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Kashyap SS, Kaur S, Devgan RK, Singh S, Singh J, Kaur M. Impact of 5' Near Gene Variants of Mannose Binding Lectin (MBL2) on Breast Cancer Risk. Biochem Genet 2024:10.1007/s10528-024-10894-3. [PMID: 39060643 DOI: 10.1007/s10528-024-10894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
The immune system plays a bifaceted role in tumour development through modulation of inflammation. MBL binds to damage-associated molecular patterns and induces inflammation through the activation of complement pathway. Dysregulated inflammation plays a major role in breast cancer pathogenesis, thereby suggesting its contribution towards breast cancer risk. Literature asserts single-nucleotide polymorphisms (SNPs) modulating serum MBL levels. Therefore, studying MBL2 SNPs in breast cancer might provide valuable insight in the disease pathogenesis. The present case-control association study aimed to elucidate the association between MBL2 5' near gene SNPs and breast cancer risk. Breast cancer patients were recruited from Government Medical College, G.N.D. Hospital, Amritsar. The age- and gender-matched genetically unrelated healthy individuals, from adjoining regions, with no history of malignancy up to three generations were recruited as controls. The SNPs of MBL2 from the 5' near gene region with putative functional significance were selected based upon the in silico analysis and literature review. The genotypic, allelic and haplotype frequencies for the studied variants were assessed and compared in the study participants by ARMS-PCR and PCR-RFLP. No difference in allelic, genotypic and haplotype frequencies was reported for rs7096206, rs7084554 and rs11003125 in both the participant groups. rs7084554 (CC) was found to confer risk towards hormone receptor-positive breast cancer. An intermediate LD was observed between rs7084554 and rs11003125. The study reports association between MBL2 variant (rs7084554) and hormone receptor-positive breast cancer risk. Further research in this direction might validate the findings.
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Affiliation(s)
- Shreya Singh Kashyap
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Surmeet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Rajiv Kumar Devgan
- Department of Radiotherapy and Oncology, Government Medical College, G.N.D. Hospital, Amritsar, Punjab, India
| | - Sumitoj Singh
- Surgery Unit II, Government Medical College, G.N.D. Hospital, Amritsar, Punjab, 143001, India
| | - Jatinder Singh
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Sahoo S, Son S, Lee HK, Lee JY, Gosu V, Shin D. Impact of nsSNPs in human AIM2 and IFI16 gene: a comprehensive in silico analysis. J Biomol Struct Dyn 2024; 42:2603-2615. [PMID: 37139544 DOI: 10.1080/07391102.2023.2206907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
AIM2 and IFI16 are the most studied members of AIM2-like receptors (ALRs) in humans and share a common N-Terminal PYD domain and C-terminal HIN domain. The HIN domain binds to dsDNA in response to the invasion of bacterial and viral DNA, and the PYD domain directs apoptosis-associated speck-like protein via protein-protein interactions. Hence, activation of AIM2 and IFI16 is crucial for protection against pathogenic assaults, and any genetic variation in these inflammasomes can dysregulate the human immune system. In this study, different computational tools were used to identify the most deleterious and disease-causing non-synonymous single nucleotide polymorphisms (nsSNPs) in AIM2 and IFI16 proteins. Molecular dynamic simulation was performed for the top damaging nsSNPs to study single amino acid substitution-induced structural alterations in AIM2 and IFI16. The observed results suggest that the variants G13V, C304R, G266R, and G266D for AIM2, and G13E and C356F are deleterious and affect structural integrity. We hope that the suggested deleterious nsSNPs and structural dynamics of AIM2 and IFI16 variants will guide future research to better understand the function of these variants with large-scale studies and may assist in fresher therapeutics focusing on these polymorphisms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sthitaprajna Sahoo
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seungwoo Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hak-Kyo Lee
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jun-Yeong Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Vijayakumar Gosu
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
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Annanya A, Priyadharshini B, Suresh V, Dilipan E. Computational Analysis of Single Nucleotide Polymorphisms in Human HIC1 Gene. Cureus 2024; 16:e56664. [PMID: 38646326 PMCID: PMC11032261 DOI: 10.7759/cureus.56664] [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: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
Background A putative tumor suppressor gene called HIC1 (hypermethylated in cancer) is situated at 17p13.3, a locus where the allelic loss occurs often in human malignancies, including breast cancer. Hypermethylated in cancer 1 protein is a protein that in humans is encoded by the HIC1 gene and it's a Homo sapiens (Human). This gene functions as a growth regulatory and tumor repressor gene. The molecular function of HIC1 gene includes DNA-binding transcription factor activity, sequence-specific DNA binding, DNA binding, histone deacetylase binding, protein binding, metal ion binding, nucleic acid binding, DNA-binding transcription repressor activity, RNA polymerase II-specific, DNA-binding transcription factor activity, RNA polymerase II-specific. The biological process of HIC1 gene includes multicellular organism development, negative regulation of Wnt signaling pathway, positive regulation of DNA damage response, signal transduction by p53 class mediator regulation of transcription, DNA-templated, negative regulation of transcription by RNA polymerase II, Wnt signaling pathway, transcription, DNA-templated, intrinsic apoptotic signaling pathway in response to DNA damage, cellular response to DNA damage stimulus. The study aimed to predict the stability and structure of the protein that will arise from single nucleotide polymorphisms (SNPs) in the human HIC1 gene. Methodology To investigate the possible negative effects associated with these SNPs, bioinformatic analysis is typically essential. The following tools were employed for forecasting harmful SNPs: scale-invariant feature transform (SIFT), Protein Analysis Through Evolutionary Relationships (PANTHER), nonsynonymous SNP by Protein Variation Effect Analyzer (PROVEAN), and nonsynonymous SNP by Single Nucleotide Polymorphism Annotation Platform (SNAP). Results The present study identified a total of 36 SNPs using the SIFT approach, which were shown to have functional significance. Twenty-six were determined to be tolerable, whereas 10 were shown to be detrimental. Out of 20 SNPs, seven (P370A, P646S, R654P, A476T, S400S, D666N, D7V) SNPs were predicted as "Possibly damaging" and seven (L9F, G468R, G490R, L482R, S12W, G489D, S12P) were identified as "probably benign", and six (R725G, G620S, A56V, E463D, D394N, L338V) were identified as "probably damaging" according to the predictions made by PANTHER tools. The majority of the pixels on the strip were red, indicating that the gene changes may have dangerous consequences. These results highlight the need for more research to fully comprehend how these mutations affect the hic1 protein's function, which is essential for the emergence of different types of cancer. Conclusion The current research has provided us with essential information about how SNPs might be used as a diagnostic marker for cancer, given that SNPs may be candidates for cellular changes caused by mutations linked to cancer.
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Affiliation(s)
- Arora Annanya
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, IND
| | - Boopathi Priyadharshini
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Vasugi Suresh
- Medical Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Elangovan Dilipan
- Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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Mao Y, Wei H, Gong Y, Peng L, Chen Y. Association of MBL2 gene polymorphisms and MBL levels with dilated cardiomyopathy in a Chinese Han population. BMC Med Genomics 2024; 17:11. [PMID: 38167099 PMCID: PMC10763076 DOI: 10.1186/s12920-023-01787-2] [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: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND It has been reported that Mannose-binding lectin 2 (MBL2) gene polymorphisms and expression levels are related to dilated cardiomyopathy (DCM). This study aimed to investigate the potential association between MBL2 gene polymorphisms and the pathogenesis of DCM. METHODS Five single nucleotide polymorphisms (SNPs) of the MBL2 gene were genotyped in 440 DCM patients and 532 controls in Southwest China. A luciferase reporter assay was used to detect the transcriptional activity the different genotypes. MBL serum levels, left ventricle ejection fraction (LVEF) and lower left ventricular end-diastolic diameter (LVEDD) were measured. RESULTS The rs11003125 C allele increased the transcriptional activity of the MBL2 promoter compared with the rs11003125 G allele. The rs11003125 CC carriers had higher MBL serum levels, LVEF and LVEDD than the rs11003125 CG and GG carriers. CONCLUSIONS Our study first revealed that MBL2 polymorphisms and serum MBL levels were associated with DCM. Allele C in rs11003125 of MBL2 may upregulate the expression levels of MBL. High serum MBL levels may be a protective factor in DCM pathogenesis.
