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Kassem PH, Montasser IF, Mahmoud RM, Ghorab RA, AbdelHakam DA, Fathi MESA, Wahed MAA, Mohey K, Ibrahim M, Hadidi ME, Masssoud YM, Salah M, Abugable A, Bahaa M, Khamisy SE, Meteini ME. Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing. BMC Med Genomics 2024; 17:202. [PMID: 39123171 PMCID: PMC11311965 DOI: 10.1186/s12920-024-01965-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing. METHODS Whole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection}. RESULTS Mutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCC and Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN). Among the 26 significantly mutated HCC genes-identified across 10 genome sequencing studies-in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants in TCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1). Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM). For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC. CONCLUSION Our results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.
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Affiliation(s)
- Perihan Hamdy Kassem
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Iman Fawzy Montasser
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Ramy Mohamed Mahmoud
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Rasha Ahmed Ghorab
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Dina A AbdelHakam
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Marwa A Abdel Wahed
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Khaled Mohey
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mariam Ibrahim
- Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed El Hadidi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates
- Bioinformatics Group, Center for Informatics Science(CIS), School of Information Technology and Computer Science(ITCS), Nile University, Giza, Egypt
| | - Yasmine M Masssoud
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Manar Salah
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Arwa Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mohamad Bahaa
- Hepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Mahmoud El Meteini
- Hepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Chen B, Qiu M, Gong R, Liu Y, Zhou Z, Wen Q, Wei X, Liang X, Jiang Y, Chen P, Wei Y, Huang Q, Mo Q, Lin Q, Yu H. Genetic variants in m5C modification genes are associated with survival of patients with HBV-related hepatocellular carcinoma. Arch Toxicol 2024; 98:1125-1134. [PMID: 38438738 DOI: 10.1007/s00204-024-03687-5] [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: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high mortality rate. The 5-methylcytosine (m5C), a type of RNA modification, plays crucial regulatory roles in HCC carcinogenesis, metastasis, and prognosis. However, a few studies have investigated the effect of genetic variants in m5C modification genes on survival of patients with hepatitis B virus (HBV)-related HCC. In the present study, we evaluated associations between 144 SNPs in 15 m5C modification genes and overall survival (OS) in 866 patients with the HBV-related HCC. Expression quantitative trait loci (eQTL) analysis and differential expression analysis were conducted to investigate biological mechanisms. As a result, we identified that two SNPs (NSUN7 rs2437325 A > G and TRDMT1 rs34434809 G > C) were significantly associated with HBV-related HCC OS with adjusted allelic hazards ratios of 1.25 (95% confidence interval = 1.05-1.48 and P = 0.011) and 1.19 (1.02-1.38 and P = 0.027), respectively, with a trend of combined risk genotypes (Ptrend < 0.001). Moreover, the results of eQTL analyses showed that both NSUN7 rs2437325 G and TRDMT1 rs34434809 C alleles were associated with a reduced mRNA expression level in 208 normal liver tissues (P = 0.007 and P < 0.001, respectively). Taken together, genetic variants in the m5C modification genes may be potential prognostic biomarkers of HBV-related HCC after hepatectomy, likely through mediating the mRNA expression of corresponding genes.
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Affiliation(s)
- Bowen Chen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Moqin Qiu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Rongbin Gong
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Zihan Zhou
- Department of Cancer Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Qiuping Wen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Xiaoxia Wei
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Yanji Jiang
- Department of Scientific Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Peiqin Chen
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
- Editorial Department of Chinese Journal of Oncology Prevention and Treatment, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Yuying Wei
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Qiongguang Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Guangxi Medical University, Nanning, 530021, China
| | - Qiuyan Mo
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China
| | - Qiuling Lin
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, China.
| | - Hongping Yu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, China.
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health Commission, Guangxi Medical University Cancer Hospital, Nanning, 530021, China.
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, 530021, China.
