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Ciocarlie T, Motofelea AC, Motofelea N, Dutu AG, Crăciun A, Costachescu D, Roi CI, Silaghi CN, Crintea A. Exploring the Role of Vitamin D, Vitamin D-Dependent Proteins, and Vitamin D Receptor Gene Variation in Lung Cancer Risk. Int J Mol Sci 2024; 25:6664. [PMID: 38928369 PMCID: PMC11203461 DOI: 10.3390/ijms25126664] [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: 04/15/2024] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Lung cancer has an unfavorable prognosis with a rate of low overall survival, caused by the difficulty of diagnosis in the early stages and resistance to therapy. In recent years, there have been new therapies that use specific molecular targets and are effective in increasing the survival chances of advanced cancer. Therefore, it is necessary to find more specific biomarkers that can identify early changes in carcinogenesis and allow the earliest possible treatment. Vitamin D (VD) plays an important role in immunity and carcinogenesis. Furthermore, the vitamin D receptor (VDR) regulates the expression of various genes involved in the physiological functions of the human organism. The genes encoding the VDR are extremely polymorphic and vary greatly between human populations. To date, there are significant associations between VDR polymorphism and several types of cancer, but the data on the involvement of VDR polymorphism in lung cancer are still conflicting. Therefore, in this review, our aim was to investigate the relationship between VDR single-nucleotide polymorphisms in humans and the degree of risk for developing lung cancer. The studies showcased different gene polymorphisms to be associated with an increased risk of lung cancer: TaqI, ApaI, BsmI, FokI, and Cdx2. In addition, there is a strong positive correlation between VD deficiency and lung cancer development. Still, due to a lack of awareness, the assessment of VD status and VDR polymorphism is rarely considered for the prediction of lung cancer evolution and their clinical applicability, despite the fact that studies have shown the highest risk for lung cancer given by TaqI gene polymorphisms and that VDR polymorphisms are associated with more aggressive cancer evolution.
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Affiliation(s)
- Tudor Ciocarlie
- Department VII Internal Medicine II, Discipline of Cardiology, University of Medicine and Pharmacy “Victor Babes”, 300041 Timisoara, Romania;
| | - Alexandru Cătălin Motofelea
- Department of Internal Medicine, University of Medicine and Pharmacy “Victor Babes”, 300041 Timisoara, Romania
| | - Nadica Motofelea
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. No. 2, 300041 Timisoara, Romania;
| | - Alina Gabriela Dutu
- Department of Molecular Sciences, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (A.G.D.); (A.C.); (C.N.S.); (A.C.)
| | - Alexandra Crăciun
- Department of Molecular Sciences, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (A.G.D.); (A.C.); (C.N.S.); (A.C.)
| | - Dan Costachescu
- Radiology Department, University of Medicine and Pharmacy “Victor Babes”, 300041 Timisoara, Romania;
| | - Ciprian Ioan Roi
- Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Sq. No. 2, 300041 Timisoara, Romania;
| | - Ciprian Nicolae Silaghi
- Department of Molecular Sciences, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (A.G.D.); (A.C.); (C.N.S.); (A.C.)
| | - Andreea Crintea
- Department of Molecular Sciences, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania; (A.G.D.); (A.C.); (C.N.S.); (A.C.)