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Affiliation(s)
- Yujie Mao
- Institute of Dermatology and Venereology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Hong Wei
- Department of Ophthalmology and Vision Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yugang Gong
- Institute of Dermatology and Venereology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Lei Peng
- Department of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Yu Chen
- Department of Cardiology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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Sharma A, Kashyap SS, Kajal NC, Malhotra B, Singh J, Kaur M. Association of mannose binding lectin with chronic obstructive pulmonary disease susceptibility and its clinical outcomes. Mol Biol Rep 2023; 50:8145-8161. [PMID: 37558798 DOI: 10.1007/s11033-023-08617-9] [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: 03/10/2023] [Accepted: 06/21/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND The physiological interactions of MBL suggest its contribution towards the pathogenesis of COPD. OBJECTIVE The present case-control study was undertaken to elucidate the role of MBL with COPD risk and clinical outcomes in north Indian cohort. METHODS Patients were enrolled as per GOLD criteria. MBL2 variants were selected based on the literature and their putative functional significance. Genotyping of six single nucleotide polymorphisms of MBL2 comprising of two coding (rs1800450, rs1800451) and four non-coding variants (rs11003125, rs7096206, rs11003123 and rs7095891) was done by using PCR-RFLP and ARMS-PCR. Serum MBL levels were analysed by sandwich ELISA. RESULTS Overall findings of the molecular genetic analysis of MBL2 indicated significant difference in frequency of three of the six studied variants, between patients and controls or among different disease severity stages. Heterozygous genotype of rs7095891 showed significant protective association towards severity of disease. Linkage disequilibrium (LD) analysis indicated a strong LD between rs1800450 and rs7095891 while intermediate LD was observed for rs11003123/rs11003125 and rs7096206/rs11003125. Haplotype analysis revealed 17.14-fold risk of developing exacerbations conferred by GGGTGG haplotype. Significantly low serum MBL levels observed in COPD patients as compared to controls. Significant difference in MBL deficiency levels were also observed for homozygous wild and variant genotypes of rs11003125 and rs7096206 respectively, as well as for all genotypes of rs11003123 than respective controls. CONCLUSION The present study reinforces the role played by MBL in the susceptibility, protection and clinical outcomes of COPD. Therefore, including the reported associations at diagnostic, prognostic and therapeutic interventions may prove helpful.
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Affiliation(s)
- Aarti Sharma
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Pb, 143005, India
| | - Shreya Singh Kashyap
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Pb, 143005, India
| | - Nirmal Chand Kajal
- Department of Pulmonary Medicine, Government Medical College, Amritsar, Pb, 143001, India
| | - Balbir Malhotra
- Department of Pulmonary Medicine, Government Medical College, Amritsar, Pb, 143001, India
| | - Jatinder Singh
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Pb, 143005, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Pb, 143005, India.
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Abid F, Khan K, Badshah Y, Ashraf NM, Shabbir M, Hamid A, Afsar T, Almajwal A, Razak S. Non-synonymous SNPs variants of PRKCG and its association with oncogenes predispose to hepatocellular carcinoma. Cancer Cell Int 2023; 23:123. [PMID: 37344815 PMCID: PMC10286404 DOI: 10.1186/s12935-023-02965-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND PRKCG encodes PKC γ, which is categorized under the classical protein kinase C family. No studies have specifically established the relationship between PRKCG nsSNPs with structural and functional variations in PKC γ in the context of hepatocellular carcinoma (HCC). The present study aims to uncover this link through in-silico and experimental studies. METHODS The 3D structure of PKC γ was predicted. Molecular Dynamic (MD) Simulations were run and estimates were made for interactions, stability, conservation and post-translational alterations between wild and mutant structures. The association of PRKCG levels with HCC survival rate was determined. Genotyping analyses were conducted to investigate the deleterious PRKCG nsSNP association with HCC. mRNA expression of PKC γ, HIF-1 alpha, AKT, SOCS3 and VEGF in the blood of controls and HCC patients was analyzed and a genetic cascade was constructed depicting these interactions. RESULTS The expression level of studied oncogenes was compared to tumour suppressor genes. Through Alphafold, the 3D structure of PKC γ was explored. Fifteen SNPs were narrowed down for in-silico analyses that were identified in exons 5, 10 and 18 and the regulatory and kinase domain of PKC γ. Root mean square deviation and fluctuation along with the radius of gyration unveiled potential changes between the wild and mutated variant structures. Mutant genotype AA (homozygous) corresponding to nsSNP, rs386134171 had more frequency in patients with OR (2.446), RR (1.564) and P-values (< 0.0029) that highlights its significant association with HCC compared to controls in which the wild genotype GG was found more prevalent. CONCLUSION nsSNP rs386134171 can be a genetic marker for HCC diagnosis and therapeutic studies. This study has laid down a road map for future studies to be conducted on HCC.
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Affiliation(s)
- Fizzah Abid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan.
| | - Arslan Hamid
- LIMES Institute (AG-Netea), University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Khan A, Waqas M, Tufail M, Halim SA, Murad W, Ahmad SU, Faheem M, Uddin J, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. In silico scanning of structural and functional deleterious nsSNPs in Arabidopsis thaliana's SOG1 protein, using molecular dynamic simulation approaches. J Biomol Struct Dyn 2023; 41:11629-11646. [PMID: 36734218 DOI: 10.1080/07391102.2023.2174187] [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: 07/28/2022] [Accepted: 01/02/2023] [Indexed: 02/04/2023]
Abstract
Suppressor of gamma response 1 (SOG1) is a member of the NAC domain family transcription factors of the DNA damage response (DDR) signaling in the plant's genome. SOG1 is directly involved in transcriptional response to DNA damage, cell cycle checkpoints and ATR or ATM-mediated activation of the DNA damage responses and repair functioning in programmed cell death and regulation of end reduplication. Different mutations in the SOG1 protein lead to severe diseases and, ultimately, cell death. Single nucleotide polymorphisms (SNPs) are an important type of genetic alteration that cause different diseases or programmed cell death. The current study applied different computational approaches to Arabidopsis thaliana L. SOG1 protein to identify the potential deleterious nsSNPs and monitor their impact on the structure, function and protein stability. Various bioinformatics tools were applied to analyze the retrieved 34 nsSNPs and interestingly extracted four deleterious nsSNPs, that is, ensvath13968004 (Q166L), tmp18998388 (P159L), ensvath01103049 (K199N) and tmp18998295 (Y190F). For example, homology modeling, conservation and conformational analysis of the mutant's models were considered to scrutinize the deviations of these variants from the native SOG1 structure. All atoms molecular dynamic simulation confirmed the significance of these mutations on the protein stability, residual and structural conformation, compactness, surface conformation, dominant motion, Gibbs free energy distribution and dynamic effects. Similarly, protein-protein interaction revealed that SOG1 operates as a hub-linking cluster of various proteins, and any changes in the SOG1 might result in the disassociation of several signal transduction cascades.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asif Khan
- Laboratory of Phytochemistry, Department of Botany, University of São Paulo, São Paulo, Brazil
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Dhodial, Pakistan
| | - Muhammad Tufail
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Waheed Murad
- Department of Botany, Abdul Wali Khan University Mardan, Pakistan
| | - Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Dhodial, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi, Pakistan
| | - Jalal Uddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
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MBL2 gene polymorphisms related to HIV-1 infection susceptibility and treatment response. Hum Immunol 2023; 84:80-88. [PMID: 36257838 DOI: 10.1016/j.humimm.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
Abstract
Human Mannose-binding lectin (MBL) is a protein encoded by MBL2 gene involved in the activation of the lectin-complement pathway. Several studies emphasized the role of MBL2 gene in several infectious diseases' susceptibility, including HIV-1 infection. We aim to investigate the impact of 10 MBL2 gene polymorphisms located in the promoter, 5'UTR and exon 1 regions on HIV-1 physiopathology. The polymorphisms genotyping of 400 individuals, which 200 were HIV-1 positive patients and 200 were controls, was performed by PCR-sequencing. Our results showed that rs503037 and rs1800451 polymorphisms are associated with a high risk of HIV-1 infection susceptibility while rs7096206 and rs11003123 showed a protective effect. A significant association between haplotype CGA and HIV-1 infection susceptibility was also found in the exon 1 region. Moreover, rs11003124, rs7084554, rs36014597 and rs11003123 polymorphisms revealed an association with treatment response outcome as measured by RNA viral load. This study highlights the importance of MBL2 polymorphisms in the modulation of HIV-1 infection susceptibility and the contribution to treatment response outcomes among Moroccan subjects.