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Lin R, Xie S, Xu F, Chen Z, Liu J, Liu X. Improvement of rat hepatocellular carcinoma model induced by diethylnitrosamine. Tissue Cell 2024; 86:102261. [PMID: 37951061 DOI: 10.1016/j.tice.2023.102261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/18/2023] [Accepted: 11/02/2023] [Indexed: 11/13/2023]
Abstract
OBJECTIVE To construct a new diethylnitrosamine (DEN)-induced rat hepatocellular carcinoma (HCC) model with short induction time, high incidence, and survival rate. METHODS 60 male Sprague-Dawley rats were randomly divided into 4 groups: the control group, the model A (MA) group, the model B (MB) group, and the model C (MC) group. The control group was intraperitoneally injected with 0.9% saline for 6 weeks. The MA group was injected with the DEN solution at 30 mg/kg three times a week for 6 weeks. The MB group was injected with the DEN solution at 30 mg/kg three times a week for 6 weeks, and discontinued the induction for 2 weeks. The MC group was injected with the DEN solution at 30 mg/kg three times a week for 8 weeks. The levels of albumin (ALB), alanine transaminase (ALT), and aspartate aminotransferase (AST) in serum were assayed. Meanwhile, the pathological conditions, apoptosis of hepatocytes, expression of NF-κBp65, and the reactive oxygen species level were detected. RESULTS All rats in the control group and the MA group survived, and none of the rats occurred HCC. HCC occurred in rats of the MB group and the MC group. The serum ALB level in the MB group was higher than that in the MC group. The serum ALT and AST levels and the number of proliferating and apoptotic hepatocyte cells in the MB group were lower than those in the MC group. The expression of ROS- and NF-κBp6- positive cells in the MA group, MB group, and MC group were significantly higher than that of the control group. CONCLUSION This study developed a new DEN-induced rat HCC model with short induction time, high incidence, and survival rate. NF-κB pathway may be one of the main pathways involved in the development of this model.
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Affiliation(s)
- Runzhui Lin
- Hepatobiliary, pancreatic and splenic surgery,Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Sitian Xie
- Burn and plastic surgery,Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Fengjie Xu
- Shantou University Medical College, Shantou 515041, China
| | - Zeming Chen
- Hepatobiliary, pancreatic and splenic surgery,Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Jianrui Liu
- Shantou University Medical College, Shantou 515041, China
| | - Xingmu Liu
- Hepatobiliary, pancreatic and splenic surgery,Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China.
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A functional variant in the RAD51 3′ UTR is associated with survival of hepatocellular carcinoma patients. Gene X 2023; 851:146964. [DOI: 10.1016/j.gene.2022.146964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 09/13/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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Huang Q, Liu Y, Qiu M, Lin Q, Wei X, Zhou Z, Liang X, Li R, Chen W, Zhou X, Yu H. Potentially functional variants of MAP3K14 in the NF-κB signaling pathway genes predict survival of HBV-related hepatocellular carcinoma patients. Front Oncol 2022; 12:990160. [PMID: 36119471 PMCID: PMC9478184 DOI: 10.3389/fonc.2022.990160] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background The NF-κB signaling pathway plays an important role in associating inflammation with tumor development and progression. However, few studies have reported that roles of genetic variants of the NF-κB signaling pathway genes in survival of patients with HBV-related hepatocellular carcinoma (HBV-HCC), especially with regards to potentially functional SNPs. Methods We used multivariate Cox proportional hazards regression to evaluate associations between 2,060 single nucleotide polymorphisms (SNPs) in 20 NF-κB signaling pathway genes and survival of 866 HBV-HCC patients, which were randomly split (1:1) into discovery and validation datasets. Expression quantitative trait loci (eQTL) analysis was conducted to identify associations between survival-associated SNPs and mRNA expression of corresponding genes. Furthermore, online database was used to assess mRNA expression of corresponding genes and survival. Finally, receiver operating characteristic (ROC) curves were used to assess the prediction accuracy of models integrating both clinical and genetic variables on HCC survival. Results A total of 6 SNPs in MAP3K14 remained significantly associated with OS of HBV-HCC patients (P<0.05, BFDP<0.8). Further eQTL analysis demonstrated that significant correlations between the rs2074292 (G>A) A allele was associated