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Yajnik CS, Wagh R, Kunte P, Asplund O, Ahlqvist E, Bhat D, Shukla SR, Prasad RB. Polygenic scores of diabetes-related traits in subgroups of type 2 diabetes in India: a cohort study. Lancet Reg Health Southeast Asia 2023; 14:100182. [PMID: 37492423 PMCID: PMC10363502 DOI: 10.1016/j.lansea.2023.100182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/08/2022] [Accepted: 03/09/2023] [Indexed: 07/27/2023]
Abstract
Background A machine-learning approach identified five subgroups of diabetes in Europeans which included severe autoimmune diabetes (SAID), severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD) and mild age-related diabetes (MARD) with partially distinct genetic aetiologies. We previously validated four of the non-autoimmune subgroups in people with young-onset type 2 diabetes (T2D) from the Indian WellGen study. Here, we aimed to apply European-derived centroids and genetic risk scores (GRSs) to the unselected (for age) WellGen to test their applicability and investigate the genetic aetiology of the Indian T2D subgroups. Methods We applied European derived centroids and GRSs to T2D participants of Indian ancestry (WellGen, n = 2217, 821 genotyped) and compared them with normal glucose tolerant controls (Pune Maternal Nutrition Study, n = 461). Findings SIDD was the predominant subgroup followed by MOD, whereas SIRD and MARD were less frequent. Weighted-GRS for T2D, obesity and lipid-related traits associated with T2D. We replicated some of the previous associations of GRS for T2D, insulin secretion, and BMI with SIDD and MOD. Unique to Indian subgroups was the association of GRS for (a) proinsulin with MOD and MARD, (b) liver-lipids with SIDD, SIRD and MOD, and (c) opposite effect of beta-cell GRS with SIDD and MARD, obesity GRS with MARD compared to Europeans. Genetic variants of fucosyltransferases were associated with T2D and MOD in Indians but not Europeans. Interpretation The similarities emphasise the applicability of some of the European-derived GRSs to T2D and its subgroups in India while the differences highlight the need for large-scale studies to identify aetiologies in diverse ancestries. The data provide robust evidence for genetically distinct aetiologies for the T2D subgroups and at least partly mirror those seen in Europeans. Funding Vetenskapsrådet, Diabetes Wellness, and Hjärt-Lungfonden (Sweden), DST (India), Wellcome Trust, Crafoord Foundation and Albert Påhlsson Foundation.
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Affiliation(s)
- Chittaranjan S. Yajnik
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Rucha Wagh
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed) University, Pune, 411021, India
| | - Pooja Kunte
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown Campus, Sydney, 2560, NSW, Australia
| | - Olof Asplund
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
| | - Dattatrey Bhat
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
| | - Sharvari R. Shukla
- Diabetes Unit, Kamalnayan Bajaj Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, 411011, India
- Symbiosis Statistical Institute, Symbiosis International University, Pune, 411005, India
| | - Rashmi B. Prasad
- Department of Clinical Sciences, Diabetes and Endocrinology, CRC, Lund University, Malmö SE-205 02, Sweden
- Institute for Molecular Medicine Finland FIMM, Helsinki University, 00290, Helsinki, Finland
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Herbert A, Pavlov F, Konovalov D, Poptsova M. Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations. Int J Mol Sci 2023; 24:ijms24054884. [PMID: 36902315 PMCID: PMC10003719 DOI: 10.3390/ijms24054884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10-116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
- Correspondence:
| | - Fedor Pavlov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Dmitrii Konovalov
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 11 Pokrovsky Bulvar, 101000 Moscow, Russia
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Bennet L, Nilsson C, Mansour‐Aly D, Christensson A, Groop L, Ahlqvist E. Adult-onset diabetes in Middle Eastern immigrants to Sweden: Novel subgroups and diabetic complications-The All New Diabetes in Scania cohort diabetic complications and ethnicity. Diabetes Metab Res Rev 2021; 37:e3419. [PMID: 33119194 PMCID: PMC8518927 DOI: 10.1002/dmrr.3419] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Middle Eastern immigrants to Europe represent a high risk population for type 2 diabetes. We compared prevalence of novel subgroups and assessed risk of diabetic macro- and microvascular complications between diabetes patients of Middle Eastern and European origin. METHODS This study included newly diagnosed diabetes patients born in Sweden (N = 10641) or Iraq (N = 286), previously included in the All New Diabetes in Scania cohort. The study was conducted between January 2008 and August 2016. Patients were followed to April 2017. Incidence rates in diabetic macro- and microvascular complications were assessed using cox-regression adjusting for the confounding effect of age at onset, sex, anthropometrics, glomerular filtration rate (eGFR) and HbA1c. FINDINGS In Iraqi immigrants versus native Swedes, severe insulin-deficient diabetes was almost twice as common (27.9 vs. 16.2% p < 0.001) but severe insulin-resistant diabetes was less prevalent. Patients born in Iraq had higher risk of coronary events (hazard ratio [HR] 1.84, 95% CI 1.06-3.12) but considerably lower risk of chronic kidney disease (CKD) than Swedes (HR 0.19; 0.05-0.76). The lower risk in Iraqi immigrants was partially attributed to better eGFR. Genetic risk scores (GRS) showed more genetic variants associated with poor insulin secretion but lower risk of insulin resistance in the Iraqi than native Swedish group. INTERPRETATION People with diabetes, born in the Middle East present with a more insulin-deficient phenotype and genotype than native Swedes. They have a higher risk of coronary events but lower risk of CKD. Ethnic differences should be considered in the preventive work towards diabetes and its complications.
