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Hallan SI, Øvrehus MA, Darshi M, Montemayor D, Langlo KA, Bruheim P, Sharma K. Metabolic Differences in Diabetic Kidney Disease Patients with Normoalbuminuria versus Moderately Increased Albuminuria. Kidney360 2023; 4:1407-1418. [PMID: 37612821 PMCID: PMC10615383 DOI: 10.34067/kid.0000000000000248] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Key Points The pathophysiological mechanisms of diabetic kidney disease (DKD) with normal (nonalbuminuric DKD) versus moderately increased albuminuria (A-DKD) are not well-understood. Fatty acid biosynthesis and oxydation, gluconeogenesis, TCA cycle, and glucose-alanine cycle were more disturbed in patients with A-DKD compared with those with nonalbuminuric DKD with identical eGFR. DKD patients with and without microalbuminuria could represent different clinical phenotypes. Background The pathophysiological mechanisms of diabetic kidney disease (DKD) with normal versus moderately increased albuminuria (nonalbuminuric DKD [NA-DKD] and A-DKD) are currently not well-understood and could have implications for diagnosis and treatment. Methods Fourteen patients with NA-DKD with urine albumin–creatinine ratio <3 mg/mmol, 26 patients with A-DKD with albumin–creatinine ratio 3–29 mg/mmol, and 60 age- and sex-matched healthy controls were randomly chosen from a population-based cohort study (Nord-Trøndelag Health Study-3, Norway). Seventy-four organic acids, 21 amino acids, 21 biogenic acids, 40 acylcarnitines, 14 sphingomyelins, and 88 phosphatidylcholines were quantified in urine. One hundred forty-six patients with diabetes from the US-based Chronic Renal Insufficiency Cohort study were used to verify main findings. Results Patients with NA-DKD and A-DKD had similar age, kidney function, diabetes treatment, and other traditional risk factors. Still, partial least-squares discriminant analysis showed strong metabolite-based separation (R2, 0.82; Q2, 0.52), with patients with NA-DKD having a metabolic profile positioned between the profiles of healthy controls and patients with A-DKD. Seventy-five metabolites contributed significantly to separation between NA-DKD and A-DKD (variable importance in projection scores ≥1.0) with propionylcarnitine (C3), phosphatidylcholine C38:4, medium-chained (C8) fatty acid octenedioic acid, and lactic acid as the top metabolites (variable importance in projection scores, 2.7–2.2). Compared with patients with NA-DKD, those with A-DKD had higher levels of short-chained acylcarnitines, higher long-chained fatty acid levels with more double bounds, higher branched-chain amino acid levels, and lower TCA cycle intermediates. The main findings were similar by random forest analysis and in the Chronic Renal Insufficiency Cohort study. Formal enrichment analysis indicated that fatty acid biosynthesis and oxydation, gluconeogenesis, TCA cycle, and glucose-alanine cycle were more disturbed in patients with A-DKD compared with those with NA-DKD with identical eGFR. We also found indications of a Warburg-like effect in patients with A-DKD (i.e. , metabolism of glucose to lactate despite adequate oxygen). Conclusion DKD patients with normoalbuminuria differ substantially in their metabolic disturbances compared with patients with moderately increase albuminuria and could represent different clinical phenotypes.
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Affiliation(s)
- Stein I Hallan
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olav Hospital, Trondheim, Norway
| | | | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Daniel Montemayor
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Knut A Langlo
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olav Hospital, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
- Department of Nephrology, University of Texas Health San Antonio, San Antonio, Texas
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Darshi M, Tumova J, Saliba A, Kim J, Baek J, Pennathur S, Sharma K. Crabtree effect in kidney proximal tubule cells via late-stage glycolytic intermediates. iScience 2023; 26:106462. [PMID: 37091239 PMCID: PMC10119590 DOI: 10.1016/j.isci.2023.106462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
The Crabtree effect is defined as a rapid glucose-induced repression of mitochondrial oxidative metabolism and has been described in yeasts and tumor cells. Using plate-based respirometry, we identified the Crabtree effect in normal (non-tumor) kidney proximal tubule epithelial cells (PTEC) but not in other kidney cells (podocytes or mesangial cells) or mammalian cells (C2C12 myoblasts). Glucose-induced repression of respiration was prevented by reducing glycolysis at the proximal step with 2-deoxyglucose and partially reversed by pyruvate. The late-stage glycolytic intermediates glyceraldehyde 3-phosphate, 3-phosphoglycerate, and phosphoenolpyruvate, but not the early-stage glycolytic intermediates or lactate, inhibited respiration in permeabilized PTEC and kidney cortex mitochondria, mimicking the Crabtree effect. Studies in diabetic mice indicated a pattern of increased late-stage glycolytic intermediates consistent with a similar pattern occurring in vivo. Our results show the unique presence of the Crabtree effect in kidney PTEC and identify the major mediators of this effect.
