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Mansouri V, Vafaee R, Mohammadi Maram M, Bandarian F, Sarabi P, Razi F, Razzaghi Z, Rezaei Tavirani M, Karimi H, Rezaei-Tavirani M. Inflammation and immunological disarrays are associated with acute exercise in type 2 diabetes. J Diabetes Metab Disord 2024; 23:1243-1250. [PMID: 38932912 PMCID: PMC11196459 DOI: 10.1007/s40200-024-01417-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/08/2024] [Indexed: 06/28/2024]
Abstract
Objective Type 2 diabetes (T2D) is the most common metabolic disorder that is associated with insulin resistance. The aim of the present study is to discover details of the molecular mechanism of exercise on control or progress of diabetic condition in patients via network analysis. Methods Gene expression profiles of patients with T2D before and after doing exercise are retrieved from Gene Expression Omnibus (GEO) and are pre-evaluated by the GEO2R program. Data are studied based on expression values, regulatory relationships between the differentially expressed genes (DEGs), gene ontology analyses, and protein-protein interaction PPI network analysis. Results A number of 118 significant DEGs were identified and classified based on fold change (FC) values as most dysregulated genes and dysregulated individuals. Action map analysis revealed that 18 DEGs appeared as the critical genes. Gene ontology analysis showed that 24 DEGs are connected to at least four pathways. JUN, IL6, IL1B, PTGS2, FOS, MYC, ATF3, CXCL8, EGR1, EGR2, NR4A1, PLK3, TTN, and UCP3 were identified as central DEGs. Conclusion Finally; JUN, IL6, IL1B, PTGS2, FOS, ATF3, CXCL8, EGR1, and EGR2 were introduced as the critical targeted genes by exercise. Since the critical genes after exercise are upregulated and mostly are known as the risk factors of T2D, it can be concluded that unsuitable exercise can develop diabetic conditions in patients. Acute exercise-induced inflammation and immune disturbances seem to be associated with the development of T2D in patients.
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Affiliation(s)
- Vahid Mansouri
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Vafaee
- Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Bandarian
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Sarabi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farideh Razi
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Razzaghi
- Laser application in medical sciences research center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Hassan Karimi
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Shaikh MAJ, Altamimi ASA, Afzal M, Gupta G, Singla N, Gilhotra R, Almalki WH, Kazmi I, Alzarea SI, Prasher P, Singh SK, Dua K. Unraveling the impact of miR-21 on apoptosis regulation in glioblastoma. Pathol Res Pract 2024; 254:155121. [PMID: 38262269 DOI: 10.1016/j.prp.2024.155121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
Glioblastoma is a prevalent form of carcinoma that exhibits a greater incidence rate across diverse demographics globally. Despite extensive global efforts, GBM continues to be a highly lethal disease that is characterized by a grim prognosis. There is a wealth of evidence suggesting that the pathophysiology of GBM is associated with the dysregulation of numerous cellular and molecular processes. The etiology of GBM may involve various cellular and molecular pathways, including EGFR, PDCD4, NF-κB, MAPK, matrix metalloproteinases, STAT, and Akt. MicroRNAs, short non-coding RNA molecules, regulate gene expression and mRNA translation after transcription but before translation to exert control over a wide range of biological functions. Extensive research has consistently demonstrated the upregulation of miRNA-21 in glioma, indicating its involvement in diverse biological pathways that facilitate tumor cell survival. By explaining the intricate interplay between miR-21 and the regulation of apoptosis in GBM, this review has the potential to significantly enhance our comprehension of the illness and provide potential targets for therapeutic intervention.
