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Sologova SS, Zavadskiy SP, Mokhosoev IM, Moldogazieva NT. Short Linear Motifs Orchestrate Functioning of Human Proteins during Embryonic Development, Redox Regulation, and Cancer. Metabolites 2022; 12:metabo12050464. [PMID: 35629968 PMCID: PMC9144484 DOI: 10.3390/metabo12050464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Short linear motifs (SLiMs) are evolutionarily conserved functional modules of proteins that represent amino acid stretches composed of 3 to 10 residues. The biological activities of two short peptide segments of human alpha-fetoprotein (AFP), a major embryo-specific and cancer-related protein, have been confirmed experimentally. This is a heptapeptide segment LDSYQCT in domain I designated as AFP14–20 and a nonapeptide segment EMTPVNPGV in domain III designated as GIP-9. In our work, we searched the UniprotKB database for human proteins that contain SLiMs with sequence similarity to the both segments of human AFP and undertook gene ontology (GO)-based functional categorization of retrieved proteins. Gene set enrichment analysis included GO terms for biological process, molecular function, metabolic pathway, KEGG pathway, and protein–protein interaction (PPI) categories. We identified the SLiMs of interest in a variety of non-homologous proteins involved in multiple cellular processes underlying embryonic development, cancer progression, and, unexpectedly, the regulation of redox homeostasis. These included transcription factors, cell adhesion proteins, ubiquitin-activating and conjugating enzymes, cell signaling proteins, and oxidoreductase enzymes. They function by regulating cell proliferation and differentiation, cell cycle, DNA replication/repair/recombination, metabolism, immune/inflammatory response, and apoptosis. In addition to the retrieved genes, new interacting genes were identified. Our data support the hypothesis that conserved SLiMs are incorporated into non-homologous proteins to serve as functional blocks for their orchestrated functioning.
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Affiliation(s)
- Susanna S. Sologova
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Sergey P. Zavadskiy
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
| | - Innokenty M. Mokhosoev
- Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Nurbubu T. Moldogazieva
- Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University, (Sechenov University), 119991 Moscow, Russia; (S.S.S.); (S.P.Z.)
- Correspondence:
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Aka TD, Saha U, Shati SA, Aziz MA, Begum M, Hussain MS, Millat MS, Uddin MS, Islam MS. Risk of type 2 diabetes mellitus and cardiovascular complications in KCNJ11, HHEX and SLC30A8 genetic polymorphisms carriers: A case-control study. Heliyon 2021; 7:e08376. [PMID: 34849419 PMCID: PMC8608605 DOI: 10.1016/j.heliyon.2021.e08376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/15/2021] [Accepted: 11/10/2021] [Indexed: 01/10/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD) are two deadly diseases caused by the complex interaction of multiple genetic loci, lifestyle and environmental factors. Genome-wide association studies described hundreds of susceptibility loci for T2DM and T2DM-related CVD, but it remains uncertain due to geographic and ethnic variations. The objective of this study was to evaluate the associations of KCNJ11 rs5219, SLC30A8 rs13266634 and HHEX rs1111875 polymorphisms with T2DM and related CVD. Methods Genotyping of all three polymorphisms was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method on 250 T2DM cases and 246 healthy controls. Both descriptive and inferential statistical methods were applied using MedCalc and IBM SPSS software programs for statistical analyses. Results A significantly increased association of KCNJ11 rs5219 (p<0.05) with T2DM was found in dominant, recessive, heterozygote, homozygote, and allele model (aOR = 2.23, 2.03, 1.90, 3.09, and 1.80, respectively). For SLC30A8 rs13266634, only dominant, heterozygote, and allele model (aOR = 3.37, 3.59, and 1.79, respectively) showed significantly increased association with T2DM. SNP rs1111875 (HHEX) also revealed 2.08, 4.18, 5.93, and 2.08-times significant association in dominant, recessive, homozygote, and allele models. Besides, a significantly reduced correlation of KCNJ11 rs5219 was found with T2DM-related CVD in the recessive and allele model (aOR = 0.40 and 0.65, respectively). Again, a significant difference was observed between T2DM-related CVD and non-CVD patients in terms of gender distribution, fasting blood glucose (FBG), systolic blood pressure (SBP), diastolic blood pressure (DBP), total cholesterol (TC), and triglycerides (TG). Conclusions Our investigation indicates that KCNJ11 rs5219, SLC30A8 rs13266634 and HHEX rs1111875 polymorphisms are associated with T2DM. Moreover, KCNJ11 rs5219 polymorphism is correlated with the risk of T2DM-related CVD.
