics Inc. Shanghai, China
| | - Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- Correspondence: Zhiyong Liang, PhD, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China. ; or Huanwen Wu, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- Correspondence: Zhiyong Liang, PhD, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China. ; or Huanwen Wu, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China.
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Elshaer M, ElManawy AI, Hammad A, Namani A, Wang XJ, Tang X. Integrated data analysis reveals significant associations of KEAP1 mutations with DNA methylation alterations in lung adenocarcinomas. Aging (Albany NY) 2020; 12:7183-7206. [PMID: 32327612 PMCID: PMC7202502 DOI: 10.18632/aging.103068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/29/2020] [Indexed: 12/17/2022]
Abstract
KEAP1 regulates the cytoprotection induced by NRF2 and has been reported to be a candidate tumor suppressor. Recent evidence has shown that mutations in several driver genes cause aberrant DNA methylation patterns, a hallmark of cancer. However, the correlation between KEAP1 mutations and DNA methylation in lung cancer has still not been investigated. In this study, we systematically carried out an integrated multi-omics analysis to explore the correlation between KEAP1 mutations and DNA methylation and its effect on gene expression in lung adenocarcinoma (LUAD). We found that most of the DNA aberrations associated with KEAP1 mutations in LAUD were hypomethylation. Surprisingly, we found several NRF2-regulated genes among the genes that showed differential DNA methylation. Moreover, we identified an 8-gene signature with altered DNA methylation pattern and elevated gene expression levels in LUAD patients with mutated KEAP1, and evaluated the prognostic value of this signature in various clinical datasets. These results establish that KEAP1 mutations are associated with DNA methylation changes capable of shaping regulatory network functions. Combining both epigenomic and transcriptomic changes along with KEAP1 mutations may provide a better understanding of the molecular mechanisms associated with the progression of lung cancer and may help to provide better therapeutic approaches.
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Affiliation(s)
- Mohamed Elshaer
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
- Labeled Compounds Department, Hot Labs Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Ahmed Islam ElManawy
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
- Agricultural Engineering Department, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed Hammad
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
- Radiation Biology Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Akhileshwar Namani
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
| | - Xiu Jun Wang
- Department of Pharmacology and Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, PR China
| | - Xiuwen Tang
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
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Lombardo D, Saitta C, Giosa D, Di Tocco FC, Musolino C, Caminiti G, Chines V, Franzè MS, Alibrandi A, Navarra G, Raimondo G, Pollicino T. Frequency of somatic mutations in TERT promoter, TP53 and CTNNB1 genes in patients with hepatocellular carcinoma from Southern Italy. Oncol Lett 2020; 19:2368-2374. [PMID: 32194736 PMCID: PMC7039085 DOI: 10.3892/ol.2020.11332] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022] Open
Abstract
Somatic mutations in the TERT promoter and in the TP53 and CTNNB1 genes are considered drivers for hepatocellular carcinoma (HCC) development. They show variable frequencies in different geographic areas, possibly depending on liver disease etiology and environmental factors. TP53, CTNNB1 and TERT genetic mutations were investigated in tumor and non-tumor liver tissues from 67 patients with HCC and liver tissue specimens from 41 control obese subjects from Southern Italy. Furthermore, TERT expression was assessed by reverse transcription-quantitative PCR. Neither CTNNB1 mutations or TP53 R249S substitution were detected in any case. The TP53 R72P polymorphism was found in 10/67 (14.9%) tumors, but was not found in either non-tumor tissues (P=0.001) or controls (P=0.009). TERT gene promoter mutations were found in 29/67 (43.3%) tumor tissues but were not found in either non-tumor (P<0.0001) or control liver specimens (P<0.0001). The most frequent mutation in the tumors was the known hot spot at -124 bp from the TERT ATG start site (-124G>A, 28 cases, 41.8%; P<0.0001). A new previously never reported TERT promoter mutation (at -297 bp from the ATG, -297C>T) was found in 5/67 (7.5%) tumors, in 0/67 (0%) non-tumor (P<0.0001), and in 0/41 (0%) controls (P=0.07). This mutation creates an AP2 consensus sequence, and was found alone (1 case) or in combination (4 cases) with the -124 bp mutation. The mutation at -124 and -297 bp induced a 33-fold (P<0.0001) and 40-fold increase of TERT expression levels, respectively. When both mutations were present, TERT expression levels were increased >300-fold (P=0.001). A new TERT promoter mutation was identified, which generates a de novo binding motif for AP2 transcription factors, and which significantly increases TERT promoter transcriptional activity.