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Wang L, Tu H, Zeng L, Gao R, Luo S, Xiong C. Identification and in silico Analysis of Nonsense SNPs of Human Colorectal Cancer Protein. J Oleo Sci 2022; 71:363-370. [PMID: 35236796 DOI: 10.5650/jos.ess21313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent disease in the world, with an estimated 1.2 million new cases each year. Spontaneous CRCs account for around 70% of all CRCs, are caused by somatic mutations. Minor variations or single-nucleotide polymorphisms (SNPs) in oncogene or tumor-suppressor genes cause familial CRC. MSH2 and MSH6 genes are located on chromosome 2. These genes products are involved in the repair of DNA replication defects. If these proteins are changed, the replication errors are not rectified, resulting in damaged DNA leading to colorectal cancer. We employed a variety of computational methodologies to find nsSNPs that are harmful to the structure and function of the MSH6 protein and could be causing CRC in our study. SIFT, PROVEAN, Poly- Phen-2, PhD-SNP, and SNPs&GO were among the in silico methods used to do the computational research. According to the findings, mutations of G932Q, E1234Q, and F1104Q are important alterations in native MSH6 protein rs35717727 that may contribute to its dysfunction and, ultimately, disease. The study also provided three-dimensional structures of the native MSH6 protein and mutations. These nsSNPs should be considered as key target mutations in many disorders involving MSH6 dysfunction in future studies. This is the first thorough study to use in silico technologies to assess MSH6 gene variants, and it will be extremely useful in planning largescale investigations and developing precision medicines to treat disorders caused by these polymorphisms. Additionally, animal models of various autoimmune disorders with these mutations could aid in determining their precise involvement.
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Affiliation(s)
- Lu Wang
- Department of Oncology, First People's Hospital of Jiujiang City
| | - Huiyang Tu
- Department of Oncology, First People's Hospital of Jiujiang City
| | - Lingzhi Zeng
- Department of Oncology, First People's Hospital of Jiujiang City
| | - Ruichen Gao
- Department of Oncology, First People's Hospital of Jiujiang City
| | - Sumei Luo
- Department of Oncology, First People's Hospital of Jiujiang City
| | - Chao Xiong
- Department of Oncology, First People's Hospital of Jiujiang City
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Ebrahim E, Teklu T, Tajebe F, Wondmagegn T, Akelew Y, Fiseha M. Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population. Diabetes Metab Syndr Obes 2022; 15:2733-2751. [PMID: 36091481 PMCID: PMC9462946 DOI: 10.2147/dmso.s375023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/29/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND T1DM is a chronic organ-specific T-cell-mediated autoimmune disease characterized by the selective destruction of β-cells in the islets of Langerhans, resulting in insulin deficiency and hyperglycemia. Genes for cytotoxic T lymphocyte-associated antigen 4 have been hypothesized as possible contender genes for T1DM vulnerability. However, it has not been studied in the Ethiopian population yet. OBJECTIVE The aim of the study was to investigate CTLA-4 exon 1 was linked to A49G polymorphism with T1DM and its biological features of CTLA-4 among T1DM patients, in Ethiopia. METHODS A case-control study was done from December 2019 to March 2020 on 210 study participants (105 T1DM patients and 105 healthy controls). Polymerase Chain Reaction amplification with forward and reverse primers was followed by restriction fragment length polymorphism and gel electrophoresis to determine gene polymorphism. Bioinformatics data of SNP was retrieved from National Centers for Biotechnology Information databases. The chi-square test and logistic regression were used. Statistical significance was defined as a P-value of less than 0.05. RESULTS The CTLA-4 (+A49G) gene polymorphism was observed on 56 (26.7%) study participants, 39 (18.57%) of T1DM patients, and 17 (0.08%) were controls. In T1DM and controls, the frequency of the A allele was 73.3% and 89.5%, while the G allele was 26.7% and 10.5%, respectively. The G allele was found to be associated with T1DM (OR=3.1; 95% CI, 1.82 -5.32; P=0.001). Statistical analysis revealed an association between the likelihood of T1DM and GG genotype of the CTLA-4 (+A49G) gene polymorphism (OR=3.11; 95% CI, 1.37-10.90; P=0.01). Further in silico analyzed the SNP to assess its biological features. CONCLUSION The study showed as CTLA-4 (+A49G) gene polymorphism is linked with T1DM in the Ethiopian population.
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Affiliation(s)
- Endris Ebrahim
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
- Correspondence: Endris Ebrahim, Email
| | - Takele Teklu
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Fitsumbrhan Tajebe
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Tadelo Wondmagegn
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yibeltal Akelew
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Mesfin Fiseha
- Hematology and Immunohematology, Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
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Prediction of Early Childhood Caries Based on Single Nucleotide Polymorphisms Using Neural Networks. Genes (Basel) 2021; 12:genes12040462. [PMID: 33805090 PMCID: PMC8064067 DOI: 10.3390/genes12040462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/11/2021] [Accepted: 03/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Several genes and single nucleotide polymorphisms (SNPs) have been associated with early childhood caries. However, they are highly age- and population-dependent and the majority of existing caries prediction models are based on environmental and behavioral factors only and are scarce in infants. Methods: We examined 6 novel and previously analyzed 22 SNPs in the cohort of 95 Polish children (48 caries, 47 caries-free) aged 2–3 years. All polymorphisms were genotyped from DNA extracted from oral epithelium samples. We used Fisher’s exact test, receiver operator characteristic (ROC) curve and uni-/multi-variable logistic regression to test the association of SNPs with the disease, followed by the neural network (NN) analysis. Results: The logistic regression (LogReg) model showed 90% sensitivity and 96% specificity, overall accuracy of 93% (p < 0.0001), and the area under the curve (AUC) was 0.970 (95% CI: 0.912–0.994; p < 0.0001). We found 90.9–98.4% and 73.6–87.2% prediction accuracy in the test and validation predictions, respectively. The strongest predictors were: AMELX_rs17878486 and TUFT1_rs2337360 (in both LogReg and NN), MMP16_rs1042937 (in NN) and ENAM_rs12640848 (in LogReg). Conclusions: Neural network prediction model might be a substantial tool for screening/early preventive treatment of patients at high risk of caries development in the early childhood. The knowledge of potential risk status could allow early targeted training in oral hygiene and modifications of eating habits.
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12
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Kalia N, Singh J, Kaur M. The ambiguous role of mannose-binding lectin (MBL) in human immunity. Open Med (Wars) 2021; 16:299-310. [PMID: 33681468 PMCID: PMC7917369 DOI: 10.1515/med-2021-0239] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 12/30/2022] Open
Abstract
Mannose-binding lectin (MBL) and lectin complement pathway have become targets of increasing clinical interest. Many aspects of MBL have been recently explored, including the structural properties that allow it to distinguish self from non-self/altered-self structures. Experimental evidences have declared the additional 5′- and 3′-variants that in amalgamation with well-known secretor polymorphisms change MBL function and concentration. Moreover, the current review highlights the differential behavior of MBL on exposure with extra/intracellular pathogens and in autoimmune diseases, stressing the fact that “high MBL levels can increase diseases susceptibility,” a paradox that needs justification. Attributable to these discrepancies, no absolute level of MBL deficiency could be defined so far and thus must be interpreted for specific diseases through case–control population-specific designs. Overall, it is evident that further research is needed about MBL and the lectin pathway of complement. Particularly, the transformative role of MBL over evolution is of interest and its role with regard to pathogenesis of different diseases and potential therapeutic targets within the respective pathways should be further explored. Apart from this, it is necessary to adopt an extensive locus-wide methodology to apprehend the clinical significance of MBL2 polymorphisms in a variety of infectious diseases by the future studies.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India.,Department of Biological Sciences, George Washington University, Washington, DC 20052, USA
| | - Jatinder Singh
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
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13
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In silico analysis of Single Nucleotide Polymorphisms in human GCH1 gene. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Španinger E, Potočnik U, Bren U. Molecular Dynamics Simulations Predict That rSNP Located in the HNF‑1α Gene Promotor Region Linked with MODY3 and Hepatocellular Carcinoma Promotes Stronger Binding of the HNF‑4α Transcription Factor. Biomolecules 2020; 10:biom10121700. [PMID: 33371430 PMCID: PMC7767403 DOI: 10.3390/biom10121700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/06/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Our study aims to investigate the impact of the Maturity-onset diabetes of the young 3 disease-linked rSNP rs35126805 located in the HNF-1α gene promotor on the binding of the transcription factor HNF-4α and consequently on the regulation of HNF-1α gene expression. Our focus is to calculate the change in the binding affinity of the transcription factor HNF-4α to the DNA, caused by the regulatory single nucleotide polymorphism (rSNP) through molecular dynamics simulations and thermodynamic analysis of acquired results. Both root-mean-square difference (RMSD) and the relative binding free energy ΔΔGbind reveal that the HNF-4α binds slightly more strongly to the DNA containing the mutation (rSNP) making the complex more stable/rigid, and thereby influencing the expression of the HNF-1α gene. The resulting disruption of the HNF-4α/HNF-1α pathway is also linked to hepatocellular carcinoma metastasis and enhanced apoptosis in pancreatic cancer cells. To the best of our knowledge, this represents the first study where thermodynamic analysis of the results obtained from molecular dynamics simulations is performed to uncover the influence of rSNP on the protein binding to DNA. Therefore, our approach can be generally applied for studying the impact of regulatory single nucleotide polymorphisms on the binding of transcription factors to the DNA.
