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Eirin A, Thaler R, Glasstetter LM, Xing L, Zhu XY, Osborne AC, Mondesir R, Bhagwate AV, Lerman A, van Wijnen AJ, Lerman LO. Obesity-driven mitochondrial dysfunction in human adipose tissue-derived mesenchymal stem/stromal cells involves epigenetic changes. Cell Death Dis 2024; 15:387. [PMID: 38824145 PMCID: PMC11144257 DOI: 10.1038/s41419-024-06774-8] [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: 08/30/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
Obesity exacerbates tissue degeneration and compromises the integrity and reparative potential of mesenchymal stem/stromal cells (MSCs), but the underlying mechanisms have not been sufficiently elucidated. Mitochondria modulate the viability, plasticity, proliferative capacity, and differentiation potential of MSCs. We hypothesized that alterations in the 5-hydroxymethylcytosine (5hmC) profile of mitochondria-related genes may mediate obesity-driven dysfunction of human adipose-derived MSCs. MSCs were harvested from abdominal subcutaneous fat of obese and age/sex-matched non-obese subjects (n = 5 each). The 5hmC profile and expression of nuclear-encoded mitochondrial genes were examined by hydroxymethylated DNA immunoprecipitation sequencing (h MeDIP-seq) and mRNA-seq, respectively. MSC mitochondrial structure (electron microscopy) and function, metabolomics, proliferation, and neurogenic differentiation were evaluated in vitro, before and after epigenetic modulation. hMeDIP-seq identified 99 peaks of hyper-hydroxymethylation and 150 peaks of hypo-hydroxymethylation in nuclear-encoded mitochondrial genes from Obese- versus Non-obese-MSCs. Integrated hMeDIP-seq/mRNA-seq analysis identified a select group of overlapping (altered levels of both 5hmC and mRNA) nuclear-encoded mitochondrial genes involved in ATP production, redox activity, cell proliferation, migration, fatty acid metabolism, and neuronal development. Furthermore, Obese-MSCs exhibited decreased mitochondrial matrix density, membrane potential, and levels of fatty acid metabolites, increased superoxide production, and impaired neuronal differentiation, which improved with epigenetic modulation. Obesity elicits epigenetic changes in mitochondria-related genes in human adipose-derived MSCs, accompanied by structural and functional changes in their mitochondria and impaired fatty acid metabolism and neurogenic differentiation capacity. These observations may assist in developing novel therapies to preserve the potential of MSCs for tissue repair and regeneration in obese individuals.
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Grants
- AG062104 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- DK122734 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R56 DK129240 NIDDK NIH HHS
- DK129240 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 DK129240 NIDDK NIH HHS
- HL158691 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- DK120292 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Li Xing
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Department of Urology, The Affiliated Zhongda Hospital, Southeast University, Nanjing, China
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Andrew C Osborne
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ronscardy Mondesir
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Aditya V Bhagwate
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Amir Lerman
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
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Eirin A, Chade AR. Cardiac epigenetic changes in VEGF signaling genes associate with myocardial microvascular rarefaction in experimental chronic kidney disease. Am J Physiol Heart Circ Physiol 2023; 324:H14-H25. [PMID: 36367693 PMCID: PMC9762979 DOI: 10.1152/ajpheart.00522.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Chronic kidney disease (CKD) is common in patients with heart failure and often results in left ventricular diastolic dysfunction (LVDD). However, the mechanisms responsible for cardiac damage in CKD-LVDD remain to be elucidated. Epigenetic alterations may impose long-lasting effects on cellular transcription and function, but their exact role in CKD-LVDD is unknown. We investigate whether changes in cardiac site-specific DNA methylation profiles might be implicated in cardiac abnormalities in CKD-LVDD. CKD-LVDD and normal control pigs (n = 6 each) were studied for 14 wk. Renal and cardiac hemodynamics were quantified by multidetector CT and echocardiography. In randomly selected pigs (n = 3/group), cardiac site-specific 5-methylcytosine (5mC) immunoprecipitation (MeDIP)- and mRNA-sequencing (seq) were performed, followed by integrated (MeDiP-seq/mRNA-seq analysis), and confirmatory ex vivo studies. MeDIP-seq analysis revealed 261 genes with higher (fold change > 1.4; P < 0.05) and 162 genes with lower (fold change < 0.7; P < 0.05) 5mC levels in CKD-LVDD versus normal pigs, which were primarily implicated in vascular endothelial growth factor (VEGF)-related signaling and angiogenesis. Integrated MeDiP-seq/mRNA-seq analysis identified a select group of VEGF-related genes in which 5mC levels were higher, but mRNA expression was lower in CKD-LVDD versus normal pigs. Cardiac VEGF signaling gene and VEGF protein expression were blunted in CKD-LVDD compared with controls and were associated with decreased subendocardial microvascular density. Cardiac epigenetic changes in VEGF-related genes are associated with impaired angiogenesis and cardiac microvascular rarefaction in swine CKD-LVDD. These observations may assist in developing novel therapies to ameliorate cardiac damage in CKD-LVDD.NEW & NOTEWORTHY Chronic kidney disease (CKD) often leads to left ventricular diastolic dysfunction (LVDD) and heart failure. Using a novel translational swine model of CKD-LVDD, we characterize the cardiac epigenetic landscape, identifying site-specific 5-methylcytosine changes in vascular endothelial growth factor (VEGF)-related genes associated with impaired angiogenesis and cardiac microvascular rarefaction. These observations shed light on the mechanisms of cardiac microvascular damage in CKD-LVDD and may assist in developing novel therapies for these patients.