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Affiliation(s)
- Manjula Darshi
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jana Tumova
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Pathophysiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Afaf Saliba
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jiwan Kim
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Judy Baek
- Department of Internal Medicine-Nephrology and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Subramaniam Pennathur
- Department of Internal Medicine-Nephrology and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kumar Sharma
- Division of Nephrology, Department of Medicine, Center for Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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Limonte CP, Valo E, Drel V, Natarajan L, Darshi M, Forsblom C, Henderson CM, Hoofnagle AN, Ju W, Kretzler M, Montemayor D, Nair V, Nelson RG, O’Toole JF, Toto RD, Rosas SE, Ruzinski J, Sandholm N, Schmidt IM, Vaisar T, Waikar SS, Zhang J, Rossing P, Ahluwalia TS, Groop PH, Pennathur S, Snell-Bergeon JK, Costacou T, Orchard TJ, Sharma K, de Boer IH. Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes. Diabetes Care 2022; 45:1416-1427. [PMID: 35377940 PMCID: PMC9210873 DOI: 10.2337/dc21-2204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/04/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Understanding mechanisms underlying rapid estimated glomerular filtration rate (eGFR) decline is important to predict and treat kidney disease in type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS We performed a case-control study nested within four T1D cohorts to identify urinary proteins associated with rapid eGFR decline. Case and control subjects were categorized based on eGFR decline ≥3 and <1 mL/min/1.73 m2/year, respectively. We used targeted liquid chromatography-tandem mass spectrometry to measure 38 peptides from 20 proteins implicated in diabetic kidney disease. Significant proteins were investigated in complementary human cohorts and in mouse proximal tubular epithelial cell cultures. RESULTS The cohort study included 1,270 participants followed a median 8 years. In the discovery set, only cathepsin D peptide and protein were significant on full adjustment for clinical and laboratory variables. In the validation set, associations of cathepsin D with eGFR decline were replicated in minimally adjusted models but lost significance with adjustment for albuminuria. In a meta-analysis with combination of discovery and validation sets, the odds ratio for the association of cathepsin D with rapid eGFR decline was 1.29 per SD (95% CI 1.07-1.55). In complementary human cohorts, urine cathepsin D was associated with tubulointerstitial injury and tubulointerstitial cathepsin D expression was associated with increased cortical interstitial fractional volume. In mouse proximal tubular epithelial cell cultures, advanced glycation end product-BSA increased cathepsin D activity and inflammatory and tubular injury markers, which were further increased with cathepsin D siRNA. CONCLUSIONS Urine cathepsin D is associated with rapid eGFR decline in T1D and reflects kidney tubulointerstitial injury.
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Affiliation(s)
- Christine P. Limonte
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Viktor Drel
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Manjula Darshi
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Clark M. Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Andrew N. Hoofnagle
- Kidney Research Institute, University of Washington, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Wenjun Ju
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Daniel Montemayor
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Viji Nair
- Division of Nephrology, University of Michigan, Ann Arbor, MI
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - John F. O’Toole
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, OH
| | - Robert D. Toto
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX
| | | | - John Ruzinski
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Insa M. Schmidt
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Tomas Vaisar
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Jing Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Janet K. Snell-Bergeon
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | | | - Kumar Sharma
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Ian H. de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
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Zhang J, Fuhrer T, Ye H, Kwan B, Montemayor D, Tumova J, Darshi M, Afshinnia F, Scialla JJ, Anderson A, Porter AC, Taliercio JJ, Rincon-Choles H, Rao P, Xie D, Feldman H, Sauer U, Sharma K, Natarajan L. High-Throughput Metabolomics and Diabetic Kidney Disease Progression: Evidence from the Chronic Renal Insufficiency (CRIC) Study. Am J Nephrol 2022; 53:215-225. [PMID: 35196658 PMCID: PMC9116599 DOI: 10.1159/000521940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/30/2021] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Metabolomics could offer novel prognostic biomarkers and elucidate mechanisms of diabetic kidney disease (DKD) progression. Via metabolomic analysis of urine samples from 995 CRIC participants with diabetes and state-of-the-art statistical modeling, we aimed to identify metabolites prognostic to DKD progression. METHODS Urine samples (N = 995) were assayed for relative metabolite abundance by untargeted flow-injection mass spectrometry, and stringent statistical criteria were used to eliminate noisy compounds, resulting in 698 annotated metabolite ions. Utilizing the 698 metabolites' ion abundance along with clinical data (demographics, blood pressure, HbA1c, eGFR, and albuminuria), we developed univariate and multivariate models for the eGFR slope using penalized (lasso) and random forest models. Final models were tested on time-to-ESKD (end-stage kidney disease) via cross-validated C-statistics. We also conducted pathway enrichment analysis and a targeted analysis of a subset of metabolites. RESULTS Six eGFR slope models selected 9-30 variables. In the adjusted ESKD model with highest C-statistic, valine (or betaine) and 3-(4-methyl-3-pentenyl)thiophene were associated (p < 0.05) with 44% and 65% higher hazard of ESKD per doubling of metabolite abundance, respectively. Also, 13 (of 15) prognostic amino acids, including valine and betaine, were confirmed in the targeted analysis. Enrichment analysis revealed pathways implicated in kidney and cardiometabolic disease. CONCLUSIONS Using the diverse CRIC sample, a high-throughput untargeted assay, followed by targeted analysis, and rigorous statistical analysis to reduce false discovery, we identified several novel metabolites implicated in DKD progression. If replicated in independent cohorts, our findings could inform risk stratification and treatment strategies for patients with DKD.