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Affiliation(s)
- Eva Španinger
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Medicine, University of Maribor, Taborska 8, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia; (E.Š.); (U.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
- Correspondence: ; Tel.: +386-2-2294-421
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15
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Rani Y, Kaur K, Sharma M, Kalia N. In silico analysis of SNPs in human phosphofructokinase, muscle (PFKM) gene: An apparent therapeutic target of aerobic glycolysis and cancer. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Lack of association between Mannose Binding Lectin-2 gene polymorphisms and periodontitis: A meta-analysis. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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17
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Mahto H, Pati A, Sahu SK, Sharma HP, Padhi A, Panda AK. Association of MBL-2 gene polymorphisms with systemic lupus erythematosus: an updated meta-analysis and trial sequential analysis. Lupus 2020; 29:1227-1237. [PMID: 32635881 DOI: 10.1177/0961203320939156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Mannose-binding lectin (MBL), an essential innate immune molecule, enhances the opsonization process and activates the complement system. Genetic variations at the promoter and coding region of the MBL-2 gene have been associated with susceptibility to systemic lupus erythematosus (SLE); however, reports remained inconsistent. The present study performs a meta-analysis of published peer-reviewed articles to draw a definitive conclusion. MATERIALS AND METHODS Published peer-reviewed articles on the association of MBL-2 gene polymorphisms and SLE were screened on various databases such as PubMed (Medline), ScienceDirect, and Google Scholar. A total of 23 eligible articles were included in the present study, comprising 3074 SLE patients and 3985 controls. Genotype and/or allele data for MBL-2 polymorphisms (A > B, A > C, A > D, A > O, Y > X and H > L) were extracted and analyzed by Comprehensive Meta-Analysis software (CMA V3.1). RESULTS The overall analysis revealed a significant association of MBL-2 (A > O) polymorphism with a predisposition to SLE in allele contrast (p = 0.000; OR = 1.261), homozygous (p = 0.005; OR = 1.482), heterozygous (p = 0.004; OR = 1.247), dominant (p = 0.000; OR = 1.303) and recessive (p = 0.025; OR = 1.356) genetic comparison model. Similar results were also observed in the comparison of allele and the dominant genetic model of MBL-2 (A > B) polymorphism in overall (allele: p = 0.000, OR = 1.46, dominant: p = 0.001, OR = 1.31) and in the Asian cohorts (allele: p = 0.007, OR = 1.43, dominant: p = 0.008, OR = 1.32). Interestingly, MBL-2 (Y-221X) polymorphism exhibited protection against the development of SLE in heterozygous (p = 0.005, OR = 0.619) and dominant genetic comparison (p = 0.01, OR = 0.672) models. CONCLUSIONS MBL-2 variants (A > O and A > B) are associated with predisposition to SLE. Conversely, promoter polymorphism (Y-221X) offers protection against SLE development.
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Affiliation(s)
- Harishankar Mahto
- Department of Bioscience and Bioinformatics, Khallikote University, Transit Campus: GMax Building, Konisi, Berhampur, Odisha, India.,Department of Botany, Ranchi University, Ranchi, Jharkhand, India
| | - Abhijit Pati
- Department of Bioscience and Bioinformatics, Khallikote University, Transit Campus: GMax Building, Konisi, Berhampur, Odisha, India
| | - Sushil K Sahu
- Department of Zoology, Ravenshaw University, Cuttack, Odisha, India
| | | | - Archana Padhi
- Department of Biology, K. C. Public School, Berhampur, Odisha, India
| | - Aditya K Panda
- Department of Bioscience and Bioinformatics, Khallikote University, Transit Campus: GMax Building, Konisi, Berhampur, Odisha, India
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18
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Höher G, Rodrigues MMDO, Waskow G, Agnes G, Von Burg PV, Onsten T, Fiegenbaum M, Almeida S. Identification of ACKR1 variants associated with altered Duffy phenotype expression in blood donors from southern Brazil. Transfus Apher Sci 2020; 59:102768. [PMID: 32276863 DOI: 10.1016/j.transci.2020.102768] [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: 11/30/2018] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/18/2022]
Abstract
The atypical chemokine receptor 1 gene (ACKR1) is responsible for the clinically significant Duffy blood group. The main antigens of this system, Fya and Fyb, can be related to a null or weak expression of the DARC protein. In the present work, we aimed to identify ACKR1 gene variants in blood donors from southern Brazil based on discrepancies between their serological and molecular typing results. Then, we analyzed the association of these variants with the expression of the Duffy phenotype. The Fy antigen types were determined via hemagglutination and real-time PCR (c.125 G > A, c.265C > T and c.-67T > C SNPs) tests in a sample composed of 382 regular repetitive voluntary blood donors to the Blood Bank of Hospital de Clínicas de Porto Alegre. An inconclusive correlation between phenotype-genotype analyses was found in 11 (2.88 %) donors, and the entire ACKR1 gene was sequenced in these samples. Our investigation found 11 genetic variants, four of which (c.-541C > T, c.21 + 150C > T, c.22-58A > G, and c.298 G > A SNPs) seem to have putative functional effects on the structure and expression of DARC undertaken for in silico analysis (SIFT, PolyPhen-2 and RegulomeDB). Molecular events can result in apparent discrepancies between red cell genotypes and phenotypes. Our findings provided insight into the molecular background of FY antigens to improve technical approaches for red cell genotyping.
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Affiliation(s)
- Gabriela Höher
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | | | - Gabriela Waskow
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Grasiela Agnes
- Laboratório de Biologia Molecular, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Pâmela Victoria Von Burg
- Laboratório de Biologia Molecular, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Tor Onsten
- Hospital de Clínicas de Porto Alegre - HCPA, Porto Alegre, Brazil
| | - Marilu Fiegenbaum
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil
| | - Silvana Almeida
- Programa de Pós-Graduação em Biociências, Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Porto Alegre, Brazil.
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19
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Kalia N, Singh J, Rauniyar AK, Kaur M. A meta-analysis of mannose-binding lectin gene polymorphisms with the risk of recurrent vulvovaginal infections. Sci Rep 2020; 10:6079. [PMID: 32269261 PMCID: PMC7142065 DOI: 10.1038/s41598-020-63261-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/27/2020] [Indexed: 12/02/2022] Open
Abstract
The genetic variants of Mannose-Binding Lectin, a vital component of innate immunity have been studied with acute/recurrent vaginal infections ((R)VVI) and presented inconclusive findings. Therefore, a systematic review and meta-analysis of published data were conducted to assess the possible role of these variations in (R)VVI. A comprehensive search was made using PubMed, Web of Science and Google scholar till June 18, 2019. A total of 12 studies met the specified criteria and were included in the analysis. Different comparisons were made on the basis of the outcome of interest that resulted in the filtering of studies for the pooled analysis to find an association using the standard genetic models. Odds ratio (OR) with 95% confidence interval (CI) was chosen as the effect measure for the data synthesis. The trim and fill technique was applied to adjust the publication bias. The meta-analysis revealed the significant association (p < 0.05) of rs1800450 polymorphism with RVVI risk (OR ≥ 3.5) in all the genetic models. The subgroup analysis identified the same association in Caucasian and Mixed ethnicity. Quantitative synthesis based on RVVC showed>3.5 fold risk of disease development accredited to rs1800450. A combined evaluation of Exon1 variants showed no association with (R)VVI. This meta-analysis suggests rs1800450 polymorphism as a genetic predisposing factor for RVVI, but to reinforce, further studies with a larger sample size are warranted.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India.