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Affiliation(s)
- Tutun Das Aka
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Urmi Saha
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Sayara Akter Shati
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Md Abdul Aziz
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Mobashera Begum
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Md Saddam Hussain
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Md Shalahuddin Millat
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Mohammad Sarowar Uddin
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur, 3814, Noakhali, Bangladesh
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Verma AK, Goyal Y, Bhatt D, Beg MMA, Dev K, Alsahli MA, Rahmani AH. Association Between CDKAL1, HHEX, CDKN2A/2B and IGF2BP2 Gene Polymorphisms and Susceptibility to Type 2 Diabetes in Uttarakhand, India. Diabetes Metab Syndr Obes 2021; 14:23-36. [PMID: 33442279 PMCID: PMC7797276 DOI: 10.2147/dmso.s284998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Current study aimed to find the association of genes polymorphism of CDKAL1, HHEX, CDKN2A/2B, and IGF2BP2 with type 2 diabetes (T2DM) in the population of Uttarakhand. RESEARCH DESIGN AND METHODS Overall 469 persons comprising 369 recently diagnosed T2DM cases and 100 healthy control were enrolled in the present study. The polymorphisms were analyzed through the PCR-RFLP technique. RESULTS For the rs10440833 variant (CDKAL1), CC genotype's frequency was significantly high among T2DM subjects than controls and increase the T2DM risk (OR: 4.46, 95% CI: 2.22-8.99, p <0.0001). The c allele was significantly found to increase the T2DM risk (OR: 2.20, 95% CI: 1.54-3.14, p <0.001). In the rs1111875 variant (HHEX), the difference of genotype frequencies among T2DM cases and control was statistically non-significant (p-0.138). We did not observe significant differences in allelic frequencies among T2DM cases and control (p-0.444). In the case of rs10811661 variant (CDKN2A/2B), frequency of both TC (OR: 3.16, 95% CI: 1.84-5.42, p <0.0001) and TT (OR: 5.84, 95% CI: 1.75-19.45, p -0.004) genotype were significantly higher in T2DM cases in comparison with control and significantly associated with higher T2DM risk. Compared to the C allele, a significant increase in T2DM risk was documented with the T allele (OR: 2.47, 95% CI: 1.55-3.92, p <0.001). For rs4402960 variant (IGF2BP2), TT genotype contributed to increased T2DM risk (OR: 4.25, 95% CI: 2.02-8.93, p -0.0001). T allele's frequency was significantly high in T2DM cases in comparison with healthy control. Except WHR, HDL-C, exercise, household chores, standing work more than 3 hours, and family history, significant differences were found between T2DM cases and healthy individuals in all other parameters. CONCLUSION Our study concluded a significant association of CDKAL1, CDKN2A/2B, and IGF2BP2 polymorphism with T2DM in the Uttarakhand population. For HHEX, the genotype and allelic frequencies difference between T2DM cases and control were statistically non-significant. However, a significant association of HHEX gene polymorphism with T2DM was observed only under the dominant model.
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Affiliation(s)
- Amit K Verma
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
- Correspondence: Amit K VermaDepartment of Biotechnology, Srinivasa Ramanujan Block, Mujeeb Bagh, Jamia Millia Islamia, Lab 413, Medical Biotechnology Lab, 4 Floor, New Delhi110025, IndiaTel +91-9027777719 Email
| | - Yamini Goyal
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Deepti Bhatt
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | | | - Kapil Dev
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Bhowmick A, Sarkar P, Baruah MP, Bodhini D, Radha V, Mohan V, Banu S. Association of SLC30A8, CDKAL1, TCF7L2 and HHEX Gene Polymorphisms with Type 2 Diabetes in the Population of North East India. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Chen CH, Wang YH, Tsai SF, Yu TM, Chen SY, Tsai FJ. Antizyme inhibitor 1 genetic polymorphisms associated with diabetic patients validated in the livers of diabetic mice. Exp Ther Med 2019; 18:3139-3146. [PMID: 31572554 DOI: 10.3892/etm.2019.7919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/06/2019] [Indexed: 11/05/2022] Open
Abstract
Diabetes mellitus (DM) is a complex disease caused by absolute or relative insulin deficiency. The C57BLKsJ-db/db mouse model is a useful animal model for studying type 2 DM (T2DM). The present study investigated the association between an antizyme inhibitor 1 (AZIN1) gene polymorphism (rs1062048) and T2DM susceptibility in 2,270 Taiwanese individuals (570 patients with T2DM and 1,700 controls). Additionally, the present study investigated AZIN1 gene and protein expression in the liver tissues of mice in three age groups (4, 16 and 32 weeks) through reverse transcription-quantitative PCR, western blotting and immunohistochemistry. The data indicated that the genotype frequency distribution of the rs1062048 single-nucleotide polymorphism differed significantly between the patients with T2DM and controls (P<0.05). Furthermore, gene and protein expression levels of AZIN1 were significantly lower in early stage and late stage T2DM mouse liver samples than in control samples. Overall, the data suggested that AZIN1 expression is involved in T2DM development.
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Affiliation(s)
- Cheng-Hsu Chen
- Department of Medical Research, Division of Basic Medical Sciences, Taichung Veterans General Hospital, Taichung 40705, Taiwan, R.O.C.,Department of Internal Medicine, Division of Nephrology, Taichung Veterans General Hospital, Taichung 40705, Taiwan, R.O.C.,Department of Life Science, Tunghai University, Taichung 40705, Taiwan, R.O.C.,School of Medicine, China Medical University, Taichung 40402, Taiwan, R.O.C
| | - Yeh-Han Wang
- Department of Anatomical Pathology, Taipei Institute of Pathology, School of Medicine, National Yang-Ming University, 11221 Taipei, Taiwan, R.O.C
| | - Shang-Feng Tsai
- Department of Internal Medicine, Division of Nephrology, Taichung Veterans General Hospital, Taichung 40705, Taiwan, R.O.C.,Department of Life Science, Tunghai University, Taichung 40705, Taiwan, R.O.C.,Department of Internal Medicine, School of Medicine, National Yang-Ming University, 11221 Taipei, Taiwan, R.O.C
| | - Tung-Min Yu
- Department of Internal Medicine, Division of Nephrology, Taichung Veterans General Hospital, Taichung 40705, Taiwan, R.O.C.,School of Medicine, China Medical University, Taichung 40402, Taiwan, R.O.C
| | - Shih-Yin Chen
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, R.O.C.,Genetics Center, Medical Research, China Medical University Hospital, Taichung 40447, Taiwan, R.O.C
| | - Fuu-Jen Tsai
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan, R.O.C.,Genetics Center, Medical Research, China Medical University Hospital, Taichung 40447, Taiwan, R.O.C.,Department of Medical Genetics, China Medical University Hospital, Taichung 40447, Taiwan, R.O.C
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