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Affiliation(s)
- Jing Zhang
- Moores Cancer Center, University of California, San Diego, California, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hongping Ye
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Brian Kwan
- Moores Cancer Center, University of California, San Diego, California, USA
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, California, USA
| | - Daniel Montemayor
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Jana Tumova
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Manjula Darshi
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Farsad Afshinnia
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan, USA
| | - Julia J. Scialla
- Departments of Medicine and Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Amanda Anderson
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna C. Porter
- Jesse Brown VA Medical Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jonathan J. Taliercio
- Cleveland Clinic Foundation, Glickman Urological & Kidney Institute, Department of Nephrology, Cleveland, Ohio, USA
| | - Hernan Rincon-Choles
- Cleveland Clinic Foundation, Glickman Urological & Kidney Institute, Department of Nephrology, Cleveland, Ohio, USA
| | - Panduranga Rao
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan, USA
| | - Dawei Xie
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Harold Feldman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kumar Sharma
- Department of Medicine, Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Loki Natarajan
- Moores Cancer Center, University of California, San Diego, California, USA
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, California, USA
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Afshinnia F, Rajendiran TM, He C, Byun J, Montemayor D, Darshi M, Tumova J, Kim J, Limonte CP, Miller RG, Costacou T, Orchard TJ, Ahluwalia TS, Rossing P, Snell-Bergeon JK, de Boer IH, Natarajan L, Michailidis G, Sharma K, Pennathur S. Circulating Free Fatty Acid and Phospholipid Signature Predicts Early Rapid Kidney Function Decline in Patients With Type 1 Diabetes. Diabetes Care 2021; 44:2098-2106. [PMID: 34244329 PMCID: PMC8740931 DOI: 10.2337/dc21-0737] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/27/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Patients with type 1 diabetes (T1D) exhibit modest lipid abnormalities as measured by traditional metrics. This study aimed to identify lipidomic predictors of rapid decline of kidney function in T1D. RESEARCH DESIGN AND METHODS In a case-control study, 817 patients with T1D from three large cohorts were randomly split into training and validation subsets. Case was defined as >3 mL/min/1.73 m2 per year decline in estimated glomerular filtration rate (eGFR), while control was defined as <1 mL/min/1.73 m2 per year decline over a minimum 4-year follow-up. Lipids were quantified in baseline serum samples using a targeted mass spectrometry lipidomic platform. RESULTS At individual lipids, free fatty acid (FFA)20:2 was directly and phosphatidylcholine (PC)16:0/22:6 was inversely and independently associated with rapid eGFR decline. When examined by lipid class, rapid eGFR decline was characterized by higher abundance of unsaturated FFAs, phosphatidylethanolamine (PE)-Ps, and PCs with an unsaturated acyl chain at the sn1 carbon, and by lower abundance of saturated FFAs, longer triacylglycerols, and PCs, PEs, PE-Ps, and PE-Os with an unsaturated acyl chain at the sn1 carbon at eGFR ≥90 mL/min/1.73 m2. A multilipid panel consisting of unsaturated FFAs and saturated PE-Ps predicted rapid eGFR decline better than individual lipids (C-statistic, 0.71) and improved the C-statistic of the clinical model from 0.816 to 0.841 (P = 0.039). Observations were confirmed in the validation subset. CONCLUSIONS Distinct from previously reported predictors of GFR decline in type 2 diabetes, these findings suggest differential incorporation of FFAs at the sn1 carbon of the phospholipids' glycerol backbone as an independent predictor of rapid GFR decline in T1D.
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Affiliation(s)
- Farsad Afshinnia
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, MI
| | - Thekkelnaycke M Rajendiran
- Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, MI.,Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Chenchen He
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, MI
| | - Jaeman Byun
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, MI
| | - Daniel Montemayor
- Division of Nephrology, University of Texas Health Science Center San Antonio, San Antonio, TX.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Manjula Darshi
- Division of Nephrology, University of Texas Health Science Center San Antonio, San Antonio, TX.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Jana Tumova
- Division of Nephrology, University of Texas Health Science Center San Antonio, San Antonio, TX.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Jiwan Kim
- Division of Nephrology, University of Texas Health Science Center San Antonio, San Antonio, TX.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Christine P Limonte
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA.,Kidney Research Institute, University of Washington, Seattle, WA
| | - Rachel G Miller
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Tina Costacou
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Trevor J Orchard
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark.,Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Peter Rossing
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Janet K Snell-Bergeon
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ian H de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA.,Kidney Research Institute, University of Washington, Seattle, WA.,Puget Sound Veterans Affairs Healthcare System, Seattle, WA
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science and Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - George Michailidis
- Department of Statistics and the Informatics Institute, University of Florida, Gainesville, FL
| | - Kumar Sharma
- Division of Nephrology, University of Texas Health Science Center San Antonio, San Antonio, TX .,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX
| | - Subramaniam Pennathur
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, MI .,Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, MI.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
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6
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Limonte CP, Valo E, Montemayor D, Afshinnia F, Ahluwalia TS, Costacou T, Darshi M, Forsblom C, Hoofnagle AN, Groop PH, Miller RG, Orchard TJ, Pennathur S, Rossing P, Sandholm N, Snell-Bergeon JK, Ye H, Zhang J, Natarajan L, de Boer IH, Sharma K. A Targeted Multiomics Approach to Identify Biomarkers Associated with Rapid eGFR Decline in Type 1 Diabetes. Am J Nephrol 2020; 51:839-848. [PMID: 33053547 PMCID: PMC7606554 DOI: 10.1159/000510830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/11/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Individuals with type 1 diabetes (T1D) demonstrate varied trajectories of estimated glomerular filtration rate (eGFR) decline. The molecular pathways underlying rapid eGFR decline in T1D are poorly understood, and individual-level risk of rapid eGFR decline is difficult to predict. METHODS We designed a case-control study with multiple exposure measurements nested within 4 well-characterized T1D cohorts (FinnDiane, Steno, EDC, and CACTI) to identify biomarkers associated with rapid eGFR decline. Here, we report the rationale for and design of these studies as well as results of models testing associations of clinical characteristics with rapid eGFR decline in the study population, upon which "omics" studies will be built. Cases (n = 535) and controls (n = 895) were defined as having an annual eGFR decline of ≥3 and <1 mL/min/1.73 m2, respectively. Associations of demographic and clinical variables with rapid eGFR decline were tested using logistic regression, and prediction was evaluated using area under the curve (AUC) statistics. Targeted metabolomics, lipidomics, and proteomics are being performed using high-resolution mass-spectrometry techniques. RESULTS At baseline, the mean age was 43 years, diabetes duration was 27 years, eGFR was 94 mL/min/1.73 m2, and 62% of participants were normoalbuminuric. Over 7.6-year median follow-up, the mean annual change in eGFR in cases and controls was -5.7 and 0.6 mL/min/1.73 m2, respectively. Younger age, longer diabetes duration, and higher baseline HbA1c, urine albumin-creatinine ratio, and eGFR were significantly associated with rapid eGFR decline. The cross-validated AUC for the predictive model incorporating these variables plus sex and mean arterial blood pressure was 0.74 (95% CI: 0.68-0.79; p < 0.001). CONCLUSION Known risk factors provide moderate discrimination of rapid eGFR decline. Identification of blood and urine biomarkers associated with rapid eGFR decline in T1D using targeted omics strategies may provide insight into disease mechanisms and improve upon clinical predictive models using traditional risk factors.