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | | | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India.
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20
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Zhang X, Li G, Zhou Z, Shao C, Huang X, Li L, Li X, Liu Y, Fan H, Li J. Molecular and computational analysis of 45 samples with a serologic weak D phenotype detected among 132,479 blood donors in northeast China. J Transl Med 2019; 17:393. [PMID: 31775789 PMCID: PMC6880393 DOI: 10.1186/s12967-019-02134-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/09/2019] [Indexed: 02/07/2023] Open
Abstract
Background RH1 is one of the most clinically important blood group antigens in the field of transfusion and in the prevention of fetal incompatibility. The molecular analysis and characterization of serologic weak D phenotypes is essential to ensuring transfusion safety. Methods Blood samples from a northeastern Chinese population were randomly screened for a serologic weak D phenotype. The nucleotide sequences of all 10 exons, adjacent flanking intronic regions, and partial 5′ and 3′ untranslated regions (UTRs) were detected for RHD genes. Predicted deleterious structural changes in missense mutations of serologicl weak D phenotypes were analyzed using SIFT, PROVEAN and PolyPhen2 software. The protein structure of serologic weak D phenotypes was predicted using Swiss-PdbViewer 4.0.1. Results A serologic weak D phenotype was found in 45 individuals (0.03%) among 132,479 blood donors. Seventeen distinct RHD mutation alleles were detected, with 11 weak D, four partial D and two DEL alleles. Further analyses resulted in the identification of two novel alleles (RHD weak D 1102A and 399C). The prediction of a three-dimensional structure showed that the protein conformation was disrupted in 16 serologic weak D phenotypes. Conclusions Two novel and 15 rare RHD alleles were identified. Weak D type 15, DVI Type 3, and RHD1227A were the most prevalent D variant alleles in a northeastern Chinese population. Although the frequencies of the D variant alleles presented herein were low, their phenotypic and genotypic descriptions add to the repertoire of reported RHD alleles. Bioinformatics analysis on RhD protein can give us more interpretation of missense variants of RHD gene.
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Affiliation(s)
- Xu Zhang
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Guiji Li
- Department of Hematology, The Forth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhuren Zhou
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Chaopeng Shao
- Department of Transfusion, the Second People's Hospital of Shenzhen, Shenzhen, China
| | - Xuying Huang
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Lichun Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Xiaofeng Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China.,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China
| | - Ying Liu
- Institute of Transfusion Medicine, Harbin Blood Center, Harbin, Heilongjiang, China
| | - Hua Fan
- Department of Hematology, The Forth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Jianping Li
- Institute of Transfusion Medicine, Liaoning Blood Center, Shenyang, Liaoning, China. .,Key Laboratory of Blood Safety Research of Liaoning Province, Shenyang, Liaoning, China. .,Institute of Transfusion Medicine, Harbin Blood Center, Harbin, Heilongjiang, China. .,Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China.
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21
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Arifuzzaman M, Mitra S, Das R, Hamza A, Absar N, Dash R. In silico analysis of nonsynonymous single-nucleotide polymorphisms (nsSNPs) of the SMPX gene. Ann Hum Genet 2019; 84:54-71. [PMID: 31583691 DOI: 10.1111/ahg.12350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/06/2019] [Accepted: 08/08/2019] [Indexed: 02/06/2023]
Abstract
Mutations in the SMPX gene can disrupt the regular activity of the SMPX protein, which is involved in the hearing process. Recent reports showing a link between nonsynonymous single-nucleotide polymorphisms (nsSNPs) in SMPX and hearing loss, thus classifying deleterious SNPs in SMPX will be an uphill task before designing a more extensive population study. In this study, damaging nsSNPs of SMPX from the dbSNP database were identified by using 13 bioinformatics tools. Initially, the impact of nsSNPs in the SMPX gene were evaluated through different in silico predictors; and the deleterious convergent changes were analyzed by energy-minimization-guided residual network analysis. In addition, the pathogenic effects of mutations in SMPX-mediated protein-protein interactions were also characterized by structural modeling and binding energy calculations. A total of four mutations (N19D, A29T, K54N, and S71L) were found to be highly deleterious by all the tools, which are located at highly conserved regions. Furthermore, all four mutants showed structural alterations, and the communities of amino acids for mutant proteins were readily changed, compared to the wild-type. Among them, A29T (rs772775896) was revealed as the most damaging nsSNP, which caused significant structural deviation of the SMPX protein, as a result reducing the binding affinity to other functional partners. These findings reflect the computational insights into the deleterious role of nsSNPs in SMPX, which might be helpful for subjecting wet-lab confirmatory analysis.
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Affiliation(s)
- Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongbuk, Republic of Korea
| | - Sarmistha Mitra
- Plasma Bioscience Research Center, Plasma-Bio Display, Kwangwoon University, Seoul, Republic of Korea
| | - Raju Das
- Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, Bangladesh
| | - Amir Hamza
- Department of Biochemistry, Hallym University, Gangwon, Republic of Korea
| | - Nurul Absar
- Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju, Republic of Korea
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22
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Akhtar M, Jamal T, Jamal H, Din JU, Jamal M, Arif M, Arshad M, Jalil F. Identification of most damaging nsSNPs in human CCR6 gene: In silico analyses. Int J Immunogenet 2019; 46:459-471. [PMID: 31364806 DOI: 10.1111/iji.12449] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 12/30/2022]
Abstract
Single nucleotide polymorphisms in CCR6 (C-C chemokine receptor type 6) gene have been found to be the possible cause of many diseases like rheumatoid arthritis, psoriasis, lupus nephritis and systemic sclerosis and other autoimmune diseases. Therefore, identification of structurally and functionally important polymorphisms in CCR6 is important in order to study its potential malfunctioning and discovering therapeutic targets. Several bioinformatics tools were used to identify most damaging nsSNPs that might be vital for CCR6 structure and function. The in silico tools included PROVEAN, SIFT, SNP&GO and PolyPhen2 followed by I-Mutant MutPred and ConSurf. Phyre2 and I-TASSER were used for protein 3-D Modelling while gene-gene interaction was predicted by STRING and GeneMANIA. Our study suggested that three nsSNPs rs1376162684, rs751102128 and rs1185426631 are the most damaging in CCR6 gene while 7 missense SNPs rs1438637216, rs139697820, rs768420505, rs1282264186, rs1394647982, rs769360638 and rs1263402382 are found to revert into stop codons. Prediction of post-transcriptional modifications highlighted the significance of rs1376162684 because it effected potential phosphorylation site. Gene-gene interactions showed relation of CCR6 with other genes depicting its importance in several pathways and co-expressions. In future, studying diseases related to CCR6 should include investigation of these 10 nsSNPs. Being the first of its type, this study also proposes future perspectives that will help in precision medicines. For such purposes, CCR6 proteins from patients of autoimmune diseases should be explored. Animal models can also be of significance find out the effects of CCR6 in diseases.
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Affiliation(s)
- Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Tazkira Jamal
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | | | - Jalal Ud Din
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Maria Arshad
- Attaur Rahman School of Applied Biosciences, NUST, Islamabad, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
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23
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Ornelas AMDM, Xavier-de-Carvalho C, Alvarado-Arnez LE, Ribeiro-Alves M, Rossi ÁD, Tanuri A, de Aguiar RS, Moraes MO, Cardoso CC. Association between MBL2 haplotypes and dengue severity in children from Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz 2019; 114:e190004. [PMID: 31141020 PMCID: PMC6534340 DOI: 10.1590/0074-02760190004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Dengue is an arthropod-borne viral disease with a majority of asymptomatic
individuals and clinical manifestations varying from mild fever to severe
and potentially lethal forms. An increasing number of genetic studies have
outlined the association between host genetic variations and dengue
severity. Genes associated to viral recognition and entry, as well as those
encoding mediators of the immune response against infection are strong
candidates for association studies. OBJECTIVES The aim of this study was to investigate the association between
MBL2, CLEC5A, ITGB3
and CCR5 genes and dengue severity in children. METHODS A matched case-control study was conducted and 19 single nucleotide
polymorphisms (SNPs) were investigated. FINDINGS No associations were observed in single SNP analysis. However, when
MBL2 SNPs were combined in haplotypes, the allele
rs7095891G/rs1800450C/ rs1800451C/rs4935047A/rs930509G/rs2120131G/rs2099902C
was significantly associated to risk of severe dengue under α = 0.05 (aOR =
4.02; p = 0.02). A second haplotype carrying rs4935047G and rs7095891G
alleles was also associated to risk (aOR = 1.91; p = 0.04). MAIN CONCLUSIONS This is the first study to demonstrate the association between
MBL2 haplotypes and dengue severity in Brazilians
including adjustment for genetic ancestry. These results reinforce the role
of mannose binding lectin in immune response to DENV.
