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Mahajan N, Luo Q, Abhyankar S, Bhatwadekar AD. Transcriptomic Profile of Lin -Sca1 +c-kit (LSK) cells in db/db mice with long-standing diabetes. BMC Genomics 2024; 25:782. [PMID: 39134978 PMCID: PMC11318115 DOI: 10.1186/s12864-024-10679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND The Lin-Sca1+c-Kit+ (LSK) fraction of the bone marrow (BM) comprises multipotent hematopoietic stem cells (HSCs), which are vital to tissue homeostasis and vascular repair. While diabetes affects HSC homeostasis overall, the molecular signature of mRNA and miRNA transcriptomic under the conditions of long-standing type 2 diabetes (T2D;>6 months) remains unexplored. METHODS In this study, we assessed the transcriptomic signature of HSCs in db/db mice, a well-known and widely used model for T2D. LSK cells of db/db mice enriched using a cell sorter were subjected to paired-end mRNA and single-end miRNA seq library and sequenced on Illumina NovaSeq 6000. The mRNA sequence reads were mapped using STAR (Spliced Transcripts Alignment to a Reference), and the miRNA sequence reads were mapped to the designated reference genome using the Qiagen GeneGlobe RNA-seq Analysis Portal with default parameters for miRNA. RESULTS We uncovered 2076 out of 13,708 mRNAs and 35 out of 191 miRNAs that were expressed significantly in db/db animals; strikingly, previously unreported miRNAs (miR-3968 and miR-1971) were found to be downregulated in db/db mice. Furthermore, we observed a molecular shift in the transcriptome of HSCs of diabetes with an increase in pro-inflammatory cytokines (Il4, Tlr4, and Tnf11α) and a decrease in anti-inflammatory cytokine IL10. Pathway mapping demonstrated inflammation mediated by chemokine, cytokine, and angiogenesis as one of the top pathways with a significantly higher number of transcripts in db/db mice. These molecular changes were reflected in an overt defect in LSK mobility in the bone marrow. miRNA downstream target analysis unveils several mRNAs targeting leukocyte migration, microglia activation, phagosome formation, and macrophage activation signaling as their primary pathways, suggesting a shift to an inflammatory phenotype. CONCLUSION Our findings highlight that chronic diabetes adversely alters HSCs' homeostasis at the transcriptional level, thus potentially contributing to the inflammatory phenotype of HSCs under long-term diabetes. We also believe that identifying HSCs-based biomarkers in miRNAs or mRNAs could serve as diagnostic markers and potential therapeutic targets for diabetes and associated vascular complications.
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Affiliation(s)
- Neha Mahajan
- Department of Ophthalmology, Indiana University School of Medicine, 1160 W Michigan St, Indianapolis, IN, 46202, USA
| | - Qianyi Luo
- Department of Ophthalmology, Indiana University School of Medicine, 1160 W Michigan St, Indianapolis, IN, 46202, USA
| | - Surabhi Abhyankar
- Department of Ophthalmology, Indiana University School of Medicine, 1160 W Michigan St, Indianapolis, IN, 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, 46202, USA
| | - Ashay D Bhatwadekar
- Department of Ophthalmology, Indiana University School of Medicine, 1160 W Michigan St, Indianapolis, IN, 46202, USA.
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Tao Y, Feng T, Zhou L, Han L. Identification of key differentially expressed immune related genes in patients with persistent atrial fibrillation: an integrated bioinformation analysis. BMC Cardiovasc Disord 2024; 24:346. [PMID: 38977948 PMCID: PMC11229288 DOI: 10.1186/s12872-024-04007-6] [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: 03/14/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
OBJECTIVE We aimed to investigate key differentially expressed immune related genes in persistent atrial fibrillation. METHODS Gene expression profiles were downloaded from Gene Expression Omnibus (GEO) using "GEO query" package. "limma" package and "sva" package were used to conduct normalization and eliminate batch effects, respectively. We screened out differentially expressed genes (DEGs) based on "limma" package with the standard of |log fold change (FC)| ≥ 1.5 and false discovery rate (FDR) < 0.05. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed by "clusterProfler" package. We further applied LASSO to select key DEGs, and intersected key DEGs with immune related genes from ImmPort database. The ROC curve of each DEIRG was constructed to evaluate its diagnostic efficiency for AF. RESULTS A total of 103 DEGs we were screened out, of them, 48 genes were down-regulated and 55 genes were up-regulated. Result of functional enrichment analysis show that, most of DEGs were related to immune response, inflammation, and oxidative stress. Ultimately, CYBB, RORB, S100A12, and CHGB were determined as key DEIRGs, each of which displayed a favor efficiency for diagnosing persistent AF. CONCLUSION CYBB, RORB, S100A12, and CHGB were identified as key DEIRGs in persistent AF, and future studies are needed to further explore the underlying roles of CYBB, RORB, S100A12, and CHGB in persistent AF.