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Veerappa A, Guda C. Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis. Front Neurosci 2024; 18:1332419. [PMID: 38660223 PMCID: PMC11041639 DOI: 10.3389/fnins.2024.1332419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Determining the key genetic variants is a crucial step to comprehensively understand substance use disorders (SUDs). In this study, utilizing whole exome sequences of five multi-generational pedigrees with SUDs, we used an integrative omics-based approach to uncover candidate genetic variants that impart susceptibility to SUDs and influence addition traits. We identified several SNPs and rare, protein-function altering variants in genes, GRIA3, NCOR1, and SHANK1; compound heterozygous variants in LNPEP, LRP1, and TBX2, that play a significant role in the neurotransmitter-neuropeptide axis, specifically in the dopaminergic circuits. We also noted a greater frequency of heterozygous and recessive variants in genes involved in the structural and functional integrity of synapse receptors, CHRNA4, CNR2, GABBR1, DRD4, NPAS4, ADH1B, ADH1C, OPRM1, and GABBR2. Variant analysis in upstream promoter regions revealed regulatory variants in NEK9, PRRX1, PRPF4B, CELA2A, RABGEF1, and CRBN, crucial for dopamine regulation. Using family-and pedigree-based data, we identified heterozygous recessive alleles in LNPEP, LRP1 (4 frameshift deletions), and TBX2 (2 frameshift deletions) linked to SUDs. GWAS overlap identified several SNPs associated with SUD susceptibility, including rs324420 and rs1229984. Furthermore, miRNA variant analysis revealed notable variants in mir-548 U and mir-532. Pathway studies identified the presence of extensive coordination among these genetic variants to impart substance use susceptibility and pathogenesis. This study identified variants that were found to be overrepresented among genes of dopaminergic circuits participating in the neurotransmitter-neuropeptide axis, suggesting pleiotropic influences in the development and sustenance of chronic substance use. The presence of a diverse set of haploinsufficient variants in varying frequencies demonstrates the existence of extraordinary coordination among them in attributing risk and modulating severity to SUDs.
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Affiliation(s)
- Avinash Veerappa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
- Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE, United States
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Yao M, Oduro PK, Akintibu AM, Yan H. Modulation of the vitamin D receptor by traditional Chinese medicines and bioactive compounds: potential therapeutic applications in VDR-dependent diseases. Front Pharmacol 2024; 15:1298181. [PMID: 38318147 PMCID: PMC10839104 DOI: 10.3389/fphar.2024.1298181] [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: 09/28/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
The Vitamin D receptor (VDR) is a crucial nuclear receptor that plays a vital role in various physiological functions. To a larger extent, the genomic effects of VDR maintain general wellbeing, and its modulation holds implications for multiple diseases. Current evidence regarding using vitamin D or its synthetic analogs to treat non-communicable diseases is insufficient, though observational studies suggest potential benefits. Traditional Chinese medicines (TCMs) and bioactive compounds derived from natural sources have garnered increasing attention. Interestingly, TCM formulae and TCM-derived bioactive compounds have shown promise in modulating VDR activities. This review explores the intriguing potential of TCM and bioactive compounds in modulating VDR activity. We first emphasize the latest information on the genetic expression, function, and structure of VDR, providing a comprehensive understanding of this crucial receptor. Following this, we review several TCM formulae and herbs known to influence VDR alongside the mechanisms underpinning their action. Similarly, we also discuss TCM-based bioactive compounds that target VDR, offering insights into their roles and modes of action.