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Affiliation(s)
- Alice Maria de Magalhães Ornelas
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Caroline Xavier-de-Carvalho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
| | - Lucia Elena Alvarado-Arnez
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em DST-AIDS, Rio de Janeiro, RJ, Brasil
| | - Átila Duque Rossi
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Renato Santana de Aguiar
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Milton Ozório Moraes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
| | - Cynthia Chester Cardoso
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
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Levy ER, Yip WK, Super M, Ferdinands JM, Mistry AJ, Newhams MM, Zhang Y, Su HC, McLaughlin GE, Sapru A, Loftis LL, Weiss SL, Hall MW, Cvijanovich N, Schwarz A, Tarquinio KM, Mourani PM, Randolph AG. Evaluation of Mannose Binding Lectin Gene Variants in Pediatric Influenza Virus-Related Critical Illness. Front Immunol 2019; 10:1005. [PMID: 31139182 PMCID: PMC6518443 DOI: 10.3389/fimmu.2019.01005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/18/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Mannose-binding lectin (MBL) is an innate immune protein with strong biologic plausibility for protecting against influenza virus-related sepsis and bacterial co-infection. In an autopsy cohort of 105 influenza-infected young people, carriage of the deleterious MBL gene MBL2_Gly54Asp(“B”) mutation was identified in 5 of 8 individuals that died from influenza-methicillin-resistant Staphylococcus aureus (MRSA) co-infection. We evaluated MBL2 variants known to influence MBL levels with pediatric influenza-related critical illness susceptibility and/or severity including with bacterial co-infections. Methods: We enrolled children and adolescents with laboratory-confirmed influenza infection across 38 pediatric intensive care units from November 2008 to June 2016. We sequenced MBL2 “low-producer” variants rs11003125(“H/L”), rs7096206(“Y/X”), rs1800450Gly54Asp(“B”), rs1800451Gly57Glu(“C”), rs5030737Arg52Cys(“D”) in patients and biologic parents. We measured serum levels and compared complement activity in low-producing homozygotes (“B/B,” “C/C”) to HYA/HYA controls. We used a population control of 1,142 healthy children and also analyzed family trios (PBAT/HBAT) to evaluate disease susceptibility, and nested case-control analyses to evaluate severity. Results: We genotyped 420 patients with confirmed influenza-related sepsis: 159 (38%) had acute lung injury (ALI), 165 (39%) septic shock, and 30 (7%) died. Although bacterial co-infection was diagnosed in 133 patients (32%), only MRSA co-infection (n = 33, 8% overall) was associated with death (p < 0.0001), present in 11 of 30 children that died (37%). MBL2 variants predicted serum levels and complement activation as expected. We found no association between influenza-related critical illness susceptibility and MBL2 variants using family trios (633 biologic parents) or compared to population controls. MBL2 variants were not associated with admission illness severity, septic shock, ALI, or bacterial co-infection diagnosis. Carriage of low-MBL producing MBL2 variants was not a risk factor for mortality, but children that died did have higher carriage of one or more B alleles (OR 2.3; p = 0.007), including 7 of 11 with influenza MRSA-related death (vs. 2 of 22 survivors: OR 14.5, p = 0.0002). Conclusions:MBL2 variants that decrease MBL levels were not associated with susceptibility to pediatric influenza-related critical illness or with multiple measures of critical illness severity. We confirmed a prior report of higher B allele carriage in a relatively small number of young individuals with influenza-MRSA associated death.
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Affiliation(s)
- Emily R Levy
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Department of Anaesthesia, Harvard Medical School, Boston, MA, United States.,Divisions of Pediatric Critical Care and Pediatric Infectious Diseases, Department of Pediatrics, Mayo Clinic, Rochester, MN, United States
| | - Wai-Ki Yip
- Foundation Medicine Inc., Cambridge, MA, United States
| | - Michael Super
- Wyss Institute at Harvard University, Boston, MA, United States
| | - Jill M Ferdinands
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Anushay J Mistry
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
| | - Margaret M Newhams
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gwenn E McLaughlin
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Anil Sapru
- Critical Care Medicine Division, Department of Pediatrics, Children's Hospital of Los Angeles, University of California, Los Angeles, Los Angeles, CA, United States
| | - Laura L Loftis
- Section of Critical Care Medicine, Department of Pediatrics, Texas Children's Hospital, Houston, TX, United States
| | - Scott L Weiss
- Department of Anesthesiology and Critical Care, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, United States
| | - Natalie Cvijanovich
- Department of Pediatrics, Benioff Children's Hospital Oakland, University California San Francisco, Oakland, CA, United States
| | - Adam Schwarz
- Department of Pediatrics, Children's Hospital of Orange County, Orange, CA, United States
| | - Keiko M Tarquinio
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Children's Healthcare of Atlanta at Egleston, Emory University School of Medicine, Atlanta, GA, United States
| | - Peter M Mourani
- Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, United States
| | | | - Adrienne G Randolph
- Division of Critical Care Medicine, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Department of Anaesthesia, Harvard Medical School, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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25
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Kalia N, Singh J, Sharma S, Kaur M. Impact of SNPs interplay across the locus of MBL2, between MBL and Dectin-1 gene, on women's risk of developing recurrent vulvovaginal infections. Cell Biosci 2019; 9:35. [PMID: 31080578 PMCID: PMC6505208 DOI: 10.1186/s13578-019-0300-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Background Human mannose binding lectin (MBL) and dendritic cell-associated C-type lectin-1 (Dectin-1) are the two prototypical PRRs of innate immunity, whose direct role in recurrent vulvovaginal infections (RVVI) defense has been defined. Previously, MBL insufficiency was proposed as a possible risk factor for the rapid progression of RVVI while, Dectin-1 was found to be playing an active role in the defense. However, the complete genetic bases for the observed low MBL levels are still lacking as our previous studies in harmony with others demonstrated the un-expected genotype–phenotype patterns. This suggested the presence of unidentified regulatory variants that may modulate sMBL levels and risk of RVVI. Therefore, the present study was designed for more inclusive locus-wide MBL2 analysis and for the possible non-linear interaction analysis of two PRRs that may impact RVVI susceptibility. Methods The present study has extended the previous findings by investigating (1) the role of chosen additional SNPs falling in the 5′ near region relating to sMBL levels and RVVI susceptibility, using polymerase chain reaction-restriction fragment length polymorphism, (2) interactions among SNPs within gene by comprehensive locus-wide haplotype analyses of two MBL2 blocks, (3) gene–gene interaction analyses between two PRRs, using multifactor dimensionality reduction. Results rs11003124_G, rs7084554_C, rs36014597_G, and rs11003123_A were observed as the minor alleles in the representative North Indian cohort. RVVI cases and its types showed an appreciably high frequency of C allele, its homozygosity and heterozygosity, explaining the observed dominant mode of inheritance of rs7084554 polymorphism in contributing 1.81 fold risk of RVVI. The rs36014597 polymorphism showed the overdominant mode of inheritance, which further depicts that the carrier of a heterozygous genotype of this polymorphism had more extreme phenotype than either of its homozygous carriers in developing 4.07 fold risk of RVVI. sMBL levels significantly varied for rs11003124, rs36014597 and rs11003123 polymorphisms in bacterial vaginosis, while for rs7084554 polymorphism in mixed infection. Independent analysis of 5′ and 3′ haplotype blocks suggested the risk-modifying effect of all the 5′ additional variants, Y/X secretor polymorphism and 3′-UTR SNP i.e. rs10824792. Combined 5′/3′ haplotype analyses depicted the importance of rs36014597; an additional 5′ variant, Y/X and rs10824792 polymorphisms from both the blocks in regulating sMBL levels and RVVI risk. Three gene–gene interaction models involving uni-variant, bi-variant and tri-variant appeared as significant predictors of RVVI risk with cross-validation consistency of 10/10, 9/10 and 5/10, respectively. Conclusions The study presented a low-cost reproducible screening design for additional 5′ variants i.e. rs11003124, rs7084554, rs36014597 and rs11003123 of MBL2 that can act as markers of susceptibility for RVVI or any other diseases. Two additional 5′ variants of MBL2 i.e. rs7084554 and rs36014597 were suggested as novel molecular markers that may contribute to RVVI risk by varying sMBL levels. Variants of two blocks were found to have more of a combined effect than the independent effect in modulating RVVI susceptibility and sMBL levels. The study presented weak synergistic interaction between MBL2 and CLEC7A in association with RVVI risk. The preliminary data will establish the foundation for the investigation of within gene and between genes interaction analyses towards RVVI susceptibility. Electronic supplementary material The online version of this article (10.1186/s13578-019-0300-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Namarta Kalia