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Affiliation(s)
- Yijing Tao
- Department of Cardiology, Changshu Hospital Affiliated to Soochow University, Changshu No. 1 People's Hospital, Changshu, 215500, China
| | - Tonghui Feng
- Department of Anesthesia Surgery, Zhejiang Hospital, Hangzhou, 310000, China.
| | - Lucien Zhou
- Independent researcher, Changshu, 215500, China.
| | - Leng Han
- Department of Cardiology, Changshu Hospital Affiliated to Soochow University, Changshu No. 1 People's Hospital, Changshu, 215500, China.
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Vinci MC, Costantino S, Damiano G, Rurali E, Rinaldi R, Vigorelli V, Sforza A, Carulli E, Pirola S, Mastroiacovo G, Raucci A, El-Osta A, Paneni F, Pompilio G. Persistent epigenetic signals propel a senescence-associated secretory phenotype and trained innate immunity in CD34 + hematopoietic stem cells from diabetic patients. Cardiovasc Diabetol 2024; 23:107. [PMID: 38553774 PMCID: PMC10981360 DOI: 10.1186/s12933-024-02195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Diabetes-induced trained immunity contributes to the development of atherosclerosis and its complications. This study aimed to investigate in humans whether epigenetic signals involved in immune cell activation and inflammation are initiated in hematopoietic stem/progenitor cells (HSPCs) and transferred to differentiated progeny. METHODS AND RESULTS High glucose (HG)-exposure of cord blood (CB)-derived HSPCs induced a senescent-associated secretory phenotype (SASP) characterized by cell proliferation lowering, ROS production, telomere shortening, up-regulation of p21 and p27genes, upregulation of NFkB-p65 transcription factor and increased secretion of the inflammatory cytokines TNFα and IL6. Chromatin immunoprecipitation assay (ChIP) of p65 promoter revealed that H3K4me1 histone mark accumulation and methyltransferase SetD7 recruitment, along with the reduction of repressive H3K9me3 histone modification, were involved in NFkB-p65 upregulation of HG-HSPCs, as confirmed by increased RNA polymerase II engagement at gene level. The differentiation of HG-HSPCs into myeloid cells generated highly responsive monocytes, mainly composed of intermediate subsets (CD14hiCD16+), that like the cells from which they derive, were characterized by SASP features and similar epigenetic patterns at the p65 promoter. The clinical relevance of our findings was confirmed in sternal BM-derived HSPCs of T2DM patients. In line with our in vitro model, T2DM HSPCs were characterized by SASP profile and SETD7 upregulation. Additionally, they generated, after myeloid differentiation, senescent monocytes mainly composed of proinflammatory intermediates (CD14hiCD16+) characterized by H3K4me1 accumulation at NFkB-p65 promoter. CONCLUSIONS Hyperglycemia induces marked chromatin modifications in HSPCs, which, once transmitted to the cell progeny, contributes to persistent and pathogenic changes in immune cell function and composition.
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Affiliation(s)
- Maria Cristina Vinci
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy.
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, University Hospital Zurich and University of Zürich, Zurich, Switzerland
- University Heart Center, University Hospital Zurich, Zurich, Switzerland
| | - Giulia Damiano
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
| | - Erica Rurali
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
| | - Raffaella Rinaldi
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
| | - Vera Vigorelli
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
| | - Annalisa Sforza
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
| | - Ermes Carulli
- Dipartimento Di Scienze Cliniche E Di Comunità, Università Di Milano, Milan, Italy
- Doctoral Programme in Translational Medicine, Università Di Milano, 20122, Milan, Italy
| | - Sergio Pirola
- Department of Cardiac Surgery, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | | | - Angela Raucci
- Unit of Experimental Cardio-Oncology and Cardiovascular Aging, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, University Hospital Zurich and University of Zürich, Zurich, Switzerland.
- University Heart Center, University Hospital Zurich, Zurich, Switzerland.
