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Damarov IS, Korbolina EE, Rykova EY, Merkulova TI. Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response. Int J Mol Sci 2024; 25:9297. [PMID: 39273245 PMCID: PMC11394919 DOI: 10.3390/ijms25179297] [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: 07/11/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.
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Affiliation(s)
- Igor S Damarov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena E Korbolina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena Y Rykova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Tatiana I Merkulova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Medina-Ruiz L, Bartolini R, Mathie H, Halawa HA, Cunningham M, Graham GJ. CCR1 and CCR2 Coexpression on Monocytes Is Nonredundant and Delineates a Distinct Monocyte Subpopulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:214-225. [PMID: 38829123 PMCID: PMC11215633 DOI: 10.4049/jimmunol.2400007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
The interactions between chemokines and their receptors, particularly in the context of inflammation, are complex, with individual receptors binding multiple ligands and individual ligands interacting with multiple receptors. In addition, there are numerous reports of simultaneous coexpression of multiple inflammatory chemokine receptors on individual inflammatory leukocyte subtypes. Overall, this has previously been interpreted as redundancy and proposed as a protective mechanism to ensure that the inflammatory response is robust. By contrast, we have hypothesized that the system is not redundant but exquisitely subtle. Our interests relate to the receptors CCR1, CCR2, CCR3, and CCR5, which, together, regulate nonneutrophilic myeloid cell recruitment to inflammatory sites. In this study, we demonstrate that although most murine monocytes exclusively express CCR2, there is a small subpopulation that is expanded during inflammation and coexpresses CCR1 and CCR2. Combinations of transcript and functional analysis demonstrate that this is not redundant expression and that coexpression of CCR1 and CCR2 marks a phenotypically distinct population of monocytes characterized by expression of genes otherwise typically associated with neutrophils. Single-cell RNA sequencing confirms this as a monodisperse population of atypical monocytes. This monocytic population has previously been described as having immunosuppressive activity. Overall, our data confirm combinatorial chemokine receptor expression by a subpopulation of monocytes but demonstrate that this is not redundant expression and marks a discrete monocytic population.
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Affiliation(s)
- Laura Medina-Ruiz
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Robin Bartolini
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Heather Mathie
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Heba A. Halawa
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Madeleine Cunningham
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gerard J. Graham
- Chemokine Research Group, Centre for Immunobiology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Kelly CJ, Lindsay SL, Smith RS, Keh S, Cunningham KT, Thümmler K, Maizels RM, Campbell JDM, Barnett SC. Development of Good Manufacturing Practice-Compatible Isolation and Culture Methods for Human Olfactory Mucosa-Derived Mesenchymal Stromal Cells. Int J Mol Sci 2024; 25:743. [PMID: 38255817 PMCID: PMC10815924 DOI: 10.3390/ijms25020743] [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: 11/23/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Demyelination in the central nervous system (CNS) resulting from injury or disease can cause loss of nerve function and paralysis. Cell therapies intended to promote remyelination of axons are a promising avenue of treatment, with mesenchymal stromal cells (MSCs) a prominent candidate. We have previously demonstrated that MSCs derived from human olfactory mucosa (hOM-MSCs) promote myelination to a greater extent than bone marrow-derived MSCs (hBM-MSCs). However, hOM-MSCs were developed using methods and materials that were not good manufacturing practice (GMP)-compliant. Before considering these cells for clinical use, it is necessary to develop a method for their isolation and expansion that is readily adaptable to a GMP-compliant environment. We demonstrate here that hOM-MSCs can be derived without enzymatic tissue digestion or cell sorting and without culture antibiotics. They grow readily in GMP-compliant media and express typical MSC surface markers. They robustly produce CXCL12 (a key secretory factor in promoting myelination) and are pro-myelinating in in vitro rodent CNS cultures. GMP-compliant hOM-MSCs are comparable in this respect to those grown in non-GMP conditions. However, when assessed in an in vivo model of demyelinating disease (experimental autoimmune encephalitis, EAE), they do not significantly improve disease scores compared with controls, indicating further pre-clinical evaluation is necessary before their advancement to clinical trials.
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Affiliation(s)
- Christopher J. Kelly
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - Susan L. Lindsay
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - Rebecca Sherrard Smith
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - Siew Keh
- New Victoria Hospital, 55 Grange Road, Glasgow G42 9LF, UK
| | - Kyle T. Cunningham
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - Katja Thümmler
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - Rick M. Maizels
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
| | - John D. M. Campbell
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
- Tissues Cells and Advanced Therapeutics, SNBTS, Jack Copland Centre, Edinburgh EH14 4BE, UK
| | - Susan C. Barnett
- School of Infection and Immunity, 120 University Place, Glasgow G12 8TA, UK; (C.J.K.); (S.L.L.); (R.M.M.)
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Larsen O, Schuermans S, Walser A, Louka S, Lillethorup IA, Våbenø J, Qvortrup K, Proost P, Rosenkilde MM. Chemokine N-terminal-derived peptides differentially regulate signaling by the receptors CCR1 and CCR5. FEBS Lett 2023; 597:3049-3060. [PMID: 37994578 DOI: 10.1002/1873-3468.14778] [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: 06/14/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
Inflammatory chemokines are often elevated in disease settings, where the largest group of CC-chemokines are the macrophage inflammatory proteins (MIP), which are promiscuous for the receptors CCR1 and CCR5. MIP chemokines, such as CCL3 and CCL5 are processed at the N terminus, which influences signaling in a highly diverse manner. Here, we investigate the signaling capacity of peptides corresponding to truncated N termini. These 3-10-residue peptides displayed weak potency but, surprisingly, retained their signaling on CCR1. In contrast, none of the peptides generated a signal on CCR5, but a CCL3-derived tetrapeptide was a positive modulator boosting the signal of several chemokine variants on CCR5. In conclusion, chemokine N termini can be mimicked to produce small CCR1-selective agonists, as well as CCR5-selective modulators.
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Affiliation(s)
- Olav Larsen
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Sara Schuermans
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anna Walser
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Stavroula Louka
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Jon Våbenø
- Helgeland Hospital Trust, Sandnessjøen, Norway
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Mette M Rosenkilde
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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