with higher mRNA expression levels of MAP3K14 (P=0.044) in normal liver tissue, which was associated with worse survival of HBV-HCC patients. In the additive model, after adjusting for age, sex, smoking status, drinking status, AFP level, cirrhosis, embolus and BCLC stage, the combined dataset showed that HBV-HCC patients carrying the rs2074292 AA and GA genotypes (HR=1.71, 95%CI= 1.29-2.27, P=0.000) (HR=1.40, 95%CI=1.10-1.77, P=0.005) have worse OS than GG genotype, respectively. The addition of risk genotypes to the prediction models increased the AUC significantly from 71.15% to 73.11% (P=0.012) and from 72.55% to 74.21% (P=0.010) for 1-year and 3-year OS, respectively. Conclusion Our study indicated that MAP3K14 rs2074292 A allele may be a potential predictor of HBV-HCC survival, likely regulating MAP3K14 mRNA expression.
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Affiliation(s)
- Qiongguang Huang
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Yingchun Liu
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Moqin Qiu
- Department of Respiratory Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qiuling Lin
- Department of Clinical Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xueyan Wei
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Zihan Zhou
- Department of Cancer Prevention and Control, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiumei Liang
- Department of Disease Process Management, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Runwei Li
- Department of Occupational and Environmental Health, Indiana University, Bloomington, IN, United States
| | - Weiyi Chen
- School of Public Health, Guangxi Medical University, Nanning, China
| | - Xianguo Zhou
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hongping Yu, ; Xianguo Zhou,
| | - Hongping Yu
- School of Public Health, Guangxi Medical University, Nanning, China
- Department of Experimental Research, Guangxi Medical University Cancer Hospital, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, China
- Key Cultivated Laboratory of Cancer Molecular Medicine, Health Commission of Guangxi Zhuang Autonomous Region, Nanning, China
- *Correspondence: Hongping Yu, ; Xianguo Zhou,
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Singh S, Singh N, Baranwal M, Sharma S. Polymorphisms in the MSH2 gene predict poor survival of North Indian lung cancer patients undergoing chemotherapy. Biomark Med 2022; 16:69-82. [PMID: 35081740 DOI: 10.2217/bmm-2021-0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To estimate if MSH2 polymorphisms, viz. rs63749993, rs2303425, rs2303426, rs4987188, rs2303428 and rs17217772, have any association with clinical outcomes in North Indian lung cancer patients. Materials & methods: PCR-RFLP was used for genotyping 500 cases. Logistic regression and survival analysis was performed by utilizing MedCalc software. Results & conclusion: Our study concluded, adenocarcinoma subjects having heterozygous genotype for rs2303425 have increased survival time (MST = 12.43, p = 0.03). In lung cancer patients undergoing paclitaxel therapy, heterozygous carriers for the rs17217772 polymorphism have reduced survival time (MST = 7.96 vs 2.63 months; HR = 2.09; p = 0.02). For rs63749993 polymorphism undergoing irinotecan therapy, subjects having mutant genotype showed poor survival (13.26 vs 6.06 months; HR = 5.37; p = 0.0004). The results suggest that MSH2 polymorphisms are involved in decreasing overall survival for patients undergoing platinum-based chemotherapy.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
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Ghaderi-Zefrehi H, Rezaei M, Sadeghi F, Heiat M. Genetic polymorphisms in DNA repair genes and hepatocellular carcinoma risk. DNA Repair (Amst) 2021; 107:103196. [PMID: 34416543 DOI: 10.1016/j.dnarep.2021.103196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/23/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent types of tumors worldwide. Its occurrence and development have been related to various risk factors, such as chronic infection with hepatitis B or C viruses and alcohol addiction. DNA repair systems play a critical role in maintaining the integrity of the genome. Defects in these systems have been related to increased susceptibility to various types of cancer. Multiple genetic polymorphisms in genes of DNA repair systems have been reported that may affect DNA repair capacity (DRC) and modulate risk to cancer. Several studies have been conducted to assess the role of polymorphisms of DNA repair genes on the HCC risk. Identifying these polymorphisms and their association with HCC risk may help to improve prevention and treatment strategies. In this study, we review investigations that evaluated the association between genetic polymorphisms of DNA repair genes and risk of HCC.