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Affiliation(s)
- Minghe Yao
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Patrick Kwabena Oduro
- Jacobs School of Medicine and Biomedical Sciences, The State University of New York, University at Buffalo, Buffalo, NY, United States
| | - Ayomide M. Akintibu
- School of Community Health and Policy, Morgan State University, Baltimore, MD, United States
| | - Haifeng Yan
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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Iwai Y, Iijima A, Kise S, Nagao C, Senda Y, Yabu K, Mano H, Nishikawa M, Ikushiro S, Yasuda K, Sakaki T. Characterization of Rickets Type II Model Rats to Reveal Functions of Vitamin D and Vitamin D Receptor. Biomolecules 2023; 13:1666. [PMID: 38002348 PMCID: PMC10669209 DOI: 10.3390/biom13111666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Vitamin D has been known to exert a wide range of physiological effects, including calcemic, osteogenic, anticancer, and immune responses. We previously generated genetically modified (GM) rats and performed a comparative analysis of their physiological properties to elucidate the roles of vitamin D and vitamin D receptor (VDR). In this study, our primary goal was to investigate the manifestations of type II rickets in rats with the VDR(H301Q) mutation, analogous to the human VDR(H305Q). Additionally, we created a double-mutant rat with the VDR(R270L/H301Q) mutation, resulting in almost no affinity for 1,25-dihydroxy-vitamin D3 (1,25D3) or 25-hydroxy-vitamin D3 (25D3). Notably, the plasma calcium concentration in Vdr(R270L/H301Q) rats was significantly lower than in wild-type (WT) rats. Meanwhile, Vdr(H301Q) rats had calcium concentrations falling between those of Vdr(R270L/H301Q) and WT rats. GM rats exhibited markedly elevated plasma parathyroid hormone and 1,25D3 levels compared to those of WT rats. An analysis of bone mineral density in the cortical bone of the femur in both GM rats revealed significantly lower values than in WT rats. Conversely, the bone mineral density in the trabecular bone was notably higher, indicating abnormal bone formation. This abnormal bone formation was more pronounced in Vdr(R270L/H301Q) rats than in Vdr(H301Q) rats, highlighting the critical role of the VDR-dependent function of 1,25D3 in bone formation. In contrast, neither Vdr(H301Q) nor Vdr(R270L/H301Q) rats exhibited symptoms of alopecia or cyst formation in the skin, which were observed in the Vdr-KO rats. These findings strongly suggest that unliganded VDR is crucial for maintaining the hair cycle and normal skin. Our GM rats hold significant promise for comprehensive analyses of vitamin D and VDR functions in future research.
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Affiliation(s)
- Yuichiro Iwai
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Ayano Iijima
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Satoko Kise
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Chika Nagao
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Yuto Senda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Kana Yabu
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Hiroki Mano
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (M.N.); (S.I.)
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (M.N.); (S.I.)
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu 939-0398, Toyama, Japan; (Y.I.); (A.I.); (S.K.); (C.N.); (Y.S.); (K.Y.); (H.M.)
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Kise S, Iijima A, Nagao C, Okada T, Nishikawa M, Ikushiro S, Nakanishi T, Sato S, Yasuda K, Sakaki T. Gene therapy for alopecia in type II rickets model rats using vitamin D receptor-expressing adenovirus vector. Sci Rep 2023; 13:18528. [PMID: 37898650 PMCID: PMC10613246 DOI: 10.1038/s41598-023-45594-2] [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: 04/18/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023] Open
Abstract
Type II rickets is a hereditary disease caused by a mutation in the vitamin D receptor (VDR) gene. The main symptoms of this disease are bone dysplasia and alopecia. Bone dysplasia can be ameliorated by high calcium intake; however, there is no suitable treatment for alopecia. In this study, we verified whether gene therapy using an adenoviral vector (AdV) had a therapeutic effect on alopecia in Vdr-KO rats. The VDR-expressing AdV was injected into six 7-week-old female Vdr-KO rats (VDR-AdV rats). On the other hand, control-AdV was injected into 7-week-old female rats (control-AdV rats); non-infected Vdr-KO rats (control rats) were also examined. The hair on the backs of the rats was shaved with hair clippers, and VDR-AdV or control-AdV was intradermally injected. Part of the back skin was collected from each rat after AdV administration. Hair follicles were observed using hematoxylin and eosin staining, and VDR expression was examined using immunostaining and western blotting. VDR-AdV rats showed significant VDR expression in the skin, enhanced hair growth, and low cyst formation, whereas control-AdV and non-infected rats did not show any of these effects. The effect of VDR-AdV lasted for nearly 60 days. These results indicate that gene therapy using VDR-AdV may be useful to treat alopecia associated with type II rickets, if multiple injections are possible after a sufficient period of time.