- 1Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Jatinder Singh
- 1Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Sujata Sharma
- 2Department of Obstetrics & Gynaecology, Bebe Nanki Mother and Child Care Centre, Government Medical College, Amritsar, India
| | - Manpreet Kaur
- 3Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
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Han SS, Yu XJ, Wang SX, Zhou FD, Yu F, Zhao MH. A novel mutation in complement 2 accompanied by susceptibility variants in C3 glomerulonephritis: A case study. Nefrologia 2019; 39:664-671. [PMID: 31014550 DOI: 10.1016/j.nefro.2019.01.008] [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: 07/27/2018] [Accepted: 01/25/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND C3 glomerulonephritis is a rare, chronic disease characterized by C3c-dominant staining on renal biopsy and is caused by inherited or acquired alternative complement pathway dysregulation. CASE PRESENTATION Here, we reported a 36-year-old man presenting with nephritic syndrome and normal renal function. Secondary causes were excluded by detailed clinical history and laboratory tests. His renal biopsy was consistent with C3 glomerulonephritis with a membranoproliferative glomerulonephritis pattern. To identify the etiology, we carried out genetic and autoantibody screening tests. The results showed he was negative for autoantibodies, while the next-generation sequencing revealed common variants of complement factor H (c.1204T>C; p.Tyr402His), (c.184G>A; p.Val62Ile) and thrombomodulin (c.1418C>T; p.Ala473Val), which have previously been reported to increase susceptibility to complement-mediated diseases. He also carried complement factor H (c.2808G>T; p.Glu936Asp) and mannose-binding lectin (c.161G>A; p.Gly54Asp), putting the patient at an increased risk of infections, which was an important trigger for C3 glomerulonephritis. A novel variant of complement 2 (c.53A>G; p.His18Arg) that might contribute to the occurrence of C3 glomerulonephritis when combined with these susceptibility variants was further identified. The patient was treated with ramipril and regular fresh frozen plasma infusion. He had a good response to treatment with well-controlled proteinuria, stable renal function and an increasing serum C3 level. CONCLUSIONS This case adds insight into the pathogenesis of C3 glomerulopathy by showing that a combination of susceptibility variants, genetic mutations and triggers might be responsible for the clinical and pathological phenotypes.
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Affiliation(s)
- Sha-Sha Han
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China
| | - Xiao-Juan Yu
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China
| | - Su-Xia Wang
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China
| | - Fu-de Zhou
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China
| | - Feng Yu
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China; Department of Nephrology, Peking University International Hospital, Beijing 102206, PR China.
| | - Ming-Hui Zhao
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Beijing 100034, PR China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, PR China; Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing 100034, PR China; Peking-Tsinghua Center for Life Sciences, PR China
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Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene. Comput Biol Chem 2019; 79:127-136. [PMID: 30802828 DOI: 10.1016/j.compbiolchem.2019.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022]
Abstract
In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.
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WITHDRAWN: A novel insight of Asp193His mutation on epigenetic methyltransferase activity of human EZH2 protein: An in-silico approach. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kalia N, Singh J, Sharma S, Kaur M. SNPs in 3'-UTR region of MBL2 increases susceptibility to recurrent vulvovaginal infections by altering sMBL levels. Immunobiology 2018; 224:42-49. [PMID: 30482481 DOI: 10.1016/j.imbio.2018.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022]
Abstract
Recurrent vulvovaginal infections (RVVI), owing to their adverse health consequences, have become a serious dilemma worldwide. Low serum levels of Mannose-Binding Lectin (sMBL), a main component of innate immunity, was found to be associated with RVVI risk, though complete genetic bases are still elusive. To reveal unrecognised regulatory variants, 3'-UTR region of MBL2 with six putative functional SNPs i.e. rs10824792, rs2120132, rs2120131, rs2165813, rs2099903 and rs2099902 was sequenced and genotyped in the present study for 109 RVVI cases and age matched healthy controls. sMBL levels were measured by enzyme-linked immunosorbent assay. The homozygous CC genotype of rs10824792 polymorphism was found to be conferring risk (OR = 2.94) of developing RVVI. Significantly high frequency of corresponding CC genotype was found in Vulvovaginal Candidiasis (VVC) and Mixed Infections (MI) relative to controls. Significantly insufficient sMBL levels were observed in RVVI and its types (Bacterial Vaginosis, VVC and MI) than controls. sMBL levels varied for rs10824792 SNP as expected from the genetic analyses. Six marker haplotype analyses have shown CTTGCT, the haplotype containing only risk allele of rs10824792, conferred risk of RVVI and its types by lowering sMBL levels. In conclusion, a 3'-UTR SNP i.e. rs10824792 was identified as novel associated genetic marker for contributing low sMBL levels and RVVI risk. Our findings contribute to the novel future research directions for the development of emerging MBL substitution as effectual therapy for RVVI.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India.
| | - Sujata Sharma
- Department of Gynaecology & Obstetrics, Bebe Nanki Mother and Child Care Centre, Government Medical College, Amritsar, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India.
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Świerzko AS, Michalski M, Sokołowska A, Nowicki M, Eppa Ł, Szala-Poździej A, Mitrus I, Szmigielska-Kapłon A, Sobczyk-Kruszelnicka M, Michalak K, Gołos A, Wierzbowska A, Giebel S, Jamroziak K, Kowalski ML, Brzezińska O, Thiel S, Jensenius JC, Kasperkiewicz K, Cedzyński M. The Role of Complement Activating Collectins and Associated Serine Proteases in Patients With Hematological Malignancies, Receiving High-Dose Chemotherapy, and Autologous Hematopoietic Stem Cell Transplantations (Auto-HSCT). Front Immunol 2018; 9:2153. [PMID: 30294330 PMCID: PMC6158352 DOI: 10.3389/fimmu.2018.02153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/31/2018] [Indexed: 12/11/2022] Open
Abstract
We conducted a prospective study of 312 patients (194 with multiple myeloma, 118 with lymphomas) receiving high-dose conditioning chemotherapy and autologous hematopoietic stem cell transplantation (auto-HSCT). Polymorphisms of MBL2 and MASP2 genes were investigated and serial measurements of serum concentrations of mannose-binding lectin (MBL), CL-LK collectin and MASP-2 as well as activities of MBL-MASP-1 and MBL-MASP-2 complex were made. Serum samples were taken before conditioning chemotherapy, before HSCT and once weekly after (totally 4-5 samples); in minority of subjects also 1 and/or 3 months post transplantation. The results were compared with data from 267 healthy controls and analyzed in relation to clinical data to explore possible associations with cancer and with chemotherapy-induced medical complications. We found a higher frequency of MBL deficiency-associated genotypes (LXA/O or O/O) among multiple myeloma patients compared with controls. It was however not associated with hospital infections or post-HSCT recovery of leukocytes, but seemed to be associated with the most severe infections during follow-up. Paradoxically, high MBL serum levels were a risk factor for prolonged fever and some infections. The first possible association of MBL2 gene 3′-untranslated region polymorphism with cancer (lymphoma) in Caucasians was noted. Heterozygosity for MASP2 gene +359 A>G mutation was relatively frequent in lymphoma patients who experienced bacteremia during hospital stay. The median concentration of CL-LK was higher in myeloma patients compared with healthy subjects. Chemotherapy induced marked increases in serum MBL and MASP-2 concentrations, prolonged for several weeks and relatively slighter decline in CL-LK level within 1 week. Conflicting findings on the influence of MBL on infections following chemotherapy of myeloma and lymphoma have been reported. Here we found no evidence for an association between MBL deficiency and infection during the short period of neutropenia following conditioning treatment before HSCT. However, we noted a possible protective effect of MBL during follow-up, and suspected that to be fully effective when able to act in combination with phagocytic cells after their recovery.