| | - Giulio Pompilio
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Via C. Parea 4, 20138, Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università Degli Studi di Milano, Milan, Italy
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Mahajan N, Luo Q, Abhyankar S, Bhatwadekar AD. Transcriptomic Profile of Lin - Sca1 + c-kit (LSK) cells in db/db mice with long-standing diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576754. [PMID: 38328165 PMCID: PMC10849703 DOI: 10.1101/2024.01.22.576754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The Lin - Sca1 + c-Kit + (LSK) fraction comprises multipotent hematopoietic stem cells (HSCs), vital to tissue homeostasis and vascular repair. While HSC homeostasis is impaired in diabetes, it is not known how chronic (>6 months) type 2 diabetes (T2D) alters the HSC transcriptome. Herein, we assessed the transcriptomic signature of HSCs in db/db mice employing mRNA and miRNA sequencing. We uncovered 2076 mRNAs and 35 miRNAs differentially expressed in db/db mice, including two novel miRNAs previously unreported in T2D. Further analysis of these transcripts showed a molecular shift with an increase in the pro-inflammatory cytokines and a decrease in anti-inflammatory cytokine expression. Also, pathway mapping unveiled inflammation and angiogenesis as one of the top pathways. These effects were reflected in bone marrow mobilopathy, retinal microglial inflammation, and neurovascular deficits in db/db mice. In conclusion, our study highlights that chronic diabetes alters HSCs' at the transcriptomic level, thus potentially contributing to overall homeostasis and neurovascular deficits of diabetes, such as diabetic retinopathy. Highlights Bone marrow mobilopathy with long-standing diabetesSwitch in LSK transcriptomic profile towards inflammation and angiogenesisDiscovered 35 miRNAs, including two novel miRNAs, miR-3968 and miR-1971LSK dysfunction reflected in inflammation and neurovascular deficits of the retina.
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Shahani P, Mahadevan A, Mondal K, Waghmare G, Datta I. Repeat intramuscular transplantation of human dental pulp stromal cells is more effective in sustaining Schwann cell survival and myelination for functional recovery after onset of diabetic neuropathy. Cytotherapy 2023; 25:1200-1211. [PMID: 37642606 DOI: 10.1016/j.jcyt.2023.07.011] [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: 06/06/2022] [Revised: 07/30/2023] [Accepted: 07/30/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AIMS Mesenchymal stromal cell (MSC) therapy for diabetic neuropathy (DN) has been extensively researched in vitro and in pre-clinical studies; however, the clinical scenario thus far has been disappointing. Temporary recovery, a common feature of these studies, indicates that either the retention of transplanted cells deteriorates with time or recovery of supportive endogenous cells, such as bone marrow-derived MSCs (BM-MSCs), does not occur, requiring further replenishment. In DN, BM-MSCs are recognized mediators of Schwann cell regeneration, and we have earlier shown that they suffer impairment in the pre-neuropathy stage. In this study, we attempted to further elucidate the mechanisms of functional recovery by focusing on changes occurring at the cellular level in the sciatic nerve, in conjunction with the biodistribution and movement patterns of the transplanted cells, to define the interval between doses. METHOD & RESULTS We found that two doses of 1 × 106 dental pulp stromal cells (DPSCs) transplanted intramuscularly at an interval of 4 weeks effectively improved nerve conduction velocity (NCV) and restored motor coordination through improving sciatic nerve architecture, Schwann cell survival and myelination. Despite very minimal recovery of endogenous BM-MSCs, a temporary restoration of NCV and motor function was achieved with the first dose of DPSC transplantation. However, this did not persist, and a repeat dose was needed to consolidate functional improvement and rehabilitate the sciatic nerve architecture. CONCLUSION Thus, repeat intramuscular transplantation of DPSCs is more effective for maintenance of Schwann cell survival and myelination for functional recovery after onset of DN.
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Affiliation(s)
- Pradnya Shahani
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kallolika Mondal
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Girish Waghmare
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Indrani Datta
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, India.
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The Long Telling Story of "Endothelial Progenitor Cells": Where Are We at Now? Cells 2022; 12:cells12010112. [PMID: 36611906 PMCID: PMC9819021 DOI: 10.3390/cells12010112] [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: 11/21/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Endothelial progenitor cells (EPCs): The name embodies years of research and clinical expectations, but where are we now? Do these cells really represent the El Dorado of regenerative medicine? Here, past and recent literature about this eclectic, still unknown and therefore fascinating cell population will be discussed. This review will take the reader through a temporal journey that, from the first discovery, will pass through years of research devoted to attempts at their definition and understanding their biology in health and disease, ending with the most recent evidence about their pathobiological role in cardiovascular disease and their recent applications in regenerative medicine.
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Rurali E, Pompilio G, Zacchigna S. Novel Targets for Old and Diseased Hearts. Int J Mol Sci 2022; 23:ijms23126627. [PMID: 35743066 PMCID: PMC9223834 DOI: 10.3390/ijms23126627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Erica Rurali
- Unità di Biologia Molecolare e Medicina Rigenerativa, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy;
- Correspondence: (E.R.); (S.Z.)
| | - Giulio Pompilio
- Unità di Biologia Molecolare e Medicina Rigenerativa, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy;
- Dipartimento di Scienze Biomediche Chirurgiche Odontoiatriche, Università degli Studi di Milano, 20122 Milan, Italy
| | - Serena Zacchigna
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Correspondence: (E.R.); (S.Z.)
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