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Affiliation(s)
- Christine P Limonte
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA,
- Kidney Research Institute, University of Washington, Seattle, Washington, USA,
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Daniel Montemayor
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas, USA
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Farsad Afshinnia
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tina Costacou
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Manjula Darshi
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas, USA
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Andrew N Hoofnagle
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rachel G Miller
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Trevor J Orchard
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Subramaniam Pennathur
- Departments of Medicine-Nephrology and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Janet K Snell-Bergeon
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hongping Ye
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas, USA
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Jing Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and UC San Diego Moores Comprehensive Cancer Center, La Jolla, California, USA
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and UC San Diego Moores Comprehensive Cancer Center, La Jolla, California, USA
| | - Ian H de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
- Kidney Research Institute, University of Washington, Seattle, Washington, USA
- Puget Sound VA Healthcare System, Seattle, Washington, USA
| | - Kumar Sharma
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas, USA
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
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7
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Onishi A, Fu Y, Patel R, Darshi M, Crespo-Masip M, Huang W, Song P, Freeman B, Kim YC, Soleimani M, Sharma K, Thomson SC, Vallon V. A role for tubular Na +/H + exchanger NHE3 in the natriuretic effect of the SGLT2 inhibitor empagliflozin. Am J Physiol Renal Physiol 2020; 319:F712-F728. [PMID: 32893663 DOI: 10.1152/ajprenal.00264.2020] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inhibitors of proximal tubular Na+-glucose cotransporter 2 (SGLT2) are natriuretic, and they lower blood pressure. There are reports that the activities of SGLT2 and Na+-H+ exchanger 3 (NHE3) are coordinated. If so, then part of the natriuretic response to an SGLT2 inhibitor is mediated by suppressing NHE3. To examine this further, we compared the effects of an SGLT2 inhibitor, empagliflozin, on urine composition and systolic blood pressure (SBP) in nondiabetic mice with tubule-specific NHE3 knockdown (NHE3-ko) and wild-type (WT) littermates. A single dose of empagliflozin, titrated to cause minimal glucosuria, increased urinary excretion of Na+ and bicarbonate and raised urine pH in WT mice but not in NHE3-ko mice. Chronic empagliflozin treatment tended to lower SBP despite higher renal renin mRNA expression and lowered the ratio of SBP to renin mRNA, indicating volume loss. This effect of empagliflozin depended on tubular NHE3. In diabetic Akita mice, chronic empagliflozin enhanced phosphorylation of NHE3 (S552/S605), changes previously linked to lesser NHE3-mediated reabsorption. Chronic empagliflozin also increased expression of genes involved with renal gluconeogenesis, bicarbonate regeneration, and ammonium formation. While this could reflect compensatory responses to acidification of proximal tubular cells resulting from reduced NHE3 activity, these effects were at least in part independent of tubular NHE3 and potentially indicated metabolic adaptations to urinary glucose loss. Moreover, empagliflozin increased luminal α-ketoglutarate, which may serve to stimulate compensatory distal NaCl reabsorption, while cogenerated and excreted ammonium balances urine losses of this "potential bicarbonate." The data implicate NHE3 as a determinant of the natriuretic effect of empagliflozin.
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Affiliation(s)
- Akira Onishi
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Yiling Fu
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Rohit Patel
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Maria Crespo-Masip
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California.,Biomedical Research Institute, University of Lleida, Lleida, Spain
| | - Winnie Huang
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Panai Song
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Brent Freeman
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Young Chul Kim
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Scott Culver Thomson
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Volker Vallon
- Department of Medicine, University of California-San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
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8
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Singh H, Miyamoto S, Darshi M, Torralba MG, Kwon K, Sharma K, Pieper R. Gut Microbial Changes in Diabetic db/db Mice and Recovery of Microbial Diversity upon Pirfenidone Treatment. Microorganisms 2020; 8:microorganisms8091347. [PMID: 32899353 PMCID: PMC7564638 DOI: 10.3390/microorganisms8091347] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/29/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
The leptin receptor-deficient db/db mouse model is an accepted in vivo model to study obesity, type 2 diabetes, and diabetic kidney disease. Healthy gastrointestinal (GI) microbiota has been linked to weight loss, improved glycemic control, and physiological benefits. We investigated the effect of various drugs on the GI microbiota of db/db mice as compared to control db/m mice. Treatment with long-acting pirfenidone (PFD) increased gut microbial diversity in diabetic db/db mice. Firmicutes, the most abundant phylum in db/m mice, decreased significantly in abundance in db/db mice but showed increased abundance with long-acting PFD treatment. Several bacterial taxa, including Lactobacillus and some Bacteroides, were less abundant in db/db mice and more abundant in long-acting-PFD-treated db/db mice. Long-acting PFD treatment reduced the abundance of Akkermansia muciniphila (5%) as compared to db/db mice (~15%). We conclude that gut microbial dysbiosis observed in db/db mice was partially reversed by long-acting PFD treatment and hypothesize that PFD has beneficial effects, in part, via its influence on the gut microbial metabolite profile. In quantitatively assessing urine metabolites, we observed a high abundance of diabetic ketoacidosis biomarkers, including 3-hydroxybutyric acid and acetoacetic acid in db/db mice, which were less abundant in the long-acting-PFD-treated db/db mice.
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Affiliation(s)
- Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA; (K.K.); (R.P.)
- Correspondence: ; Tel.: +1-301-795-7684
| | - Satoshi Miyamoto
- Department of Medicine, University of Texas Health, San Antonio, TX 77030, USA; (S.M.); (M.D.); (K.S.)
| | - Manjula Darshi
- Department of Medicine, University of Texas Health, San Antonio, TX 77030, USA; (S.M.); (M.D.); (K.S.)
| | | | - Keehwan Kwon
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA; (K.K.); (R.P.)
| | - Kumar Sharma
- Department of Medicine, University of Texas Health, San Antonio, TX 77030, USA; (S.M.); (M.D.); (K.S.)
| | - Rembert Pieper
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA; (K.K.); (R.P.)