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Affiliation(s)
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, India.
| | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, India
| | - Ritu Gilhotra
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Energy Acres, Dehradun 248007, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
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Rabby MG, Rahman MH, Islam MN, Kamal MM, Biswas M, Bonny M, Hasan MM. In silico identification and functional prediction of differentially expressed genes in South Asian populations associated with type 2 diabetes. PLoS One 2023; 18:e0294399. [PMID: 38096208 PMCID: PMC10721103 DOI: 10.1371/journal.pone.0294399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
Type 2 diabetes (T2D) is one of the major metabolic disorders in humans caused by hyperglycemia and insulin resistance syndrome. Although significant genetic effects on T2D pathogenesis are experimentally proved, the molecular mechanism of T2D in South Asian Populations (SAPs) is still limited. Hence, the current research analyzed two Gene Expression Omnibus (GEO) and 17 Genome-Wide Association Studies (GWAS) datasets associated with T2D in SAP to identify DEGs (differentially expressed genes). The identified DEGs were further analyzed to explore the molecular mechanism of T2D pathogenesis following a series of bioinformatics approaches. Following PPI (Protein-Protein Interaction), 867 potential DEGs and nine hub genes were identified that might play significant roles in T2D pathogenesis. Interestingly, CTNNB1 and RUNX2 hub genes were found to be unique for T2D pathogenesis in SAPs. Then, the GO (Gene Ontology) showed the potential biological, molecular, and cellular functions of the DEGs. The target genes also interacted with different pathways of T2D pathogenesis. In fact, 118 genes (including HNF1A and TCF7L2 hub genes) were directly associated with T2D pathogenesis. Indeed, eight key miRNAs among 2582 significantly interacted with the target genes. Even 64 genes were downregulated by 367 FDA-approved drugs. Interestingly, 11 genes showed a wide range (9-43) of drug specificity. Hence, the identified DEGs may guide to elucidate the molecular mechanism of T2D pathogenesis in SAPs. Therefore, integrating the research findings of the potential roles of DEGs and candidate drug-mediated downregulation of marker genes, future drugs or treatments could be developed to treat T2D in SAPs.
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Affiliation(s)
- Md. Golam Rabby
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Khulna, Bangladesh
| | - Md. Hafizur Rahman
- Department of Agro Product Processing Technology, Jashore University of Science and Technology, Khulna, Bangladesh
- Faculty of Food Sciences and Safety, Department of Quality Control and Safety Management, Khulna Agricultural University, Khulna, Bangladesh
| | - Md. Numan Islam
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Khulna, Bangladesh
| | - Md. Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Khulna, Bangladesh
| | - Mrityunjoy Biswas
- Department of Agro Product Processing Technology, Jashore University of Science and Technology, Khulna, Bangladesh
| | - Mantasa Bonny
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Khulna, Bangladesh
| | - Md. Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Khulna, Bangladesh
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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Islam MN, Rabby MG, Hossen MM, Kamal MM, Zahid MA, Syduzzaman M, Hasan MM. In silico functional and pathway analysis of risk genes and SNPs for type 2 diabetes in Asian population. PLoS One 2022; 17:e0268826. [PMID: 36037214 PMCID: PMC9423640 DOI: 10.1371/journal.pone.0268826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Type 2 diabetes (T2D) has earned widespread recognition as a primary cause of death, disability, and increasing healthcare costs. There is compelling evidence that hereditary factors contribute to the development of T2D. Clinical trials in T2D have mostly focused on genes and single nucleotide polymorphisms (SNPs) in protein-coding areas. Recently, it was revealed that SNPs located in noncoding areas also play a significant impact on disease vulnerability. It is required for cell type-specific gene expression. However, the precise mechanism by which T2D risk genes and SNPs work remains unknown. We integrated risk genes and SNPs from genome-wide association studies (GWASs) and performed comprehensive bioinformatics analyses to further investigate the functional significance of these genes and SNPs. We identified four intriguing transcription factors (TFs) associated with T2D. The analysis revealed that the SNPs are engaged in chromatin interaction regulation and/or may have an effect on TF binding affinity. The Gene Ontology (GO) study revealed high enrichment in a number of well-characterized signaling pathways and regulatory processes, including the STAT3 and JAK signaling pathways, which are both involved in T2D metabolism. Additionally, a detailed KEGG pathway analysis identified two major T2D genes and their prospective therapeutic targets. Our findings underscored the potential functional significance of T2D risk genes and SNPs, which may provide unique insights into the disease’s pathophysiology.