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Affiliation(s)
- Daniele Lombardo
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Carlo Saitta
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Internal Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Domenico Giosa
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Francesca Casuscelli Di Tocco
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Cristina Musolino
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Giuseppe Caminiti
- Department of Internal Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Valeria Chines
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Maria Stella Franzè
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Angela Alibrandi
- Department of Economics, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Giuseppe Navarra
- Department of Human Pathology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Giovanni Raimondo
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Clinical and Experimental Medicine, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
| | - Teresa Pollicino
- Division of Clinical and Molecular Hepatology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy.,Department of Human Pathology, University Hospital 'G. Martino' of Messina, 98124 Messina, Italy
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10
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Zhang L, Wang Y, Qin Z, Li R, Cong R, Ji C, Meng X, Wang Y, Xia J, Song N. TP53 codon 72 Polymorphism and bladder cancer risk: a meta-analysis and emphasis on the role of tumor or smoking status. J Cancer 2018; 9:3522-3531. [PMID: 30310509 PMCID: PMC6171014 DOI: 10.7150/jca.26264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/27/2018] [Indexed: 01/08/2023] Open
Abstract
Background: Various studies had explored the relationship between TP53 codon 72 polymorphisms and the risk of bladder cancer (BC). However, their results remained inconsistent and the definite role of smoking or tumor status associated with this polymorphism in BC cases was seldom involved. Hence, this meta-analysis was to disclose such associations. Methods: Systematical and comprehensive retrieval of online databases PubMed, PMC, EMBASE and Web of Science were conducted to obtain eligible studies, up to May 30th, 2018. Pooled odds ratios (ORs) with 95% confidence intervals (CI) were utilized to assess the associations between TP53 codon 72 polymorphisms and BC susceptibilities under five genetic comparison models. Results: Ultimately, this meta-analysis enrolled 22 applicable studies with 3,791 BC cases and 4,917 controls. Our results suggested that the variant genotypes were associated with BC risk in Asian subgroup (allele model: OR=1.19, 95% CI=1.04-1.34; dominant model: OR=1.27, 95% CI=1.06-1.52; homozygote model: OR=1.36, 95% CI=1.03-1.80), while negative outcomes were presented in Caucasians. In the relationship between TP53 codon 72 polymorphisms and BC tumor stage in Asian group, positive results were presented in allele model: OR=1.68, 95% CI=1.04-2.72; dominant model: OR=2.46, 95% CI=1.08-5.61; heterozygous model: OR=2.32, 95% CI=1.04-5.14; homozygote model: OR=2.66, 95% CI=1.04-6.81. However, no evidence was revealed between this polymorphism and BC tumor grade. Besides, significant associations were displayed between TP53 codon 72 polymorphism and smoking status (allele model: OR=1.40, 95% CI=1.06-1.84; dominant model OR=1.72, 95% CI=1.18-2.50; heterozygous model: OR=1.77, 95% CI=1.19-2.64). Conclusion: Taken together, our results shed light on that TP53 codon 72 polymorphism was significantly associated with the susceptibility to BC in Asians. In addition, positive associations were also revealed between this polymorphism and tumor stage/smoking status in BC cases.