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9
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Kwan B, Fuhrer T, Zhang J, Darshi M, Van Espen B, Montemayor D, de Boer IH, Dobre M, Hsu CY, Kelly TN, Raj DS, Rao PS, Saraf SL, Scialla J, Waikar SS, Sharma K, Natarajan L. Metabolomic Markers of Kidney Function Decline in Patients With Diabetes: Evidence From the Chronic Renal Insufficiency Cohort (CRIC) Study. Am J Kidney Dis 2020; 76:511-520. [PMID: 32387023 DOI: 10.1053/j.ajkd.2020.01.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 10/08/2019] [Accepted: 01/17/2020] [Indexed: 02/01/2023]
Abstract
RATIONALE & OBJECTIVE Biomarkers that provide reliable evidence of future diabetic kidney disease (DKD) are needed to improve disease management. In a cross-sectional study, we previously identified 13 urine metabolites that had levels reduced in DKD compared with healthy controls. We evaluated associations of these 13 metabolites with future DKD progression. STUDY DESIGN Prospective cohort. SETTING & PARTICIPANTS 1,001 Chronic Renal Insufficiency Cohort (CRIC) participants with diabetes with estimated glomerular filtration rates (eGFRs) between 20 and 70mL/min/1.73m2 were followed up prospectively for a median of 8 (range, 2-10) years. PREDICTORS 13 urine metabolites, age, race, sex, smoked more than 100 cigarettes in lifetime, body mass index, hemoglobin A1c level, blood pressure, urinary albumin, and eGFR. OUTCOMES Annual eGFR slope and time to incident kidney failure with replacement therapy (KFRT; ie, initiation of dialysis or receipt of transplant). ANALYTICAL APPROACH Several clinical metabolite models were developed for eGFR slope as the outcome using stepwise selection and penalized regression, and further tested on the time-to-KFRT outcome. A best cross-validated (final) prognostic model was selected based on high prediction accuracy for eGFR slope and high concordance statistic for incident KFRT. RESULTS During follow-up, mean eGFR slope was-1.83±1.92 (SD) mL/min/1.73m2 per year; 359 (36%) participants experienced KFRT. Median time to KFRT was 7.45 years from the time of entry to the CRIC Study. In our final model, after adjusting for clinical variables, levels of metabolites 3-hydroxyisobutyrate (3-HIBA) and 3-methylcrotonyglycine had a significant negative association with eGFR slope, whereas citric and aconitic acid were positively associated. Further, 3-HIBA and aconitic acid levels were associated with higher and lower risk for KFRT, respectively (HRs of 2.34 [95% CI, 1.51-3.62] and 0.70 [95% CI, 0.51-0.95]). LIMITATIONS Subgroups for whom metabolite signatures may not be optimal, nontargeted metabolomics by flow-injection analysis, and 2-stage modeling approaches. CONCLUSIONS Urine metabolites may offer insights into DKD progression. If replicated in future studies, aconitic acid and 3-HIBA could identify individuals with diabetes at high risk for GFR decline, potentially leading to improved clinical care and targeted therapies.
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Affiliation(s)
- Brian Kwan
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA; Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - Manjula Darshi
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | | | - Daniel Montemayor
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Ian H de Boer
- Department of Medicine, University of Washington, Seattle, WA
| | - Mirela Dobre
- Division of Nephrology and Hypertension, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH
| | - Chi-Yuan Hsu
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA
| | - Dominic S Raj
- Division of Kidney Disease and Hypertension, George Washington University, Washington, DC
| | - Panduranga S Rao
- Department of Medicine, University of Michigan, Ann Arbor, Ann Arbor, MI
| | - Santosh L Saraf
- Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Julia Scialla
- Department of Medicine and Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC; Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA; Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Sushrut S Waikar
- Renal Division, Brigham and Women's Hospital, Boston, MA; Renal Section, Boston University Medical Center, Boston, MA
| | - Kumar Sharma
- Center of Renal Precision Medicine, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX.
| | - Loki Natarajan
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA; Moores Cancer Center, University of California, San Diego, La Jolla, CA.
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10
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Mulder S, Heerspink HJL, Darshi M, Kim JJ, Laverman GD, Sharma K, Pena MJ. Effects of dapagliflozin on urinary metabolites in people with type 2 diabetes. Diabetes Obes Metab 2019; 21:2422-2428. [PMID: 31264758 DOI: 10.1111/dom.13823] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/07/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
AIM To assess the effects of the sodium-glucose co-transporter-2 (SGLT2) inhibitor dapagliflozin on a pre-specified panel of 13 urinary metabolites linked to mitochondrial metabolism in people with type 2 diabetes and elevated urine albumin levels. MATERIALS AND METHODS Urine and plasma samples were used from a double-blind, randomized, placebo-controlled crossover trial in 31 people with type 2 diabetes, with an albumin:creatinine ratio >100 mg/g, and who were on a stable dose of an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Dapagliflozin or placebo treatment periods each lasted 6 weeks, with a 6-week washout period in between. Urinary and plasma metabolites were quantified by gas-chromatography mass spectrometry, corrected for creatinine level, and then combined into a single-valued urinary metabolite index. Fractional excretion of the metabolites was calculated. RESULTS All 13 urinary metabolites were detectable. After 6 weeks of dapagliflozin therapy, nine of the 13 metabolites were significantly increased from baseline. The urinary metabolite index increased by 42% (95% confidence interval [CI] 8.5 to 85.6; P = .01) with placebo versus 121% (95% CI 69 to 189; P < .001) with dapaglifozin. The placebo-adjusted effect was 56% (95% CI 11 to 118; P = .012). In plasma, seven of the 13 metabolites were detectable, and none was modified by dapagliflozin. CONCLUSIONS Dapagliflozin significantly increased a panel of urinary metabolites previously linked to mitochondrial metabolism. These data support the hypothesis that SGLT2 inhibitors improve mitochondrial function, and improvements in mitochondrial function could be a mechanism for kidney protection. Future studies with longer treatment duration and clinical outcomes are needed to confirm the clinical impact of these findings.
