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Hasona NA, Elsabahy M, Shaker OG, Zaki O, Ayeldeen G. The Implication of Growth Arrest-Specific 5 rs145204276 Polymorphism and Serum Expression of Sirtuin 1, Transforming Growth Factor-Beta, and microRNA-182 in Breast Cancer. Clin Med Insights Oncol 2024; 18:11795549241227415. [PMID: 38322669 PMCID: PMC10846042 DOI: 10.1177/11795549241227415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/01/2024] [Indexed: 02/08/2024] Open
Abstract
Background Breast cancer (BC) patients have a higher chance of survival if it is diagnosed at an early stage, which is essential for efficient treatment of the condition. The results of an elevated risk of cancer, including BC, previously associated with the ins/del polymorphism rs145204276 in the promoter region of growth arrest-specific 5 (GAS5) are still up for debate. Thus, this study aimed to appraise the frequency of the GAS5 rs145204276 variant with BC risk and demonstrate the potential impact of the sirtuin 1 (SIRT-1), transforming growth factor-beta (TGF-β), and microRNA-182 (miR-182) expression and their diagnostic value in BC. Methods Blood samples of 155 patients with BC and fibroadenoma and 80 healthy controls were analyzed for GAS5 rs145204276 single nucleotide polymorphism (SNP), SIRT-1, TGF-β, and miRNA-182 expression levels. Results Ins/ins genotype and ins allele frequencies for GAS5 rs145204276 were considerably higher in BC patients compared with controls. Patients with BC had significantly greater serum levels of TGF-β, miR-182, and SIRT-1 expression. Conclusions The SIRT-1, TGF-β, and miR-182 genes provide novel, noninvasive diagnostic biomarkers for BC.
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Affiliation(s)
- Nabil A Hasona
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Mahmoud Elsabahy
- Badr University in Cairo Research Center, Badr University in Cairo, Badr City, Egypt
| | - Olfat G Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Othman Zaki
- Department of Clinical Pathology, Faculty of Medicine, Damietta University, New Damietta, Egypt
| | - Ghada Ayeldeen
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Giza, Egypt
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Zeng Z, Mao C, Vo A, Li X, Nugent JO, Khan SA, Clare SE, Luo Y. Deep learning for cancer type classification and driver gene identification. BMC Bioinformatics 2021; 22:491. [PMID: 34689757 PMCID: PMC8543824 DOI: 10.1186/s12859-021-04400-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Background Genetic information is becoming more readily available and is increasingly being used to predict patient cancer types as well as their subtypes. Most classification methods thus far utilize somatic mutations as independent features for classification and are limited by study power. We aim to develop a novel method to effectively explore the landscape of genetic variants, including germline variants, and small insertions and deletions for cancer type prediction.
Results We proposed DeepCues, a deep learning model that utilizes convolutional neural networks to unbiasedly derive features from raw cancer DNA sequencing data for disease classification and relevant gene discovery. Using raw whole-exome sequencing as features, germline variants and somatic mutations, including insertions and deletions, were interactively amalgamated for feature generation and cancer prediction. We applied DeepCues to a dataset from TCGA to classify seven different types of major cancers and obtained an overall accuracy of 77.6%. We compared DeepCues to conventional methods and demonstrated a significant overall improvement (p < 0.001). Strikingly, using DeepCues, the top 20 breast cancer relevant genes we have identified, had a 40% overlap with the top 20 known breast cancer driver genes. Conclusion Our results support DeepCues as a novel method to improve the representational resolution of DNA sequencings and its power in deriving features from raw sequences for cancer type prediction, as well as discovering new cancer relevant genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04400-4.
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Affiliation(s)
- Zexian Zeng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 750 N Lake Shore Drive Room 11-189, Chicago, IL, 60611, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chengsheng Mao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 750 N Lake Shore Drive Room 11-189, Chicago, IL, 60611, USA
| | - Andy Vo
- Committee on Developmental Biology and Regenerative Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Janna Ore Nugent
- Research Computing Services, Northwestern University, Chicago, IL, USA
| | - Seema A Khan
- Department of Surgery, Feinberg School of Medicine, Northwestern University, NMH/Prentice Women's Hospital Room 4-420 250 E Superior, Chicago, IL, 60611, USA.
| | - Susan E Clare
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Robert H Lurie Medical Research Center Room 4-113 250 E Superior, Chicago, IL, 60611, USA.
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 750 N Lake Shore Drive Room 11-189, Chicago, IL, 60611, USA.