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Affiliation(s)
- Md. Numan Islam
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Golam Rabby
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Munnaf Hossen
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, China
| | - Md. Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Ashrafuzzaman Zahid
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Syduzzaman
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Division of Plant Science, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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Interactive bioinformatics analysis for the screening of hub genes and molecular docking of phytochemicals present in kitchen spices to inhibit CDK1 in cervical cancer. Comput Biol Med 2022; 149:105994. [DOI: 10.1016/j.compbiomed.2022.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/07/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
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Khokhar M, Roy D, Tomo S, Gadwal A, Sharma P, Purohit P. Novel Molecular Networks and Regulatory MicroRNAs in Type 2 Diabetes Mellitus: Multiomics Integration and Interactomics Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e32437. [PMID: 38935970 PMCID: PMC11135235 DOI: 10.2196/32437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/18/2021] [Accepted: 12/27/2021] [Indexed: 06/29/2024]
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a metabolic disorder with severe comorbidities. A multiomics approach can facilitate the identification of novel therapeutic targets and biomarkers with proper validation of potential microRNA (miRNA) interactions. OBJECTIVE The aim of this study was to identify significant differentially expressed common target genes in various tissues and their regulating miRNAs from publicly available Gene Expression Omnibus (GEO) data sets of patients with T2DM using in silico analysis. METHODS Using differentially expressed genes (DEGs) identified from 5 publicly available T2DM data sets, we performed functional enrichment, coexpression, and network analyses to identify pathways, protein-protein interactions, and miRNA-mRNA interactions involved in T2DM. RESULTS We extracted 2852, 8631, 5501, 3662, and 3753 DEGs from the expression profiles of GEO data sets GSE38642, GSE25724, GSE20966, GSE26887, and GSE23343, respectively. DEG analysis showed that 16 common genes were enriched in insulin secretion, endocrine resistance, and other T2DM-related pathways. Four DEGs, MAML3, EEF1D, NRG1, and CDK5RAP2, were important in the cluster network regulated by commonly targeted miRNAs (hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-124-3p, hsa-mir-1-3p), which are involved in the advanced glycation end products (AGE)-receptor for advanced glycation end products (RAGE) signaling pathway, culminating in diabetic complications and endocrine resistance. CONCLUSIONS This study identified tissue-specific DEGs in T2DM, especially pertaining to the heart, liver, and pancreas. We identified a total of 16 common DEGs and the top four common targeting miRNAs (hsa-let-7b-5p, hsa-miR-124-3p, hsa-miR-1-3p, and has-miR-155-5p). The miRNAs identified are involved in regulating various pathways, including the phosphatidylinositol-3-kinase-protein kinase B, endocrine resistance, and AGE-RAGE signaling pathways.
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Affiliation(s)
- Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Dipayan Roy
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Sojit Tomo
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Ashita Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
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Milchram L, Fischer A, Huber J, Soldo R, Sieghart D, Vierlinger K, Blüml S, Steiner G, Weinhäusel A. Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041452. [PMID: 35209238 PMCID: PMC8876797 DOI: 10.3390/molecules27041452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022]
Abstract
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.05 were identified between seropositive and seronegative RA for the human samples. Correlation with the clinical disease activity index revealed an inverse correlation of antibodies against self-proteins found in pathways relevant for antigen presentation and immune regulation. The PIA model showed n = 1291 significant DIRAGs within acute disease. Significant DIRAGs for (I) seropositive, (II) seronegative and (III) PIA were subjected to the Reactome pathway browser which also revealed pathways relevant for antigen presentation and immune regulation; of these, seven overlapping pathways had high significance. We therefore conclude that the PIA model reflects the biological similarities of the disease pathogenesis. Our data show that protein array analysis can elucidate biological differences and pathways relevant in disease as well be a useful additional layer of omics information.