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Affiliation(s)
- Skander Mulder
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Manjula Darshi
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas
| | - Jiwan J Kim
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas
| | - Gozewijn D Laverman
- Department of Internal Medicine, ZiekenhuisGroep Twente, Almelo, The Netherlands
| | - Kumar Sharma
- Division of Nephrology, UT Health Science Center San Antonio, San Antonio, Texas
| | - Michelle J Pena
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, Groningen, The Netherlands
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11
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Onishi A, Fu Y, Darshi M, Crespo-Masip M, Huang W, Song P, Patel R, Kim YC, Nespoux J, Freeman B, Soleimani M, Thomson S, Sharma K, Vallon V. Effect of renal tubule-specific knockdown of the Na +/H + exchanger NHE3 in Akita diabetic mice. Am J Physiol Renal Physiol 2019; 317:F419-F434. [PMID: 31166707 PMCID: PMC6732454 DOI: 10.1152/ajprenal.00497.2018] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023] Open
Abstract
Na+/H+ exchanger isoform 3 (NHE3) contributes to Na+/bicarbonate reabsorption and ammonium secretion in early proximal tubules. To determine its role in the diabetic kidney, type 1 diabetic Akita mice with tubular NHE3 knockdown [Pax8-Cre; NHE3-knockout (KO) mice] were generated. NHE3-KO mice had higher urine pH, more bicarbonaturia, and compensating increases in renal mRNA expression for genes associated with generation of ammonium, bicarbonate, and glucose (phosphoenolpyruvate carboxykinase) in proximal tubules and H+ and ammonia secretion and glycolysis in distal tubules. This left blood pH and bicarbonate unaffected in nondiabetic and diabetic NHE3-KO versus wild-type mice but was associated with renal upregulation of proinflammatory markers. Higher renal phosphoenolpyruvate carboxykinase expression in NHE3-KO mice was associated with lower Na+-glucose cotransporter (SGLT)2 and higher SGLT1 expression, indicating a downward tubular shift in Na+ and glucose reabsorption. NHE3-KO was associated with lesser kidney weight and glomerular filtration rate (GFR) independent of diabetes and prevented diabetes-associated albuminuria. NHE3-KO, however, did not attenuate hyperglycemia or prevent diabetes from increasing kidney weight and GFR. Higher renal gluconeogenesis may explain similar hyperglycemia despite lower SGLT2 expression and higher glucosuria in diabetic NHE3-KO versus wild-type mice; stronger SGLT1 engagement could have affected kidney weight and GFR responses. Chronic kidney disease in humans is associated with reduced urinary excretion of metabolites of branched-chain amino acids and the tricarboxylic acid cycle, a pattern mimicked in diabetic wild-type mice. This pattern was reversed in nondiabetic NHE3-KO mice, possibly reflecting branched-chain amino acids use for ammoniagenesis and tricarboxylic acid cycle upregulation to support formation of ammonia, bicarbonate, and glucose in proximal tubule. NHE3-KO, however, did not prevent the diabetes-induced urinary downregulation in these metabolites.
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Affiliation(s)
- Akira Onishi
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Yiling Fu
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Maria Crespo-Masip
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
- Biomedical Research Institute (IRBLleida), University of Lleida, Lleida, Spain
| | - Winnie Huang
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Panai Song
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Rohit Patel
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Young Chul Kim
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Josselin Nespoux
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Brent Freeman
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | | | - Scott Thomson
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health San Antonio, San Antonio, Texas
| | - Volker Vallon
- Department of Medicine, University of California San Diego and Veterans Affairs San Diego Healthcare System, San Diego, California
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12
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Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science 2019; 364:364/6436/eaau8650. [PMID: 30975860 DOI: 10.1126/science.aau8650] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.
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Affiliation(s)
- Francine E Garrett-Bakelman
- Weill Cornell Medicine, New York, NY, USA.,University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Ruben C Gur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ling Lin
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Jad Nasrini
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Lynn Taylor
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sara Ahadi
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aditya Ambati
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Songjie Chen
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Marisa Covington
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | - Brian E Crucian
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | - David F Dinges
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | - Ryan P Hillary
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Peng Jiang
- Northwestern University, Evanston, IL, USA
| | | | | | | | | | | | | | | | - Tyler M Moore
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Hemal H Patel
- University of California, San Diego, La Jolla, CA, USA
| | | | - Varsha Rao
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rintaro Saito
- University of California, San Diego, La Jolla, CA, USA
| | - Denis N Salins
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Michael B Stenger
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | | | | | | | - Jing Zhang
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - John B Charles
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | - Craig E Kundrot
- Space Life and Physical Sciences Division, NASA Headquarters, Washington, DC, USA.
| | - Graham B I Scott
- National Space Biomedical Research Institute, Baylor College of Medicine, Houston, TX, USA.
| | | | - Mathias Basner
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | | | | | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | | | - Brinda K Rana
- University of California, San Diego, La Jolla, CA, USA.