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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Rahimi N, Azizi M, Bahari G, Narouie B, Hashemi M. Association of EGLN2 rs10680577 Polymorphism with the Risk and Clinicopathological Features of Patients with Prostate Cancer. Asian Pac J Cancer Prev 2020; 21:1221-1226. [PMID: 32458625 PMCID: PMC7541883 DOI: 10.31557/apjcp.2020.21.5.1221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Indexed: 11/25/2022] Open
Abstract
Several studies have evaluated the association between EGLN2 4-bp insertion/deletion (ins/del) polymorphism (rs10680577) and many cancers. However, up to date, no study has inspected the impact of rs10680577 polymorphism on prostate cancer (PCa) risk. This case-control study was achieved on 170 pathologically confirmed PCa patients and 196 cancer free men to inspect whether rs10680577 variant is related to the risk and clinicopathological features of patients with PCa. Genotyping was performed by mismatched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The findings did not support an association between the variant with the risk and clinicopathological characteristics of PCa patients. When we pooled our results with six preceding studies, the findings suggested that rs10680577 variant significantly augmented the risk of overall cancer in heterozygous (OR=1.38, 95 % CI=1.26-1.52, p<0.00001, ins/del vs ins/ins), homozygous (OR=1.66, 95 % CI=1.05-2.61, p=0.029, del/del vs ins/ins), codominant (OR=1.44, 95%CI=1.32-1.58, p<0.00001, ins/del+del/del vs ins/ins), and allele (OR=1.32, 95%CI=1.18-1.49, p<0.00001, del vs ins) genetic models. Additional well designed studies with larger sample sizes are necessary to confirm our findings.
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Affiliation(s)
- Nahid Rahimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahsa Azizi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Gholamreza Bahari
- Children and Adolescent Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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Zhang S, Zhu K, Zhang Z, Wang H, Wang X. Association between an indel polymorphism within the distal promoter of EGLN2 and cancer risk: An updated meta-analysis. Mol Genet Genomic Med 2019; 7:e00936. [PMID: 31414584 PMCID: PMC6785434 DOI: 10.1002/mgg3.936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/03/2019] [Accepted: 08/05/2019] [Indexed: 01/11/2023] Open
Abstract
Background The association between a 4‐bp indel polymorphism (rs10680577) within the distal promoter of EGLN2 and cancer risk has been investigated by several case–control studies in recent years, but investigation results were inconsistent. Thus, a systematic assessment of the association was performed based on a literature review and pooled analysis. Methods Two investigators independently retrieved relevant studies from PubMed, Chinese National Knowledge Infrastructure (CNKI), Embase, and Google Scholar. The fixed or random effects model was selected to calculate odds ratios (ORs) with 95% confidence intervals (CIs) based on heterogeneity level. All analyses including heterogeneity assessment, subgroup analysis, sensitivity analysis, and publication bias assessment were performed using RevMan 5.3 software and Stata 12.0 software. Results A total of six relevant studies with 3,406 cases and 5,147 controls were included in the final analysis. The overall pooled analysis showed that EGLN2 rs10680577 polymorphism was significantly associated with cancer risk under all genetic models. However, subgroup analysis based on cancer type showed that the polymorphism was significantly associated with the risk of digestive system cancer under all genetic models, and with the risk of lung cancer under dominant model, heterozygote comparison model, and allele comparison model. Subgroup analysis based on population sources showed a significant association in Chinese population under all genetic models. Conclusion The present result suggests that EGLN2 rs10680577 polymorphism is associated with cancer risk, and may act as a promising predictive biomarker for cancer risk, especially in Chinese population. However, further well‐designed studies are warranted to confirm these results.
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Affiliation(s)
- Shulong Zhang
- Department of General Surgery, Xuhui District Central Hospital of Shanghai, Shanghai, China
| | - Kaihua Zhu
- Department of General Surgery, Xuhui District Central Hospital of Shanghai, Shanghai, China
| | - Zuoliang Zhang
- Department of General Surgery, Xuhui District Central Hospital of Shanghai, Shanghai, China
| | - Hui Wang
- Department of General Surgery, Xuhui District Central Hospital of Shanghai, Shanghai, China
| | - Xiaolong Wang
- Department of General Surgery, Xuhui District Central Hospital of Shanghai, Shanghai, China
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Zhu J, Luo JZ, Li CB. Correlations of an Insertion/Deletion Polymorphism (rs10680577) in the RERT-lncRNA with the Susceptibility, Clinicopathological Features, and Prognosis of Lung Cancer. Biochem Genet 2018; 57:147-158. [PMID: 30073577 DOI: 10.1007/s10528-018-9883-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022]
Abstract
The aim of this study was to investigate the correlations of an Ins/Del polymorphism (rs10680577) in the RERT-lncRNA with the susceptibility, clinicopathological features, and prognosis of lung cancer. A total of 376 patients with lung cancer and 419 healthy subjects were enrolled in this study. The genotype of rs10680577 was performed using polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis. Quantitative real-time PCR was used to measure RERT-lncRNA and EGLN2 expressions. Subjects with Del allele of rs10680577 exhibited an elevated risk of lung cancer. The expressions of RERT-lncRNA and EGLN2 in tumor tissues were higher than adjacent normal tissues, manifesting a positive correlation. Compared to patients with Ins/Ins genotype carriers, those with Ins/Del + Del/Del genotype carriers had upregulated expressions of RERT-lncRNA and EGLN2. Moreover, Ins/Del + Del/Del genotype and expressions of RERT-lncRNA and EGLN2 were associated with age, smoking habits, and TNM stage in lung cancer patients. Besides, patients with Ins/Ins genotype of rs10680577 had a longer OS than those with Ins/Del + Del/Del genotype carriers, and patients with lower expressions of RERT-lncRNA and EGLN2 presented a shorter OS than those with higher expressions. COX multivariate analysis demonstrated that Ins/Del + Del/Del genotype and higher expressions of RERT lncRNA and EGLN2 were risk factors affecting the prognosis of lung cancer. The Ins/Del polymorphism (rs10680577) in RERT-lncRNA was correlated with the risk, major clinicopathological features, and prognosis of lung cancer patients, and the patients with Ins/Del + Del/Del genotype carriers had higher expressions of RERT-lncRNA and EGLN2 than those with Ins/Ins carriers.