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Affiliation(s)
- Lisa Milchram
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Anita Fischer
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Jasmin Huber
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Regina Soldo
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Daniela Sieghart
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Stephan Blüml
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Günter Steiner
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
- Correspondence:
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Shawki HA, Abo-hashem EM, Youssef MM, Shahin M, Elzehery R. PPARɣ2, aldose reductase, and TCF7L2 gene polymorphisms: relation to diabetes mellitus. J Diabetes Metab Disord 2022; 21:241-250. [PMID: 35673413 PMCID: PMC9167404 DOI: 10.1007/s40200-021-00963-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/25/2021] [Indexed: 01/05/2023]
Abstract
Purpose Diabetes mellitus (DM) is a growing global health concern. Genetic factors play a pivotal role in the development of diabetes. Therefore, the present work aimed to study the relation between peroxisome proliferator-activate receptors (PPARɣ2) (rs3856806), aldose reductase (AR) (rs759853), transcription factor 7 like 2 (TCF7L2) (rs7903146) gene polymorphism with diabetes in the Egyptian population. Methods The study included 260 diabetics and 120 healthy subjects. Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism. Results Regression analysis revealed that PPARɣ2 TT, TCF7L2 TT were suggested to be independent risk predictors for T1DM and TCF7L2 TC, CC genotype were suggested to be independent protective factors against T1DM development. On the other hand, PPARɣ2 TT, AR TT genotypes were suggested to be independent risk predictors for T2DM susceptibility, and PPARɣ2 CT genotypes were suggested to be independent protective factors against T2DM development. Conclusion The present study revealed that PPARγ2 (rs3856806), TCF7L2 (rs7903146) and AR (rs759853) gene polymorphism may play an important role in the susceptibility of diabetes. Therefore, these polymorphisms may have a prognostic value for diabetes in the Egyptian population. Further work is required to confirm the role of these polymorphisms in diabetes.
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Affiliation(s)
- Hadeel Ahmed Shawki
- grid.10251.370000000103426662Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt ,grid.10251.370000000103426662Mansoura Ophthalmic Center, Mansoura University, Mansoura, Egypt
| | - Ekbal M. Abo-hashem
- grid.10251.370000000103426662Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Magdy M. Youssef
- grid.10251.370000000103426662Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Maha Shahin
- grid.10251.370000000103426662Mansoura Ophthalmic Center, Mansoura University, Mansoura, Egypt
| | - Rasha Elzehery
- grid.10251.370000000103426662Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Liu S, Ren W, Yu J, Li C, Tang S. Identification of Hub Genes Associated with Diabetes Mellitus and Tuberculosis Using Bioinformatic Analysis. Int J Gen Med 2021; 14:4061-4072. [PMID: 34354368 PMCID: PMC8331204 DOI: 10.2147/ijgm.s318071] [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: 05/04/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose To investigate the potential pathophysiological association between tuberculosis (TB) and diabetes mellitus (DM) using bioinformatic analyses. Patients and Methods Gene expression datasets for healthy controls (HCs), TB patients, DM patients, TB+DM patients (GSE114192), and metformin-treated cells (GSE102677) were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified from pairwise dataset comparisons TB vs HCs and DM vs HCs. DEGs were verified by comparing them to DEGs for TB+DM vs HCs. Enrichment analysis of DEGs common to all three dataset comparisons was conducted using DAVID. The protein–protein interaction (PPI) network was established via STRING and visualised in Cytoscape. Hub genes were identified using the Cytoscape plug-in cytoHubba and then were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. Targeted miRNA prediction analysis identified metformin treatment-induced gene expression changes in peripheral blood mononuclear cells. Results A total of 422 DEGs were common to all three dataset comparisons. Functional enrichment analysis revealed these DEGs were enriched for functional terms of type I interferon signaling pathway, innate immune response, inflammatory response, and infectious diseases. Ten hub genes identified using PPI network analysis were screened for interactions with metformin target gene INS using cytoHubba based on maximal clique centrality (MCC) score. Subsequently, five hub genes were predicted to functionally interact with INS, including STAT1, IFIT3, RSAD2, IFI44L, and XAF1, as verified by RT-qPCR. Meanwhile, seven miRNAs (miR-3680-3p, miR-3059-5p, miR-629-3p, miR-29b-2-5p, miR-514b-5p, miR-4755-5p, miR-4691-3p) were associated with regulation of hub genes. Notably, six hub genes (STAT1, IFIT3, RSAD2, ISG15, IFI44, IFI6) were down-regulated in cells exposed to both metformin and Mycobacterium tuberculosis antigens. Conclusion Network hub genes hold promise as disease status biomarkers and as metformin treatment targets for alleviating TB and DM. This study describes a strategy for exploring pathogenic mechanisms of diseases such as TB and DM.