| | - Scott M Smith
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
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13
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Saulnier PJ, Darshi M, Wheelock KM, Looker HC, Fufaa GD, Knowler WC, Weil EJ, Tanamas SK, Lemley KV, Saito R, Natarajan L, Nelson RG, Sharma K. Urine metabolites are associated with glomerular lesions in type 2 diabetes. Metabolomics 2018; 14:84. [PMID: 30830355 PMCID: PMC6461445 DOI: 10.1007/s11306-018-1380-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/02/2018] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Little is known about the association of urine metabolites with structural lesions in persons with diabetes. OBJECTIVES We examined the relationship between 12 urine metabolites and kidney structure in American Indians with type 2 diabetes. METHODS Data were from a 6-year clinical trial that assessed renoprotective efficacy of losartan, and included a kidney biopsy at the end of the treatment period. Metabolites were measured in urine samples collected within a median of 6.5 months before the research biopsy. Associations of the creatinine-adjusted urine metabolites with kidney structural variables were examined by Pearson's correlations and multivariable linear regression after adjustment for age, sex, diabetes duration, hemoglobin A1c, mean arterial pressure, glomerular filtration rate (iothalamate), and losartan treatment. RESULTS Participants (n = 62, mean age 45 ± 10 years) had mean ± standard deviation glomerular filtration rate of 137 ± 50 ml/min and median (interquartile range) urine albumin:creatinine ratio of 34 (14-85) mg/g near the time of the biopsy. Urine aconitic and glycolic acids correlated positively with glomerular filtration surface density (partial r = 0.29, P = 0.030 and r = 0.50, P < 0.001) and total filtration surface per glomerulus (partial r = 0.32, P = 0.019 and r = 0.43, P = 0.001). 2-ethyl 3-OH propionate correlated positively with the percentage of fenestrated endothelium (partial r = 0.32, P = 0.019). Citric acid correlated negatively with mesangial fractional volume (partial r=-0.36, P = 0.007), and homovanillic acid correlated negatively with podocyte foot process width (partial r=-0.31, P = 0.022). CONCLUSIONS Alterations of urine metabolites may associate with early glomerular lesions in diabetic kidney disease.
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Affiliation(s)
- Pierre-Jean Saulnier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- Clinical Investigation Center CIC1402, CHU Poitiers, University of Poitiers, INSERM, Poitiers, France
| | | | - Kevin M Wheelock
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Helen C Looker
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Gudeta D Fufaa
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - E Jennifer Weil
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Stephanie K Tanamas
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | | | - Rintaro Saito
- University of California San Diego, San Diego, CA, USA
| | | | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA.
- National Institutes of Health, 1550 East Indian School Road, Phoenix, AZ, 85014-4972, USA.
| | - Kumar Sharma
- University of California San Diego, San Diego, CA, USA
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14
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Abstract
Diabetic kidney disease (DKD) is the leading cause of morbidity and mortality in diabetic patients. Defining risk factors for DKD using a reductionist approach has proven challenging. Integrative omics-based systems biology tools have shed new insights in our understanding of DKD and have provided several key breakthroughs for identifying novel predictive and diagnostic biomarkers. In this review, we highlight the role of the Warburg effect in DKD and potential regulating factors such as sphingomyelin, fumarate, and pyruvate kinase muscle isozyme M2 in shifting glucose flux from complete oxidation in mitochondria to the glycolytic pathway and its principal branches. With the development of highly sensitive instruments and more advanced automatic bioinformatics tools, we believe that omics analyses and imaging techniques will focus more on singular-cell-level studies, which will allow in-depth understanding of DKD and pave the path for personalized kidney precision medicine.
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Affiliation(s)
- Guanshi Zhang
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health, San Antonio, TX; Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX
| | - Manjula Darshi
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health, San Antonio, TX; Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, University of Texas Health, San Antonio, TX; Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX.
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15
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Hallan S, Afkarian M, Zelnick LR, Kestenbaum B, Sharma S, Saito R, Darshi M, Barding G, Raftery D, Ju W, Kretzler M, Sharma K, de Boer IH. Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients. EBioMedicine 2017; 26:68-77. [PMID: 29128444 PMCID: PMC5832558 DOI: 10.1016/j.ebiom.2017.10.027] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [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] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 01/17/2023] Open
Abstract
Chronic kidney disease (CKD) is a public health problem with very high prevalence and mortality. Yet, there is a paucity of effective treatment options, partly due to insufficient knowledge of underlying pathophysiology. We combined metabolomics (GCMS) with kidney gene expression studies to identify metabolic pathways that are altered in adults with non-diabetic stage 3-4 CKD versus healthy adults. Urinary excretion rate of 27 metabolites and plasma concentration of 33 metabolites differed significantly in CKD patients versus controls (estimate range-68% to +113%). Pathway analysis revealed that the citric acid cycle was the most significantly affected, with urinary excretion of citrate, cis-aconitate, isocitrate, 2-oxoglutarate and succinate reduced by 40-68%. Reduction of the citric acid cycle metabolites in urine was replicated in an independent cohort. Expression of genes regulating aconitate, isocitrate, 2-oxoglutarate and succinate were significantly reduced in kidney biopsies. We observed increased urine citrate excretion (+74%, p=0.00009) and plasma 2-oxoglutarate concentrations (+12%, p=0.002) in CKD patients during treatment with a vitamin-D receptor agonist in a randomized trial. In conclusion, urinary excretion of citric acid cycle metabolites and renal expression of genes regulating these metabolites were reduced in non-diabetic CKD. This supports the emerging view of CKD as a state of mitochondrial dysfunction.
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Affiliation(s)
- Stein Hallan
- Center for Renal Translational Medicine/Institute for Metabolomic Medicine, University of California San Diego, San Diego, CA, United States; Department of Clinical and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Nephrology, St. Olav Hospital, Trondheim, Norway.