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Affiliation(s)
- Satoko Kise
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Ayano Iijima
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Chika Nagao
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Tadashi Okada
- Department of Food and Nutrition, Okayama Gakuin University, 787 Aruki, Kurashiki, Okayama, 710-8511, Japan
| | - Miyu Nishikawa
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Tomoko Nakanishi
- Center of Biomedical Research Resources, Juntendo University School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Shigeto Sato
- Center of Biomedical Research Resources, Juntendo University School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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Kashyap J, Kumari N, Ponnusamy K, Tyagi RK. Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194891. [PMID: 36396100 DOI: 10.1016/j.bbagrm.2022.194891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Vitamin D receptor (VDR) is a member of the nuclear receptor superfamily. It is a primary regulator of calcium and phosphate homeostasis required for skeleton and bone mineralization. Vitamin D in active form 1α,25 dihydroxyvitamin-D3 mediates its cellular functions by binding to VDR. Active VDR forms heterodimers with partner RXR (retinoid X receptor) to execute its physiological actions. HVDRR (Hereditary Vitamin D-Resistant Rickets) is a rare genetic disorder that occurs because of generalized resistance to the 1α,25(OH)2D3. HVDRR is caused by the polymorphic variations in VDR gene leading to defective intestinal calcium absorption and mineralization of newly forming bones. Using point and deletion SNPs of VDR we have studied several HVDRR-associated SNP variants for their subcellular dynamics, transcriptional functions, 'genome bookmarking', heterodimeric interactions with RXR, and receptor stability. We previously reported that VDR is a 'mitotic bookmarking factor' that remains constitutively associated with the mitotic chromatin to inherit 'transcriptional memory', however the mechanistic details remained unclear. We document that 'genome bookmarking' property by VDR is critically impaired by naturally occurring HVDRR-associated point and deletion variants found in patients. Furthermore, these HVDRR-associated SNP variants of VDR were found to be compromised in transcriptional function, nuclear translocation, protein stability and intermolecular interactions with its heterodimeric partner RXR. Intriguingly, majority of these disease-allied functional defects failed to be rescued by RXR. Our findings suggest that the HVDRR-associated SNP variations influence the normal functioning of the receptor, and this derived understanding may help in the management of disease with precisely designed small molecule modulators.
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Affiliation(s)
- Jyoti Kashyap
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Neha Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; Special Centre for Systems Medicine (Concurrent Faculty), Jawaharlal Nehru University, New Delhi 110067, India.
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Kise S, Iijima A, Nagao C, Okada T, Mano H, Nishikawa M, Ikushiro S, Kanemoto Y, Kato S, Nakanishi T, Sato S, Yasuda K, Sakaki T. Functional analysis of vitamin D receptor (VDR) using adenovirus vector. J Steroid Biochem Mol Biol 2023; 230:106275. [PMID: 36854350 DOI: 10.1016/j.jsbmb.2023.106275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/09/2023] [Accepted: 02/25/2023] [Indexed: 02/27/2023]
Abstract
Recently, we generated type II rickets model rats, including Vdr(R270L), Vdr(H301Q), Vdr(R270L/H301Q), and Vdr-knockout (KO), by genome editing. All generated animals showed symptoms of rickets, including growth retardation and abnormal bone formation. Among these, only Vdr-KO rats exhibited abnormal skin formation and alopecia. To elucidate the relationship between VDR function and rickets symptoms, each VDR was expressed in human HaCaT-VDR-KO cells using an adenovirus vector. We also constructed an adenovirus vector expressing VDR(V342M) corresponding to human VDR(V346M) which causes alopecia. We compared the nuclear translocation of VDRs after adding 1α,25-dihydroxyvitamin D3 (1,25D3) or 25-hydroxyvitamin D3 (25D3) at final concentrations of 10 and 100 nM, respectively. Both 25D3 and 1,25D3 induced the nuclear translocation of wild type VDR and VDR(V342M). Conversely, VDR(R270L) translocation was observed in the presence of 100 nM 25D3, with almost no translocation following treatment with 10 nM 1,25D3. VDR(R270L/H301Q) failed to undergo nuclear translocation. These results were consistent with their affinity for each ligand. Notably, VDR(R270L/H301Q) may exist in an unliganded form under physiological conditions, and factors interacting with VDR(R270L/H301Q) may be involved in the hair growth cycle. Thus, this novel system using an adenovirus vector could be valuable in elucidating vitamin D receptor functions.