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Affiliation(s)
- Hossein Ghaderi-Zefrehi
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Gillman R, Lopes Floro K, Wankell M, Hebbard L. The role of DNA damage and repair in liver cancer. Biochim Biophys Acta Rev Cancer 2020; 1875:188493. [PMID: 33316376 DOI: 10.1016/j.bbcan.2020.188493] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma is rapidly becoming a major cause of global mortality due to the ever-increasing prevalence of obesity. DNA damage is known to play an important role in cancer initiation, however DNA repair systems are also vital for the survival of cancer cells. Given the function of the liver and its exposure to the gut, it is likely that DNA damage and repair would be of particular importance in hepatocellular carcinoma. However, many contemporary reports have neglected the role of individual pathways of DNA damage and repair in their hypotheses. This review, therefore, aims to provide a concise overview for researchers in the field of liver cancer to understand the pathways of DNA damage and repair and their individual roles in hepatocellular carcinoma.
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Affiliation(s)
- Rhys Gillman
- Department of Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Kylie Lopes Floro
- Department of Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia; Department of Radiation Oncology, Townsville University Hospital, Townsville, Queensland, Australia
| | - Miriam Wankell
- Department of Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia; Australian Institute for Tropical Health and Medicine, Townsville, Queensland, Australia
| | - Lionel Hebbard
- Department of Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia; Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia; Australian Institute for Tropical Health and Medicine, Townsville, Queensland, Australia.
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9
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Ramirez-Valles EG, Rodríguez-Pulido A, Barraza-Salas M, Martínez-Velis I, Meneses-Morales I, Ayala-García VM, Alba-Fierro CA. A Quest for New Cancer Diagnosis, Prognosis and Prediction Biomarkers and Their Use in Biosensors Development. Technol Cancer Res Treat 2020; 19:1533033820957033. [PMID: 33107395 PMCID: PMC7607814 DOI: 10.1177/1533033820957033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Traditional techniques for cancer diagnosis, such as nuclear magnetic resonance, ultrasound and tissue analysis, require sophisticated devices and highly trained personnel, which are characterized by elevated operation costs. The use of biomarkers has emerged as an alternative for cancer diagnosis, prognosis and prediction because their measurement in tissues or fluids, such as blood, urine or saliva, is characterized by shorter processing times. However, the biomarkers used currently, and the techniques used for their measurement, including ELISA, western-blot, polymerase chain reaction (PCR) or immunohistochemistry, possess low sensitivity and specificity. Therefore, the search for new proteomic, genomic or immunological biomarkers and the development of new noninvasive, easier and cheaper techniques that meet the sensitivity and specificity criteria for the diagnosis, prognosis and prediction of this disease has become a relevant topic. The purpose of this review is to provide an overview about the search for new cancer biomarkers, including the strategies that must be followed to identify them, as well as presenting the latest advances in the development of biosensors that possess a high potential for cancer diagnosis, prognosis and prediction, mainly focusing on their relevance in lung, prostate and breast cancers.