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Affiliation(s)
- Shengsheng Liu
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China.,Multidisciplinary Diagnosis and Treatment Centre for Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China.,Department of Tuberculosis, Anhui Chest Hospital, Anhui, 230022, People's Republic of China
| | - Weicong Ren
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China
| | - Jiajia Yu
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China.,Multidisciplinary Diagnosis and Treatment Centre for Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China
| | - Chuanyou Li
- Department of Bacteriology and Immunology, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China
| | - Shenjie Tang
- Multidisciplinary Diagnosis and Treatment Centre for Tuberculosis, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People's Republic of China
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Chan JY, Bensellam M, Lin RCY, Liang C, Lee K, Jonas JC, Laybutt DR. Transcriptome analysis of islets from diabetes-resistant and diabetes-prone obese mice reveals novel gene regulatory networks involved in beta-cell compensation and failure. FASEB J 2021; 35:e21608. [PMID: 33977593 DOI: 10.1096/fj.202100009r] [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: 01/03/2021] [Revised: 03/23/2021] [Accepted: 04/05/2021] [Indexed: 01/02/2023]
Abstract
The mechanisms underpinning beta-cell compensation for obesity-associated insulin resistance and beta-cell failure in type 2 diabetes remain poorly understood. We used a large-scale strategy to determine the time-dependent transcriptomic changes in islets of diabetes-prone db/db and diabetes-resistant ob/ob mice at 6 and 16 weeks of age. Differentially expressed genes were subjected to cluster, gene ontology, pathway and gene set enrichment analyses. A distinctive gene expression pattern was observed in 16 week db/db islets in comparison to the other groups with alterations in transcriptional regulators of islet cell identity, upregulation of glucose/lipid metabolism, and various stress response genes, and downregulation of specific amino acid transport and metabolism genes. In contrast, ob/ob islets displayed a coordinated downregulation of metabolic and stress response genes at 6 weeks of age, suggestive of a preemptive reconfiguration in these islets to lower the threshold of metabolic activation in response to increased insulin demand thereby preserving beta-cell function and preventing cellular stress. In addition, amino acid transport and metabolism genes were upregulated in ob/ob islets, suggesting an important role of glutamate metabolism in beta-cell compensation. Gene set enrichment analysis of differentially expressed genes identified the enrichment of binding motifs for transcription factors, FOXO4, NFATC1, and MAZ. siRNA-mediated knockdown of these genes in MIN6 cells altered cell death, insulin secretion, and stress gene expression. In conclusion, these data revealed novel gene regulatory networks involved in beta-cell compensation and failure. Preemptive metabolic reconfiguration in diabetes-resistant islets may dampen metabolic activation and cellular stress during obesity.
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Affiliation(s)
- Jeng Yie Chan
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mohammed Bensellam
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Pôle D'endocrinologie, Diabète et Nutrition, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Ruby C Y Lin
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Cassandra Liang
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kailun Lee
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jean-Christophe Jonas
- Pôle D'endocrinologie, Diabète et Nutrition, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - D Ross Laybutt
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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Gupta MK, Ramakrishna V. Identification of targeted molecules in cervical cancer by computational approaches. A THERANOSTIC AND PRECISION MEDICINE APPROACH FOR FEMALE-SPECIFIC CANCERS 2021:213-222. [DOI: 10.1016/b978-0-12-822009-2.00011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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13
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Lam ATN, Aksit MA, Vecchio-Pagan B, Shelton CA, Osorio DL, Anzmann AF, Goff LA, Whitcomb DC, Blackman SM, Cutting GR. Increased expression of anion transporter SLC26A9 delays diabetes onset in cystic fibrosis. J Clin Invest 2020; 130:272-286. [PMID: 31581148 DOI: 10.1172/jci129833] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Diabetes is a common complication of cystic fibrosis (CF) that affects approximately 20% of adolescents and 40%-50% of adults with CF. The age at onset of CF-related diabetes (CFRD) (marked by clinical diagnosis and treatment initiation) is an important measure of the disease process. DNA variants associated with age at onset of CFRD reside in and near SLC26A9. Deep sequencing of the SLC26A9 gene in 762 individuals with CF revealed that 2 common DNA haplotypes formed by the risk variants account for the association with diabetes. Single-cell RNA sequencing (scRNA-Seq) indicated that SLC26A9 is predominantly expressed in pancreatic ductal cells and frequently coexpressed with CF transmembrane conductance regulator (CFTR) along with transcription factors that have binding sites 5' of SLC26A9. These findings were replicated upon reanalysis of scRNA-Seq data from 4 independent studies. DNA fragments derived from the 5' region of SLC26A9-bearing variants from the low-risk haplotype generated 12%-20% higher levels of expression in PANC-1 and CFPAC-1 cells compared with the high- risk haplotype. Taken together, our findings indicate that an increase in SLC26A9 expression in ductal cells of the pancreas delays the age at onset of diabetes, suggesting a CFTR-agnostic treatment for a major complication of CF.