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Alejandro R Chade
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, Missouri
- Department of Medicine, University of Missouri-Columbia, Columbia, Missouri
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Rajagopalan KS, Glasstetter LM, Zhu XY, Thaler R, Tang H, Jordan KL, Saadiq IM, Herrmann SM, Chade AR, Irazabal MV, Lerman LO, Eirin A. Renal Ischemia Induces Epigenetic Changes in Apoptotic, Proteolytic, and Mitochondrial Genes in Swine Scattered Tubular-like Cells. Cells 2022; 11:1803. [PMID: 35681498 PMCID: PMC9180447 DOI: 10.3390/cells11111803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Scattered tubular-like cells (STCs) are dedifferentiated renal tubular cells endowed with progenitor-like characteristics to repair injured parenchymal cells. STCs may be damaged and rendered ineffective by renal artery stenosis (RAS), but the underlying processes remain unclear. We hypothesized that RAS alters the epigenetic landscape on DNA and the ensuing gene transcriptional profile of swine STCs. METHODS CD24+/CD133+ STCs were isolated from pig kidneys after 10 weeks of RAS or sham (n = 3 each) and their whole 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles were examined by 5mC and 5hmC immunoprecipitation sequencing (MeDIP-/hMeDIP-seq, respectively). A subsequent integrated (MeDIP/hMeDIP-seq/mRNA-seq) analysis was performed by comparing all online available gene sets using Gene Set Enrichment Analysis. Apoptosis, proteolysis, and mitochondrial structure and function were subsequently evaluated in vitro. RESULTS Differential expression (DE) analysis revealed 239 genes with higher and 236 with lower 5mC levels and 275 genes with higher and 315 with lower 5hmC levels in RAS-STCs compared to Normal-STCs (fold change ≥1.4 or ≤0.7, p ≤ 0.05). Integrated MeDIP-/hMeDIP-seq/mRNA-seq analysis identified several overlapping (DE-5mC/mRNA and DE-5hmC/mRNA levels) genes primarily implicated in apoptosis, proteolysis, and mitochondrial functions. Furthermore, RAS-STCs exhibited decreased apoptosis, mitochondrial matrix density, and ATP production, and increased intracellular amino acid concentration and ubiquitin expression. CONCLUSIONS Renal ischemia induces epigenetic changes in apoptosis-, proteolysis-, and mitochondria-related genes, which correlate with alterations in the transcriptomic profile and corresponding function of swine STCs. These observations may contribute to developing novel targeted interventions to preserve the reparative potency of STCs in renal disease.
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Affiliation(s)
- Kamalnath S. Rajagopalan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Logan M. Glasstetter
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55901, USA;
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Kyra L. Jordan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Ishran M. Saadiq
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Sandra M. Herrmann
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Alejandro R. Chade
- Department of Physiology and Biophysics, Medicine and Radiology, University of Mississippi Medical Center, Jackson, MS 55901, USA;
| | - Maria V. Irazabal
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Lilach O. Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55901, USA; (K.S.R.); (L.M.G.); (X.-Y.Z.); (H.T.); (K.L.J.); (I.M.S.); (S.M.H.); (M.V.I.); (L.O.L.)
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Farahani RA, Zhu XY, Tang H, Jordan KL, Lerman LO, Eirin A. Renal ischemia alters expression of mitochondria-related genes and impairs mitochondrial structure and function in swine scattered tubular-like cells. Am J Physiol Renal Physiol 2020; 319:F19-F28. [PMID: 32463728 DOI: 10.1152/ajprenal.00120.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Scattered tubular-like cells (STCs) are dedifferentiated surviving tubular epithelial cells that repair neighboring injured cells. Experimental renal artery stenosis (RAS) impairs STC reparative potency by inducing mitochondrial injury, but the exact mechanisms of mitochondrial damage remain unknown. We hypothesized that RAS alters expression of mitochondria-related genes, contributing to mitochondrial structural damage and dysfunction in swine STCs. CD24+/CD133+ STCs were isolated from pig kidneys after 10 wk of RAS or sham (n = 3 each). mRNA sequencing was performed, and nuclear DNA (nDNA)-encoded mitochondrial genes and mitochondrial DNA (mtDNA)-encoded genes were identified. Mitochondrial structure, ATP generation, biogenesis, and expression of mitochondria-associated microRNAs were also assessed. There were 96 nDNA-encoded mitochondrial genes upregulated and 12 mtDNA-encoded genes downregulated in RAS-STCs versus normal STCs. Functional analysis revealed that nDNA-encoded and mtDNA-encoded differentially expressed genes were primarily implicated in mitochondrial respiration and ATP synthesis. Mitochondria from RAS STCs were swollen and showed cristae remodeling and loss and decreased ATP production. Immunoreactivity of the mitochondrial biogenesis marker peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α and expression of the mitochondria-associated microRNAs miR-15a, miR-181a, miR-196a, and miR-296-3p, which target several mtDNA genes, were higher in RAS-STCs compared with normal STCs, suggesting a potential modulation of mitochondria-related gene expression. These results demonstrate that RAS induces an imbalance in mtDNA- and nDNA-mitochondrial gene expression, impairing mitochondrial structure and function in swine STCs. These observations support development of gene gain- and loss-of-function strategies to ameliorate mitochondrial damage and preserve the reparative potency of STCs in patients with renal ischemia.