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Affiliation(s)
- Satoko Kise
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Ayano Iijima
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Chika Nagao
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tadashi Okada
- Health Sciences Research Center, Iryo Sosei University, 5-5-1 Chuodai Iino, Iwaki, Fukushima 970-8551, Japan; Research Institute of Innovative Medicine (RIIM), Tokiwa Foundation, 57 Kaminodai Jyoban Kamiyunagayamachi, Iwaki, Fukushima 972-8322, Japan
| | - Hiroki Mano
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Miyu Nishikawa
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yoshiaki Kanemoto
- Research Institute of Innovative Medicine (RIIM), Tokiwa Foundation, 57 Kaminodai Jyoban Kamiyunagayamachi, Iwaki, Fukushima 972-8322, Japan
| | - Shigeaki Kato
- Health Sciences Research Center, Iryo Sosei University, 5-5-1 Chuodai Iino, Iwaki, Fukushima 970-8551, Japan; Research Institute of Innovative Medicine (RIIM), Tokiwa Foundation, 57 Kaminodai Jyoban Kamiyunagayamachi, Iwaki, Fukushima 972-8322, Japan
| | - Tomoko Nakanishi
- Center of Biomedical Research Resources, Juntendo University School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan
| | - Shigeto Sato
- Center of Biomedical Research Resources, Juntendo University School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Khan AS, Parvez N, Ahsan T, Shoily SS, Sajib AA. A comprehensive in silico exploration of the impacts of missense variants on two different conformations of human pirin protein. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:225. [PMID: 35967515 PMCID: PMC9362109 DOI: 10.1186/s42269-022-00917-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pirin, a member of the cupin superfamily, is an iron-binding non-heme protein. It acts as a coregulator of several transcription factors, especially the members of NFκB transcription factor family. Based on the redox state of its iron cofactor, it can assume two different conformations and thereby act as a redox sensor inside the nucleus. Previous studies suggested that pirin may be associated with cancer, inflammatory diseases as well as COVID-19 severities. Hence, it is important to explore the pathogenicity of its missense variants. In this study, we used a number of in silico tools to investigate the effects of missense variants of pirin on its structure, stability, metal cofactor binding affinity and interactions with partner proteins. In addition, we used protein dynamics simulation to elucidate the effects of selected variants on its dynamics. Furthermore, we calculated the frequencies of haplotypes containing pirin missense variants across five major super-populations (African, Admixed American, East Asian, European and South Asian). RESULTS Among a total of 153 missense variants of pirin, 45 were uniformly predicted to be pathogenic. Of these, seven variants can be considered for further experimental studies. Variants R59P and L116P were predicted to significantly destabilize and damage pirin structure, substantially reduce its affinity to its binding partners and alter pirin residue fluctuation profile via changing the flexibility of several key residues. Additionally, variants R59Q, F78V, G98D, V151D and L220P were found to impact pirin structure and function in multiple ways. As no haplotype was identified to be harboring more than one missense variant, further interrogation of the individual effects of these seven missense variants is highly recommended. CONCLUSIONS Pirin is involved in the transcriptional regulation of several genes and can play an important role in inflammatory responses. The variants predicted to be pathogenic in this study may thus contribute to a better understanding of the underlying molecular mechanisms of various inflammatory diseases. Future studies should be focused on clarifying if any of these variants can be used as disease biomarkers. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-022-00917-7.