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Affiliation(s)
- Anh-Thu N Lam
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melis A Aksit
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Briana Vecchio-Pagan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - Celeste A Shelton
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Ariel Precision Medicine, Pittsburgh, Pennsylvania, USA
| | - Derek L Osorio
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Arianna F Anzmann
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Loyal A Goff
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Scott M Blackman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Mallepalli S, Gupta MK, Vadde R. Neuroblastoma: An Updated Review on Biology and Treatment. Curr Drug Metab 2020; 20:1014-1022. [PMID: 31878853 DOI: 10.2174/1389200221666191226102231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is the second leading extracranial solid tumors of early childhood and clinically characterized by the presence of round, small, monomorphic cells with excess nuclear pigmentation (hyperchromasia).Owing to a lack of definitive treatment against NB and less survival rate in high-risk patients, there is an urgent requirement to understand molecular mechanisms associated with NB in a better way, which in turn can be utilized for developing drugs towards the treatment of NB in human. OBJECTIVES In this review, an approach was adopted to understand major risk factors, pathophysiology, the molecular mechanism associated with NB, and various therapeutic agents that can serve as drugs towards the treatment of NB in humans. CONCLUSION Numerous genetic (e.g., MYCN amplification), perinatal, and gestational factors are responsible for developing NB. However, no definite environmental or parental exposures responsible for causing NB have been confirmed to date. Though intensive multimodal treatment approaches, namely, chemotherapy, surgery & radiation, may help in improving the survival rate in children, these approaches have several side effects and do not work efficiently in high-risk patients. However, recent studies suggested that numerous phytochemicals, namely, vincristine, and matrine have a minimal side effect in the human body and may serve as a therapeutic drug during the treatment of NB. Most of these phytochemicals work in a dose-dependent manner and hence must be prescribed very cautiously. The information discussed in the present review will be useful in the drug discovery process as well as treatment and prevention on NB in humans.
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Affiliation(s)
- Suresh Mallepalli
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa-516003, A.P., India
| | - Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa-516003, A.P., India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa-516003, A.P., India
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15
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Gouda G, Gupta MK, Donde R, Kumar J, Parida M, Mohapatra T, Dash SK, Pradhan SK, Behera L. Characterization of haplotypes and single nucleotide polymorphisms associated with Gn1a for high grain number formation in rice plant. Genomics 2020; 112:2647-2657. [PMID: 32087244 DOI: 10.1016/j.ygeno.2020.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/07/2020] [Accepted: 02/18/2020] [Indexed: 01/03/2023]
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16
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Gupta MK, Vadde R, Sarojamma V. Curcumin - A Novel Therapeutic Agent in the Prevention of Colorectal Cancer. Curr Drug Metab 2020; 20:977-987. [DOI: 10.2174/1389200220666191007153238] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/11/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
Background:
Colorectal cancer is the third important cause of cancer-associated deaths across the world.
Hence, there is an urgent need for understanding the complete mechanism associated with colorectal cancer, which in
turn can be utilized toward early detection as well as the treatment of colorectal cancer in humans. Though colorectal
cancer is a complex process and chemotherapy is the first step toward the treatment of colorectal cancer, recently
several studies suggested that dietary phytochemicals may also aid significantly in reducing colorectal cancer risk in
human. However, only few phytochemicals, specifically curcumin derived from the rhizomes of Curcuma longa,
have better chemotherapeutic property, which might be because of its ability to regulate the activity of key factors
associated with the initiation, promotion, as well as progression of tumors.