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Affiliation(s)
- Anna S Świerzko
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Mateusz Michalski
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Anna Sokołowska
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Mateusz Nowicki
- Department of Hematology, Copernicus Memorial Hospital in Łódź Comprehensive Cancer Center and Traumatology, Łódź, Poland
| | - Łukasz Eppa
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Agnieszka Szala-Poździej
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Iwona Mitrus
- Department of Bone Marrow Transplantation and Oncohematology, Cancer Center and Institute of Oncology, Gliwice, Poland
| | | | | | - Katarzyna Michalak
- Department of Bone Marrow Transplantation and Oncohematology, Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Aleksandra Gołos
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | - Sebastian Giebel
- Department of Bone Marrow Transplantation and Oncohematology, Cancer Center and Institute of Oncology, Gliwice, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marek L Kowalski
- Department of Immunology and Allergy, Medical University of Łódz, Łódź, Poland
| | - Olga Brzezińska
- Department of Immunology and Allergy, Medical University of Łódz, Łódź, Poland.,Department of Rheumatology, Medical University of Łódz, Łódź, Poland
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | - Maciej Cedzyński
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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Kalia N, Kaur M, Sharma S, Singh J. A Comprehensive in Silico Analysis of Regulatory SNPs of Human CLEC7A Gene and Its Validation as Genotypic and Phenotypic Disease Marker in Recurrent Vulvovaginal Infections. Front Cell Infect Microbiol 2018; 8:65. [PMID: 29616193 PMCID: PMC5869923 DOI: 10.3389/fcimb.2018.00065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 02/26/2018] [Indexed: 01/25/2023] Open
Abstract
Recurrent Vulvovaginal infections (RVVI) are the commonly reported microbiological syndrome affecting millions of women globally. Various molecules of innate immune system are instrumental in clearance of these microbial pathogens, thus suggested as one of the most important contributing factor in determining the disease outcome. Dendritic cell-associated C-type lectin-1 (Dectin-1) is an important molecule of innate immunity that is primarily known for its role in antifungal defenses. However, role of dectin-1 in recognition of other pathogens is also documented. The intracellular expression of dectin-1 was shown to be up-regulated by Mannose Binding Lectin (MBL)-mediated opsonophagocytosis of pathogens. Dectin-1 is encoded by CLEC7A, postulated to be a candidate gene in modulating risk of developing RVVI. In this study, we identified CLEC7A causal variants using in silico analysis. To assess their impact on susceptibility to RVVI, these causal variants along with serum dectin-1 levels (sDectin-1) were investigated using polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) and Enzyme Linked Immnosorbent Assay (ELISA) respectively, under a case-control design. Furthermore, effect of these polymorphisms was also assessed on sMBL levels. In silico analysis revealed 9 putative functional conserved SNPs of CLEC7A. Association analysis revealed a significantly lower risk of developing RVVI and its types in carriers of CLEC7A rs3901533 G allele and its homozygous genotypes (p < 0.05). The heterozygous genotype was associated with significant protection against RVVI (p = 0.004). Haplotypes GGG and GTA showed significant protection against RVVI (p < 0.0001; p = 0.0003), Bacterial Vaginosis (p = 0.03; p = 0.002), Vulvovaginal Candidiasis (p = 0.03; p = 0.01) and Mixed Infections (p = 0.007; p = 0.04). Mean sDectin-1 levels were significantly high in RVVI and its types compared to controls (p < 0.05). Further, genotype-phenotype stratification showed significant differences within/between cases groups and controls. The CLEC7A rs3901533 polymorphism was also found to be associated with sMBL levels. The present study contributed novel insights into the role of dectin-1 in RVVI. CLEC7A rs3901533 polymorphism and high sDectin-1 levels along with low sMBL levels were found to be associated with RVVI susceptibility. Thus, screening of women with RVVI for these novel associations may lead to better diagnosis and treatment. Also genotyping method used in this study constitutes a simple and reliable assay, which can be confidently, used as a cheaper alternative for genotyping these variants in clinical settings. Finally, new restorative markers for other infectious diseases might be found by exploring nine functionally identified CLEC7A SNPs.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Sujata Sharma
- Department of Gynaecology & Obstetrics, Bebe Nanki Mother and Child Care Centre, Government Medical College, Amritsar, India
| | - Jatinder Singh
- Department of Molecular Biology & Biochemistry, Guru Nanak Dev University, Amritsar, India
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Arshad M, Bhatti A, John P. Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study. PLoS One 2018; 13:e0188143. [PMID: 29329296 PMCID: PMC5766082 DOI: 10.1371/journal.pone.0188143] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/01/2017] [Indexed: 12/02/2022] Open
Abstract
Genetic polymorphisms in TAGAP gene have been associated with many diseases including rheumatoid arthritis, multiple sclerosis and other autoimmune disorders. Identifying functional SNPs in such disease associated genes is an uphill task hence before planning larger population study, it is better to scrutinize putative functional SNPs. In this study we used various computational approaches to identify nsSNPs which are deleterious to the structure and/or function of TAGAP protein that might be causing these diseases. Computational analysis was performed by five different in silico tools including SIFT, PROVEAN, PolyPhen-2, PhD-SNP and SNPs&GO. The study concludes that mutations of Glycine → Glutamic Acid at position 120, Glycine → Tryptophan at position 141 and Valine → Methionine at position 151 are major mutations in native TAGAP protein which might contribute to its malfunction and ultimately causing disease. The study also proposed 3D structures of native TAGAP protein and its three mutants. Future studies should consider these nsSNPs as main target mutations in various diseases involving TAGAP malfunction. This is the first comprehensive study, where TAGAP gene variants were analyzed using in silico tools hence will be of great help while considering large scale studies and also in developing precision medicines for cure of diseases related to these polymorphisms. Furthermore, animal models of various autoimmune diseases and having these mutations might be of help in exploring their precise roles.
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Affiliation(s)
- Maria Arshad
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Attya Bhatti
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Peter John
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
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Kalia N, Singh J, Sharma S, Arora H, Kaur M. Genetic and Phenotypic Screening of Mannose-Binding Lectin in Relation to Risk of Recurrent Vulvovaginal Infections in Women of North India: A Prospective Cohort Study. Front Microbiol 2017; 8:75. [PMID: 28197138 PMCID: PMC5281598 DOI: 10.3389/fmicb.2017.00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 12/25/2022] Open
Abstract
Recurrent Vulvovaginal Infections (RVVI) is common problem associated with women of reproductive age. The function and deleterious effect of Mannose Binding Lectin 2 (MBL2) common polymorphisms are reported to be associated with various diseases. However, the role of MBL2 promoter gene polymorphisms and their combined effect with structural variant along with Serum Mannose Binding Lectin (sMBL) levels in RVVI has not been investigated. The study included 258 RVVI cases and 203 age matched healthy controls. These were investigated for the distribution of MBL2 codon 54 and promoter polymorphisms by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). sMBL levels were quantified by Enzyme Linked Immnosorbent Assay (ELISA). The frequency of X allele and its genotypes was significantly high in cases than controls conferring risk toward RVVI and its types (p < 0.05). The HXPA (OR; 2.0), LXQB (OR; 1.43) haplotypes were associated with susceptibility to RVVI cases while haplotype LYQB significantly protected against RVVI (OR; 0.58), Bacterial Vaginosis (BV) (OR; 0.27) and Mixed Infections (MI) cases (OR; 0.62) with high frequency observed in controls (p < 0.05). Mean sMBL levels were significantly low in RVVI, BV, Vulvovaginal Candidiasis (VVC), and MI cases compared to controls (p < 0.05). VVC patient showed significantly low sMBL levels than RVVI and MI cases (p < 0.05). The mean sMBL levels segregated based on MBL2 genotypes and haplotypes showed significant difference in different cases groups with controls. The findings of the present study suggested that MBL2 Y/X polymorphism and low sMBL levels were associated with susceptibility to RVVI either it is BV, VVC, or MI. Thus MBL deficiency in women with RVVI may contribute to decreased efficiency in clearing of pathogens. Hence, specific measures like administration of purified or recombinant MBL might decrease the incidence of vaginal infections recurrences and more-effective treatment.
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Affiliation(s)
- Namarta Kalia
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University Amritsar, India
| | - Jatinder Singh
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University Amritsar, India
| | - Sujata Sharma
- Department of Gynaecology and Obstetrics, Bebe Nanki Mother and Child Care Centre, Government Medical College Amritsar, India
| | - Hardesh Arora
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University Amritsar, India
| | - Manpreet Kaur
- Department of Human Genetics, Guru Nanak Dev University Amritsar, India
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