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Affiliation(s)
- Louise Bennet
- Department of Clinical SciencesLund UniversityMalmöSweden
- Department of Family MedicineLund UniversityMalmöSweden
| | - Christopher Nilsson
- Department of Clinical SciencesLund UniversityMalmöSweden
- Department of NephrologySkåne University HospitalMalmöSweden
| | - Dina Mansour‐Aly
- Department of Clinical Sciences, Genomics, Diabetes and EndocrinologyLund University Diabetes CentreLund UniversityMalmöSweden
| | - Anders Christensson
- Department of Clinical SciencesLund UniversityMalmöSweden
- Department of NephrologySkåne University HospitalMalmöSweden
| | - Leif Groop
- Department of Clinical SciencesLund UniversityMalmöSweden
- Finnish Institute of Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | - Emma Ahlqvist
- Department of Clinical SciencesLund UniversityMalmöSweden
- Department of Clinical Sciences, Genomics, Diabetes and EndocrinologyLund University Diabetes CentreLund UniversityMalmöSweden
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Orlov MA, Ryasik AA, Sorokin AA. [Destabilization of the DNA Duplex of Actively Replicating Promoters of T7-Like Bacteriophages]. Mol Biol (Mosk) 2018; 52:793-800. [PMID: 30363054 DOI: 10.1134/s0026898418050117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
Abstract
The relation between the processes of replication and transcription has been actively studied over several decades, but detailed mechanisms for their interaction have not been established reliably. Among the initiating transcription promoters of bacteria and bacteriophages, there are both promoters having an additional function of the secondary origin of replication (OR) and promoters not participating in this process. In this paper, we describe the stability of DNA by Stress-Induced Duplex Destabilization (SIDD) profiles for a complete set of promoters and the primary OR of the bacteriophage T7 genome. It has been shown that, among the native T7 promoters, only those that have an additional function of secondary OR are characterized by high destabilization. These include the phiOL and phiOR promoters adjoining the 5' and 3' terminal repeats of bacteriophage T7, and of six other T7 group phages. In each case, these two promoters are located in the regions of DNA with high destabilization of the duplex. Additionally, the genomes of seven representatives of the T7 group without annotated phiOL and phiOR have been considered. For three of them, high peaks of SIDD profiles have been found near the ends of the genomic DNA that may be due to the presence of similar phiOL and phiOR promoters. Probably, such promoters can be found in the genomes of other bacteriophages. Thus, for the promoters of bacteriophages, we have a confirmation of the relationship of SIDD as a DNA duplex parameter and the DNA replication initiation on promoters, serving as secondary OR.
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Affiliation(s)
- M A Orlov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.,
| | - A A Ryasik
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| | - A A Sorokin
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
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Kouzine F, Wojtowicz D, Baranello L, Yamane A, Nelson S, Resch W, Kieffer-Kwon KR, Benham CJ, Casellas R, Przytycka TM, Levens D. Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. Cell Syst 2017; 4:344-356.e7. [PMID: 28237796 DOI: 10.1016/j.cels.2017.01.013] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022]
Abstract
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.
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