Objectives:
In the present review, the authors made an attempt to summarize the physiochemical properties of curcumin,
which in turn prevent colorectal cancer via regulating numerous cell signaling as well as genetic pathways.
Conclusions:
Accumulated evidence suggested that curcumin suppresses tumour/colon cancer in various ways, (a)
restricting cell cycle progression, or stimulating apoptosis, (b) restricting angiogenesis, anti-apoptotic proteins expression,
cell survival signaling pathways & their cross-communication and (c) regulating immune responses. The
information discussed in the present review will be useful in the drug discovery process as well as the treatment and
prevention of colorectal cancer in humans.
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Affiliation(s)
- Manoj K. Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa 516003, A.P, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa 516003, A.P, India
| | - Vemula Sarojamma
- Department of Microbiology, Sri Venkateswara Medical College, Tirupathi 517501, A.P, India
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Gupta MK, Gouda G, Donde R, Vadde R. Tumor Heterogeneity: Challenges and Perspectives for Gastrointestinal Cancer Therapy. IMMUNOTHERAPY FOR GASTROINTESTINAL MALIGNANCIES 2020:1-15. [DOI: 10.1007/978-981-15-6487-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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18
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Gupta MK, Vadde R. Applications of Computational Biology in Gastrointestinal Malignancies. IMMUNOTHERAPY FOR GASTROINTESTINAL MALIGNANCIES 2020:231-251. [DOI: 10.1007/978-981-15-6487-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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19
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El-Kenawy A, Benarba B, Neves AF, de Araujo TG, Tan BL, Gouri A. Gene surgery: Potential applications for human diseases. EXCLI JOURNAL 2019; 18:908-930. [PMID: 31762718 PMCID: PMC6868916 DOI: 10.17179/excli2019-1833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
Gene therapy became in last decade a new emerging therapeutic era showing promising results against different diseases such as cancer, cardiovascular diseases, diabetes, and neurological disorders. Recently, the genome editing technique for eukaryotic cells called CRISPR-Cas (Clustered Regulatory Interspaced Short Palindromic Repeats) has enriched the field of gene surgery with enhanced applications. In the present review, we summarized the different applications of gene surgery for treating human diseases such as cancer, diabetes, nervous, and cardiovascular diseases, besides the molecular mechanisms involved in these important effects. Several studies support the important therapeutic applications of gene surgery in a large number of health disorders and diseases including β-thalassemia, cancer, immunodeficiencies, diabetes, and neurological disorders. In diabetes, gene surgery was shown to be effective in type 1 diabetes by triggering different signaling pathways. Furthermore, gene surgery, especially that using CRISPR-Cas possessed important application on diagnosis, screening and treatment of several cancers such as lung, liver, pancreatic and colorectal cancer. Nevertheless, gene surgery still presents some limitations such as the design difficulties and costs regarding ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases) use, off-target effects, low transfection efficiency, in vivo delivery-safety and ethical issues.
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Affiliation(s)
- Ayman El-Kenawy
- Department of Pathology, College of Medicine, Taif University, Saudi Arabia
- Department of Molecular Biology, GEBRI, University of Sadat City, P.O. Box 79, Sadat City, Egypt
| | - Bachir Benarba
- Laboratory Research on Biological Systems and Geomatics, Faculty of Nature and Life Sciences, University of Mascara, Algeria
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Goias, Catalao, Brazil
| | - Thaise Gonçalves de Araujo
- Laboratory of Genetics and Biotechnology, Institute of Biotechnology, Federal University of Uberlandia, Patos de Minas, MG, Brazil
| | - Bee Ling Tan
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Adel Gouri
- Laboratory of Medical Biochemistry, Faculty of Medicine, University of Annaba, Algeria
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Gupta MK, Sarojamma V, Vadde R. Diabetes and Pancreatic Cancer: A Bidirectional Relationship Perspective. EXPLORING PANCREATIC METABOLISM AND MALIGNANCY 2019:35-51. [DOI: 10.1007/978-981-32-9393-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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