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Affiliation(s)
- Eda G Ramirez-Valles
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | | | - Marcelo Barraza-Salas
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Isaac Martínez-Velis
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Iván Meneses-Morales
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Víctor M Ayala-García
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
| | - Carlos A Alba-Fierro
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Dgo, Mexico
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10
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Liu JY, Zou T, Yin JY, Wang Z, Wang Y, Liu ZQ, Chen J, Chen ZW. Genetic Variants in DNA Mismatch Repair Pathway predict prognosis of Lung Cancer patients with receiving Platinum-Based Chemotherapy. J Cancer 2020; 11:5281-5288. [PMID: 32742474 PMCID: PMC7391198 DOI: 10.7150/jca.46150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022] Open
Abstract
Objective: To investigate the relationships between genetic variants in DNA mismatch repair pathway genes and the prognosis of platinum-based chemotherapy in lung cancer patients. Methods: 346 lung cancer patients who received at least two cycles of platinum-based chemotherapy were recruited in this study. A total of 35 single nucleotide polymorphisms in 7 DNA mismatch repair genes were genotyped to investigate their associations with platinum-based chemotherapy prognosis. Result: The results revealed that patients carried MSH2 rs4608577 TT genotype had a significantly shorter progression free survival than patients with GG or GT genotypes (Additive model: P=0.003, OR =0.94, 95% CI =0.33-1.57). Patients with SAPCD1 rs707937 TT genotype had a significantly longer overall survival than patients with GG or GT genotypes (Additive model: P=0.0003, OR=0.75, 95% CI =0.35-1.14). Eight SNPs and fourteen SNPs were related to progression free survival and overall survival in subgroup analyses, respectively. Conclusion: Our findings suggest that the MSH2 rs4608577 and SAPCD1 rs707937 may be potential clinical biomarkers for predicting platinum-based chemotherapy prognosis in lung cancer patients.
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Affiliation(s)
- Jun-Yan Liu
- Department of Orthopaedics, The First Affiliated Hospital of the University of South China, Hengyang 421001, China
| | - Ting Zou
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, P.R.China
| | - Ji-Ye Yin
- Departments of Clinical Pharmacology, Xinagya Hospital, Central South University, Changsha 410008, China.,Institute of Clinical Pharmacology and Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China
| | - Zhan Wang
- Department of Medical Oncology, Lung cancer and Gastrointestinal unit, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha 410013, China
| | - Ying Wang
- Hunan clinical research center in gynecologic cancer, Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha 410013, China
| | - Zhao-Qian Liu
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, P.R.China.,Departments of Clinical Pharmacology, Xinagya Hospital, Central South University, Changsha 410008, China
| | - Juan Chen
- Department of Pharmacy, Xinagya Hospital, Central South University, Changsha 410008, China
| | - Zhi-Wei Chen
- Department of Orthopaedics, The First Affiliated Hospital of the University of South China, Hengyang 421001, China
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11
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Gong X, Huang A. Differential expression and diagnostic significance of P53, MutS homologs 2, tropomyosin-4 in alpha-fetoprotein-negative hepatocellular carcinoma. J Clin Lab Anal 2020; 34:e23353. [PMID: 32363617 PMCID: PMC7439328 DOI: 10.1002/jcla.23353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Current study aimed to explore the value of P53, MutS homologs 2 (MSH2), and tropomyosin-4 (Tm-4) combined with inflammatory factors, life-history traits in the differential diagnosis of alpha-fetoprotein-negative hepatocellular carcinoma (AFP-Negative HCC). METHODS A testing cohort including 280 AFP-Negative HCC patients and 300 controls was included. Three external validation cohorts from 3 centers were used to assess the novel logistic regression model including 400 AFP-Negative HCC patients and 400 controls. RESULTS Compared with the control group, the levels of P53, MSH2, and Tm-4 protein in si-P53 group, si-MSH2 group, and si-Tm-4 group were significantly reduced (P < .05). The P53, MSH2, Tm-4, neutrophil to lymphocyte ratio (NLR), monocytes to lymphocyte ratio (MLR), hypersensitive C-reactive protein (hs-CRP), tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6) levels, and the smoking, drinking, and occupational exposure to chemicals rates in patients were significantly higher than those in controls (P < .05). ROC analyses showed that the area under curve (AUC) of NLR, MLR, hs-CRP, TNF-α, IL-6, P53, MSH2, Tm-4, drinking, smoking, and occupational exposure to chemicals were 0.798, 0.803, 0.560, 0.644, 0.808, 0.681, 0.830, 0.694, 0.582, 0.581, and 0.567, respectively. A novel logistic regression model was built and has a high value in identifying AFP-Negative HCC with AUC of 0.917, sensitivity of 85.2%, and specificity of 88.3%. In the validation cohorts, this model also showed good diagnostic efficiency (AUC = 0.898 with Dazu Branch cohort, AUC = 0.924 with Jinshan Branch cohort, and AUC = 0.907 with Liangping Branch cohort). CONCLUSION Current model has potential significance for the noninvasive diagnosis of AFP-Negative HCC.