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Affiliation(s)
- Rahele A Farahani
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hui Tang
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Kyra L Jordan
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
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Renal Artery Stenosis Alters Gene Expression in Swine Scattered Tubular-Like Cells. Int J Mol Sci 2019; 20:ijms20205069. [PMID: 31614781 PMCID: PMC6829501 DOI: 10.3390/ijms20205069] [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: 09/23/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Scattered tubular-like cells (STCs) proliferate and differentiate to support neighboring injured renal tubular cells during recovery from insults. Renal artery stenosis (RAS) induces renal ischemia and hypertension and leads to loss of kidney function, but whether RAS alters renal endogenous repair mechanisms, such as STCs, remains unknown. We hypothesize that RAS in swine modifies the messenger RNA (mRNA) profile of STCs, blunting their in vitro reparative capacity. Methods: CD24+/CD133+ STCs were isolated from pig kidneys after 10-weeks of RAS or sham (n = 3 each) and their gene cargo analyzed using high-throughput mRNAseq. Expression profiles for upregulated and downregulated mRNAs in RAS-STCs were functionally interpreted by gene ontology analysis. STC activation was assessed by counting the total number of STCs in pig kidney sections using flow cytometry, whereas cell proliferation was assessed in vitro. Results: Of all expressed genes, 1430 genes were upregulated and 315 downregulated in RAS- versus Normal-STCs. Expression of selected candidate genes followed the same fold change directions as the mRNAseq findings. Genes upregulated in RAS-STCs were involved in cell adhesion, extracellular matrix remodeling, and kidney development, whereas those downregulated in RAS-STCs are related to cell cycle and cytoskeleton. The percentage of STCs from dissociated kidney cells was higher in RAS versus Normal pigs, but their proliferation rate was blunted. Conclusions: Renal ischemia and hypertension in swine induce changes in the mRNA profile of STCs, associated with increased STC activation and impaired proliferation. These observations suggest that RAS may alter the reparative capacity of STCs.
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Eirin A, Zhu XY, Puranik AS, Woollard JR, Tang H, Dasari S, Lerman A, van Wijnen AJ, Lerman LO. Comparative proteomic analysis of extracellular vesicles isolated from porcine adipose tissue-derived mesenchymal stem/stromal cells. Sci Rep 2016; 6:36120. [PMID: 27786293 PMCID: PMC5081562 DOI: 10.1038/srep36120] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) isolated from mesenchymal stem/stromal cells (MSCs) contribute to recovery of damaged tissue. We have previously shown that porcine MSC-derived EVs transport mRNA and miRNA capable of modulating cellular pathways in recipient cells. To identify candidate factors that contribute to the therapeutic effects of porcine MSC-derived EVs, we characterized their protein cargo using proteomics. Porcine MSCs were cultured from abdominal fat, and EVs characterized for expression of typical MSC and EV markers. LC-MS/MS proteomic analysis was performed and proteins classified. Functional pathway analysis was performed and five candidate proteins were validated by western blot. Proteomics analysis identified 5,469 distinct proteins in MSCs and 4,937 in EVs. The average protein expression was higher in MSCs vs. EVs. Differential expression analysis revealed 128 proteins that are selectively enriched in EVs versus MSCs, whereas 563 proteins were excluded from EVs. Proteins enriched in EVs are linked to a broad range of biological functions, including angiogenesis, blood coagulation, apoptosis, extracellular matrix remodeling, and regulation of inflammation. Excluded are mostly nuclear proteins, like proteins involved in nucleotide binding and RNA splicing. EVs have a selectively-enriched protein cargo with a specific biological signature that MSCs may employ for intercellular communication to facilitate tissue repair.
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Affiliation(s)
- Alfonso Eirin
- Divisions of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Xiang-Yang Zhu
- Divisions of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - John R. Woollard
- Divisions of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Hui Tang
- Divisions of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Amir Lerman
- Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | | | - Lilach O. Lerman
- Divisions of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
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