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Affiliation(s)
- Auroni Semonti Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, 1100 Bangladesh
| | - Nahid Parvez
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, 1100 Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349 Bangladesh
| | - Sabrina Samad Shoily
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000 Bangladesh
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Ahsan T, Shoily SS, Fatema K, Sajib AA. Impacts of 119 missense variants at functionally important sites of drug-metabolizing human cytosolic sulfotransferase SULT1A1: An in silico study. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Li L, Liu S, Yu J. Autoimmune thyroid disease and type 1 diabetes mellitus: same pathogenesis; new perspective? Ther Adv Endocrinol Metab 2020; 11:2042018820958329. [PMID: 32973994 PMCID: PMC7493255 DOI: 10.1177/2042018820958329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Autoimmune thyroid disease (AITD) and type 1 diabetes mellitus (T1DM) are two common autoimmune diseases that can occur concomitantly. In general, patients with diabetes have a high risk of AITD. It has been proposed that a complex genetic basis together with multiple nongenetic factors make a variable contribution to the pathogenesis of T1DM and AITD. In this paper, we summarize current knowledge in the field regarding potential pathogenic factors of T1DM and AITD, including human leukocyte antigen, autoimmune regulator, lymphoid protein tyrosine phosphatase, forkhead box protein P3, cytotoxic T lymphocyte-associated antigen, infection, vitamin D deficiency, and chemokine (C-X-C motif) ligand. These findings offer an insight into future immunotherapy for autoimmune diseases.
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Affiliation(s)
- Liyan Li
- Department of Endocrinology, First People’s Hospital of Jinan, Jinan, People’s Republic of China
| | - Shudong Liu
- Department of Endocrinology, Shandong Rongjun General Hospital, Jinan, People’s Republic of China
| | - Junxia Yu
- Department of Endocrinology, Tengzhou Central People’s Hospital, 181 Xingtan Road, Tengzhou, Shandong Province, 277500, People’s Republic of China
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Vesnina A, Prosekov A, Kozlova O, Atuchin V. Genes and Eating Preferences, Their Roles in Personalized Nutrition. Genes (Basel) 2020; 11:genes11040357. [PMID: 32230794 PMCID: PMC7230842 DOI: 10.3390/genes11040357] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
At present, personalized diets, which take into account consumer genetic characteristics, are growing popular. Nutrigenetics studies the effect of gene variations on metabolism and nutrigenomics, which branches off further and investigates how nutrients and food compounds affect genes. This work deals with the mutations affecting the assimilation of metabolites, contributing to nutrigenetic studies. We searched for the genes responsible for eating preferences which allow for the tailoring of personalized diets. Presently, genetic nutrition is growing in demand, as it contributes to the prevention and/or rehabilitation of non-communicable diseases, both monogenic and polygenic. In this work, we showed single-nucleotide polymorphisms in genes-missense mutations that change the functions of coded proteins, resulting in a particular eating preferences or a disease. We studied the genes influencing food preferences-particularly those responsible for fats and carbohydrates absorption, food intolerance, metabolism of vitamins, taste sensations, oxidation of xenobiotics, eating preferences and food addiction. As a result, 34 genes were identified that affect eating preferences. Significant shortcomings were found in the methods/programs for developing personalized diets that are used today, and the weaknesses were revealed in the development of nutrigenetics (inconsistency of data on SNP genes, ignoring population genetics data, difficult information to understand consumer, etc.). Taking into account all the shortcomings, an approximate model was proposed in the review for selecting an appropriate personalized diet. In the future, it is planned to develop the proposed model for the compilation of individual diets.
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Affiliation(s)
- Anna Vesnina
- Department of Bionanotechnology, Kemerovo State University, 650043 Kemerovo, Russia; (A.V.); (O.K.)
| | - Alexander Prosekov
- Laboratory of Biocatalysis, Kemerovo State University, 650043 Kemerovo, Russia;
| | - Oksana Kozlova
- Department of Bionanotechnology, Kemerovo State University, 650043 Kemerovo, Russia; (A.V.); (O.K.)
| | - Victor Atuchin
- Laboratory of Optical Materials and Structures, Institute of Semiconductor Physics, 630090 Novosibirsk, Russia
- Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, 630090 Novosibirsk, Russia
- Research and Development Department, Kemerovo State University, 650000 Kemerovo, Russia
- Correspondence: ; Tel.: +7-(383)-3308889
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