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Affiliation(s)
- Xuyang Gong
- Infectious Disease and Molecular Biology Laboratory, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- Infectious Disease and Molecular Biology Laboratory, Chongqing Medical University, Chongqing, China
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Yushchuk ND, Sleptsova SS, Malov SI, Bilukina IF, Semenov SI, Stepanenko LA, Ogarkov OB, Savilov ED, Malov IV. [Assessment of external risk factors of hepatocellular cancer development and markers of genetic predisposition to its development in the ethnic group of yakut - men]. TERAPEVT ARKH 2020; 92:56-61. [PMID: 32598664 DOI: 10.26442/00403660.2020.01.000505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 01/10/2023]
Abstract
AIM To establish the main external and genetically determined risk factors for the development of hepatocellular cancer in the ethnic group of male Yakuts living in the Republic of Sakha (Yakutia) [RS (Y)] in the epidemiologically unfavorable conditions of the incidence of viral hepatitis. MATERIALS AND METHODS A total of 97 male Yakuts were examined, including 44 people diagnosed with hepatocellular cancer and 53 people diagnosed with chronic viral hepatitis. HCC risk factors were identified by analyzing medical records and questioning patients. In the experimental and control groups, genetic studies of single nucleotide polymorphisms of genes mapped on the X-chromosome and involved in the activation of antiviral immunity along the TLR7 signaling pathway were performed. RESULTS AND DISCUSSION In 100% of patients with hepatocellular cancer, infection with hepatitis B, C, D viruses or co - infection with these agents was detected. Every fourth patient with HCC in the RS (Y) was infected with hepatitis D. The course of hepatocellular cancer associated with HDV was characterized by rapid progression of liver cirrhosis, development of portal hypertension, bleeding from varicose veins of the stomach and esophagus (36.4%) and edematous ascitic syndrome (63.6%). In addition to viral agents, additional risk factors for liver cancer were identified, such as alcohol abuse, overweight, diabetes mellitus, and smoking. Among the studied variation sites of genes localized on the X-chromosome and encoding the reaction of innate antiviral immunity, no genetic marker was found with a sufficient degree of confidence determining the likelihood of hepatocellular cancer developing. CONCLUSIONS The high incidence of hepatocellular carcinoma of the male population in the RS (Y) is due to the widespread prevalence of parenteral viral hepatitis, especially viral hepatitis D. Due to the introduction of mass vaccination of the population against hepatitis B in the Russian Federation in the foreseeable future in the RS (Y) we should see a decrease in the proportion of hepatocellular cancer associated with hepatitis B and D viruses, and therefore the focus should be on the treatment and prevention of hepatitis C virus and non - infectious risk factors.