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Affiliation(s)
- Jing Zhu
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China
| | - Jin-Zhu Luo
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China
| | - Cheng-Bin Li
- Department of Laboratory Medicine, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, 434020, Hubei, China.
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Ma Q, Mao Z, Du J, Liao S, Zheng Y, Zhi M, Zhang J, Wang Y. Association between an insertion/deletion polymorphism in the interleukin-1α gene and the risk of colorectal cancer in a Chinese population. Int J Biol Markers 2018; 33:1724600818785069. [PMID: 30016900 DOI: 10.1177/1724600818785069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Previous studies have reported that polymorphisms in the interleukin-1 gene may be involved in tumorigenesis and tumor progression. AIM The purpose of the present study was to evaluate whether an insertion/deletion polymorphism, rs3783553, located in the miR-122 target gene interleukin-1α, was associated with the risk of colorectal cancer. METHODS Genomic DNA was extracted from peripheral venous blood of 382 patients with colorectal cancer and 433 controls, and the polymorphism was genotyped using a polymerase chain reaction assay. RESULTS Significantly decreased colorectal cancer risk was observed to be associated with the interleukin-1α rs3783553 insertion/insertion genotype ( P=0.0001; OR=0.41; 95% CI 0.26, 0.65) and the insertion allele ( P<0.001; OR=0.68; 95% CI 0.55, 0.83). Stratification analysis based on clinical and pathological features also revealed that the "TTCA" insertion allele of rs3783553 contributes to slow the progression of colorectal cancer. CONCLUSION These results suggest that the rs3783553 polymorphism could be a useful genetic marker to predict the size/extent of colorectal cancer.
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Affiliation(s)
- Qizhao Ma
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Zhigang Mao
- 2 Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Jipei Du
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Shiping Liao
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yanjiang Zheng
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Maohui Zhi
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Ji Zhang
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yufang Wang
- 1 West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
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Hashemi M, Danesh H, Bizhani F, Sattarifard H, Hashemi SM, Bahari G. Detection of a 4-bp Insertion/deletion Polymorphism within the Promoter of EGLN2 Using Mismatch PCR-RFLP and Its Association with Susceptibility to Breast Cancer. Asian Pac J Cancer Prev 2018; 19:923-926. [PMID: 29693343 PMCID: PMC6031807 DOI: 10.22034/apjcp.2018.19.4.923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It has been shown that a 4-bp insertion/deletion (ins/del) polymorphism of EGLN2 influences the risk of several cancers. However, to date, no study has inspected the impact of the 4-bp ins/del polymorphism on breast cancer (BC) risk. A case-control study, including 134 breast cancer patients and 154 healthy women, was here conducted to examine the possible association between EGLN2 4-bp ins/del polymorphism and BC risk in a southeast Iranian population. A mismatched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was designed for genotyping of the variant. Our findings did not support any association between the 4-bp ins/del polymorphism and the risk of BC in the codominant, dominant, recessive and allele inheritance models tested. When links between the EGLN2 4-bp ins/del polymorphism and clinicopathological characteristics of the patients were evaluate the variant was only associated with HER2 status. More studies with larger sample sizes and diverse ethnicities are warranted to verify our finding.
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Affiliation(s)
- Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
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Kennel KB, Burmeister J, Schneider M, Taylor CT. The PHD1 oxygen sensor in health and disease. J Physiol 2018; 596:3899-3913. [PMID: 29435987 DOI: 10.1113/jp275327] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
The hypoxia-inducible factor (HIF) co-ordinates the adaptive transcriptional response to hypoxia in metazoan cells. The hypoxic sensitivity of HIF is conferred by a family of oxygen-sensing enzymes termed HIF hydroxylases. This family consists of three prolyl hydroxylases (PHD1-3) and a single asparagine hydroxylase termed factor inhibiting HIF (FIH). It has recently become clear that HIF hydroxylases are functionally non-redundant and have discrete but overlapping physiological roles. Furthermore, altered abundance or activity of these enzymes is associated with a number of pathologies. Pharmacological HIF-hydroxylase inhibitors have recently proven to be both tolerated and therapeutically effective in patients. In this review, we focus on the physiology, pathophysiology and therapeutic potential of the PHD1 isoform, which has recently been implicated in diseases including inflammatory bowel disease, ischaemia and cancer.
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Affiliation(s)
- Kilian B Kennel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Julius Burmeister
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Cormac T Taylor
- UCD Conway Institute & School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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