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Affiliation(s)
- Lei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yi Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Zhiqiang Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Ran Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Chengjian Ji
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Xianghu Meng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yamin Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Jiadong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Ninghong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
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11
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Abstract
Molecular pathological epidemiology (MPE) is a new discipline which emerged as an integrated approach of molecular pathology and epidemiology and was introduced for the first time by Professor Shuji Ogino and Professor Meir Stampfer in the year of 2010. MPE studies in hepatocellular carcinoma (HCC) investigate the relationship among risk factors, molecular biomarkers, and initiation, progression, and prognosis of HCC, which can be used for exploring the molecular mechanisms of HCC and for the molecular classification of the high risk population. Type 2 diabetes mellitus (DM) has been confirmed as an established risk factor for HCC, and MPE can be helpful to better understand the underlying molecular mechanisms. On December 20, 2017, the first China-Japan Symposium on HCC-MPE was held successfully in Beijing. HCC-MPE provides the opportunities and challenges to solve some problems of HCC, and I believe that it can be helpful to improve the early diagnosis, molecular typing, personalized prevention and treatment, and prognosis of HCC.
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12
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Variants of ubiquitin-specific peptidase 24 play a crucial role in lung cancer malignancy. Oncogene 2015; 35:3669-80. [PMID: 26568301 DOI: 10.1038/onc.2015.432] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 09/15/2015] [Accepted: 10/05/2015] [Indexed: 12/24/2022]
Abstract
Ubiquitin is a critical modifier regulating the degradation and function of its target proteins during posttranslational modification. Here we found that ubiquitin-specific peptidase 24 (USP24) is highly expressed in cell lines with enhanced malignancy and in late-stage lung cancer clinical samples. Studying single-nucleotide polymorphisms (SNPs) of USP24 using genomic DNA of lung cancer patients revealed an increase in SNP 7656C/T. When using RNA specimens instead of the genomic DNA of lung cancer patients, we found significant increases in the ratios of variants 930C/T and 7656T/C, suggesting that variants at these two sites are not only caused by the SNP of DNA but also by the RNA editing. USP24-930T and USP24-7656C increase USP24 expression levels by increasing RNA stability. Knocking down USP24 increased Suv39h1 level through a decrease in mouse double-minute 2 homolog levels, thus enhancing lysine-9 methylation of histone H3, and resulting in the prevention of lung cancer malignancy. In conclusion, as USP24 variant analysis revealed a higher ratio of variants in blood specimens of lung cancer patients than that in normal individuals, USP24-930T and USP24-7656C might be useful as diagnostic markers for cancer detection.
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13
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Chen R, Liu S, Ye H, Li J, Du Y, Chen L, Liu X, Ding Y, Li Q, Mao Y, Ai S, Zhang P, Ma W, Yang H. Association of p53 rs1042522, MDM2 rs2279744, and p21 rs1801270 polymorphisms with retinoblastoma risk and invasion in a Chinese population. Sci Rep 2015; 5:13300. [PMID: 26289323 PMCID: PMC4642541 DOI: 10.1038/srep13300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) of p53 rs1042522, MDM2 rs2279744 and p21 rs1801270, all in the p53 pathway, which plays a crucial role in DNA damage and genomic instability, were reported to be associated with cancer risk and pathologic characteristics. This case-control study was designed to analyse the association between these SNPs and retinoblastoma (RB) in a Chinese Han population. These SNPs in 168 RB patients and 185 adult controls were genotyped using genomic DNA from venous blood. No significant difference was observed in allele or genotypic frequencies of these SNPs between Chinese RB patients and controls (all P > 0.05). However, the rs1042522 GC genotype showed a protective effect against RB invasion, as demonstrated by event-free survival (HR = 0.53, P = 0.007 for GC versus GG/CC). This effect was significant for patients with a lag time >1 month and no pre-enucleation treatment (P = 0.007 and P = 0.010, respectively), indicating an interaction between p53 rs1042522 and clinical characteristics, including lag time and pre-enucleation treatment status. Thus, the rs1042522 SNP may be associated with RB invasion in the Han Chinese population; however, further large and functional studies are needed to assess the validity of this association.
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Affiliation(s)
- Rongxin Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Shu Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Huijing Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiali Li
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Yi Du
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Lingyan Chen
- Divisions of Genetics and Molecular Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Xiaoman Liu
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Yungang Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qian Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuxiang Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Siming Ai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Ping Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wenfang Ma
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huasheng Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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