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Affiliation(s)
- N D Yushchuk
- A.I. Evdokimov Moscow State University of Medicine and Dentistry
| | - S S Sleptsova
- M.K. Ammosov North-Eastern Federal University, Medical Institute
| | - S I Malov
- Irkutsk State Medical University.,Irkutsk State Medical Academy of Continuing Education
| | - I F Bilukina
- M.K. Ammosov North-Eastern Federal University, Medical Institute
| | - S I Semenov
- M.K. Ammosov North-Eastern Federal University, Medical Institute
| | | | - O B Ogarkov
- Irkutsk State Medical Academy of Continuing Education.,Scientific Center of Family Health and Human Reproduction
| | - E D Savilov
- Irkutsk State Medical Academy of Continuing Education.,Scientific Center of Family Health and Human Reproduction
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Li X, Wu Y, Suo P, Liu G, Li L, Zhang X, Chen S, Xu M, Song L. Identification of a novel germline frameshift mutation p.D300fs of PMS1 in a patient with hepatocellular carcinoma: A case report and literature review. Medicine (Baltimore) 2020; 99:e19076. [PMID: 32000458 PMCID: PMC7004782 DOI: 10.1097/md.0000000000019076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RATIONALE PMS1 is one of the mismatch repair (MMR) genes with potential crucial roles in carcinogenesis. Very few reports have been identified on germline PMS1 mutations with definite disease phenotype. Here we report a case of hepatocellular carcinoma (HCC) with a novel potential pathogenic germline PMS1 mutation. PATIENT CONCERNS A 46-year-old Chinese male with Hepatitis B infection history presented a single cancerous nodule (10×12×10 mm) at the left lobe of liver. The nodule was considered malignant by type-B ultrasonic and computed tomography (CT) examinations. DIAGNOSIS AND INTERVENTION Liver lobectomy was performed to remove the liver cancerous nodule and postoperative TACE was performed for recurrence prevention. Pathological examination on resected tumor tissue confirmed the diagnosis of HCC. Whole-exome sequencing (WES) identified the c.900delT (p.D300fs) heterozygous germline mutation of PMS1, along with 253 nonsynonymous single nucleotide variations (SNVs), 14 Insertion or deletion mutations (INDELs) and 21 genes with copy number variations (CNVs). Three-dimensional prediction of protein tertiary structure suggested that the conformation of the enzyme active site and the ligand binding site might be changed due to the protein truncation. OUTCOMES The patient was still alive in good condition with no sign of recurrence in 12 months follow-up period. LESSONS The affected pathways in this case were unique from previously reported HCC patients with no PMS1 germline mutations. The novel PMS1 germline mutation may increase cancer risk. The roles of PMS1 germline mutations in carcinogenesis need further investigation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lele Song
- HaploX Biotechnology, Co., Ltd
- Department of Radiotherapy, the Eighth Medical Center of the Chinese PLA General Hospital, PR China
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Zhao X, Dai D, Li X, Shen B, Chen X, Shu Y, Wang D. A polymorphism within the mismatch repair gene predicts prognosis and adjuvant chemotherapy benefit in gastric cancer. Gastric Cancer 2019; 22:1121-1129. [PMID: 30989434 DOI: 10.1007/s10120-019-00962-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Defective mismatch repair (dMMR) and microsatellite instability (MSI) correlate with gastric cancer (GC) outcome. We hypothesized that MMR genetic polymorphisms that have low-penetrant effects but may cause heterogeneous MMR capability among individuals also affect GC outcome. METHODS The polymorphisms rs1800734 in MLH1, rs2303428 and rs3732183 in MSH2, rs735943 in EXO1, and rs11797 in TREX1 were selected and analyzed in independent discovery and validation sets that included 167 and 593 patients, respectively. MSI was determined. RESULTS In both the discovery and validation sets, the rs2303428 TC + CC genotype correlated with poor overall survival (OS) in non-cardia (P < 0.05) but not in cardia GC. Multivariate models showed that for OS of patients with non-cardia GC, the rs2303428 TC + CC genotype was an independent predictor in the validation set (HR 1.54; 95% CI 1.02-2.32; P = 0.040) and had a trend to be an independent predictor in the discovery set (HR 1.70; 95% CI 0.96-3.01; P = 0.067). Furthermore, in both patient sets, fluoropyrimidines-based adjuvant chemotherapy improved OS for non-cardia patients with the rs2303428 TC + CC genotype (HR 0.14; 95% CI 0.04-0.57; P = 0.006; and HR 0.29; 95% CI 0.15-0.58; P < 0.001, respectively) but not for those with the TT genotype. The rs2303428 genotypes were not associated with MSI frequency. The rs2303428 TC + CC genotype correlated with reduced expressions for thymidylate synthetase, P-glycoprotein and ERCC1 (P < 0.05) in non-cardia GC. CONCLUSIONS The rs2303428 genotypes may predict prognosis and adjuvant chemotherapy benefit in non-cardia GC patients.
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Affiliation(s)
- Xiaohui Zhao
- Department of Medical Oncology, The Cancer Therapy Center, Affiliated Hospital of Jiangsu University, Road Jiefang, Zhenjiang, 212001, Jiangsu, China.,Department of Pathology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dongfang Dai
- Department of Medical Oncology, The Cancer Therapy Center, Affiliated Hospital of Jiangsu University, Road Jiefang, Zhenjiang, 212001, Jiangsu, China
| | - Xiaoqin Li
- Department of Medical Oncology, The Cancer Therapy Center, Affiliated Hospital of Jiangsu University, Road Jiefang, Zhenjiang, 212001, Jiangsu, China
| | - Bo Shen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaofeng Chen
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Road Guangzhou, Nanjing, 210029, China
| | - Yongqian Shu
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Road Guangzhou, Nanjing, 210029, China.
| | - Deqiang Wang
- Department of Medical Oncology, The Cancer Therapy Center, Affiliated Hospital of Jiangsu University, Road Jiefang, Zhenjiang, 212001, Jiangsu, China. .,Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Road Guangzhou, Nanjing, 210029, China.
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Si W, Kang S, Sun H, Chen J, Cao S, Li Y. Genetic polymorphisms in hMSH2 and hMLH1 genes are associated with prognosis in epithelial ovarian cancer patients. Int J Gynecol Cancer 2019; 29:1148-1155. [DOI: 10.1136/ijgc-2019-000368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 12/29/2022] Open
Abstract
ObjectiveDNA mismatch repair deficiency is not only thought to promote tumorigenesis but is also suggested to be associated with platinum-based chemotherapy treatment. In this study, we investigated the effects of two genetic polymorphisms in the hMSH2 and hMLH1 genes on the risk of epithelial ovarian cancer and the clinical outcome of patients treated with platinum-based chemotherapy.MethodsA case-control study was performed in 536 epithelial ovarian cancer patients and 532 control women. Genotypes of two polymorphisms were determined by the polymerase chain reaction/ligase detection reaction method. Pearson Chi-square test was used to evaluate genotype distributions and allele frequencies in the patients and controls. Kaplan-Meier survival curves, and univariate and multivariate Cox regression models were used to analyze the effect of polymorphisms on patients’ prognoses.ResultsThe genotype and allele frequencies of the rs2303428 and rs1800734 polymorphisms were not significantly different between the case and control groups. Compared with wild homozygous genotype, the presence of variant alleles (heterozygous and variant homozygous genotypes) did not affect the risk of developing epithelial ovarian cancer. However, survival analysis showed that the rs2303428 polymorphism was related to the prognosis of epithelial ovarian cancer patients. Compared with the TT genotype, patients carrying the C allele had a shorter progression-free survival during the 3- and 5-year follow-up (HR 1.41, 95% CI 1.07 to 1.87 and HR 1.56, 95% CI 1.12 to 2.16, respectively). For the rs1800734 polymorphism, the A allele may significantly increase patients’ progression-free survival compared with the GG genotype in the 5-year follow-up (HR 0.66, 95% CI 0.44 to 0.98).ConclusionOur research suggests that genetic polymorphisms in hMSH2 and hMLH1 may indicate the clinical progression of epithelial ovarian cancer patients treated with platinum-based chemotherapy.
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