| | - Maryam Afkarian
- Kidney Research Institute, University of Washington, Seattle, WA, United States; Division of Nephrology, Department of Medicine, University of California, Davis, CA, United States
| | - Leila R Zelnick
- Kidney Research Institute, University of Washington, Seattle, WA, United States; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Bryan Kestenbaum
- Kidney Research Institute, University of Washington, Seattle, WA, United States; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Shoba Sharma
- University of Texas Health San Antonio, San Antonio, TX, United States
| | - Rintaro Saito
- Center for Renal Translational Medicine/Institute for Metabolomic Medicine, University of California San Diego, San Diego, CA, United States
| | - Manjula Darshi
- Center for Renal Translational Medicine/Institute for Metabolomic Medicine, University of California San Diego, San Diego, CA, United States
| | - Gregory Barding
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, United States
| | - Wenjun Ju
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI, United States; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Matthias Kretzler
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI, United States; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Kumar Sharma
- Center for Renal Translational Medicine/Institute for Metabolomic Medicine, University of California San Diego, San Diego, CA, United States; Department of Nephrology and Hypertension, Veterans Administration San Diego HealthCare System, San Diego, CA, United States
| | - Ian H de Boer
- Kidney Research Institute, University of Washington, Seattle, WA, United States; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, United States
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16
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Sastri M, Darshi M, Mackey M, Ramachandra R, Ju S, Phan S, Adams S, Stein K, Douglas CR, Kim JJ, Ellisman MH, Taylor SS, Perkins GA. Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50. J Cell Sci 2017; 130:3248-3260. [PMID: 28808085 DOI: 10.1242/jcs.201400] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 01/06/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
Each mitochondrial compartment contains varying protein compositions that underlie a diversity of localized functions. Insights into the localization of mitochondrial intermembrane space-bridging (MIB) components will have an impact on our understanding of mitochondrial architecture, dynamics and function. By using the novel visualizable genetic tags miniSOG and APEX2 in cultured mouse cardiac and human astrocyte cell lines and performing electron tomography, we have mapped at nanoscale resolution three key MIB components, Mic19, Mic60 and Sam50 (also known as CHCHD3, IMMT and SAMM50, respectively), in the environment of structural landmarks such as cristae and crista junctions (CJs). Tagged Mic19 and Mic60 were located at CJs, distributed in a network pattern along the mitochondrial periphery and also enriched inside cristae. We discovered an association of Mic19 with cytochrome c oxidase subunit IV. It was also found that tagged Sam50 is not uniformly distributed in the outer mitochondrial membrane and appears to incompletely overlap with Mic19- or Mic60-positive domains, most notably at the CJs.
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Affiliation(s)
- Mira Sastri
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Manjula Darshi
- Howard Hughes Medical Institute, University of California, San Diego, CA 92093, USA
| | - Mason Mackey
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Saeyeon Ju
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Stephen Adams
- Department of Pharmacology, University of California, San Diego, CA 92093, USA
| | - Kathryn Stein
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Christopher R Douglas
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Jiwan John Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA.,Howard Hughes Medical Institute, University of California, San Diego, CA 92093, USA.,Department of Pharmacology, University of California, San Diego, CA 92093, USA
| | - Guy A Perkins
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093, USA
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17
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Börgeson E, Wallenius V, Syed GH, Darshi M, Lantero Rodriguez J, Biörserud C, Ragnmark Ek M, Björklund P, Quiding-Järbrink M, Fändriks L, Godson C, Sharma K. AICAR ameliorates high-fat diet-associated pathophysiology in mouse and ex vivo models, independent of adiponectin. Diabetologia 2017; 60:729-739. [PMID: 28188334 PMCID: PMC6518112 DOI: 10.1007/s00125-017-4211-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 08/29/2016] [Accepted: 12/05/2016] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS In this study, we aimed to evaluate the therapeutic potential of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), an activator of AMP-activated protein kinase, for ameliorating high-fat diet (HFD)-induced pathophysiology in mice. We also aimed to determine whether the beneficial effects of AICAR were dependent on adiponectin. Furthermore, human adipose tissue was used to examine the effect of AICAR ex vivo. METHODS Six-week-old male C57BL/6J wild-type and Adipoq -/- mice were fed a standard-fat diet (10% fat) or an HFD (60% fat) for 12 weeks and given vehicle or AICAR (500 μg/g) three times/week from weeks 4-12. Diet-induced pathophysiology was examined in mice after 11 weeks by IPGTT and after 12 weeks by flow cytometry and western blotting. Human adipose tissue biopsies from obese (BMI 35-50 kg/m2) individuals were incubated with vehicle or AICAR (1 mmol/l) for 6 h at 37°C, after which inflammation was characterised by ELISA (TNF-α) and flow cytometry. RESULTS AICAR attenuated adipose inflammation in mice fed an HFD, promoting an M1-to-M2 macrophage phenotype switch, while reducing infiltration of CD8+ T cells. AICAR treatment of mice fed an HFD partially restored glucose tolerance and attenuated hepatic steatosis and kidney disease, as evidenced by reduced albuminuria (p < 0.05), urinary H2O2 (p < 0.05) and renal superoxide levels (p < 0.01) in both wild-type and Adipoq -/- mice. AICAR-mediated protection occurred independently of adiponectin, as similar protection was observed in wild-type and Adipoq -/- mice. In addition, AICAR promoted an M1-to-M2 macrophage phenotype switch and reduced TNF-α production in tissue explants from obese human patients. CONCLUSIONS/INTERPRETATION AICAR may promote metabolic health and protect against obesity-induced systemic diseases in an adiponectin-independent manner. Furthermore, AICAR reduced inflammation in human adipose tissue explants, suggesting by proof-of-principle that the drug may reduce obesity-induced complications in humans. TRIAL REGISTRATION ClinicalTrials.gov NCT02322073.
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Affiliation(s)
- Emma Börgeson
- The Wallenberg Laboratory for Cardiovascular and Metabolic Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Bruna Stråket 16, S-413 45, Gothenburg, Sweden.
- Centre for Renal Translational Medicine, Institute of Metabolomic Medicine, UC San Diego Health Sciences, San Diego VA HealthCare System, Stein Clinical Research Building, Room 406, mail code 0711, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Veteran's Affairs (VA), San Diego VA HealthCare System, Veterans Medical Research Foundation, San Diego, CA, USA.
| | - Ville Wallenius
- Department of Gastrosurgical Research and Education, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gulam H Syed
- Division of Infectious Diseases, School of Medicine, University of California, San Diego, CA, USA
| | - Manjula Darshi
- Centre for Renal Translational Medicine, Institute of Metabolomic Medicine, UC San Diego Health Sciences, San Diego VA HealthCare System, Stein Clinical Research Building, Room 406, mail code 0711, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Juan Lantero Rodriguez
- The Wallenberg Laboratory for Cardiovascular and Metabolic Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Bruna Stråket 16, S-413 45, Gothenburg, Sweden
| | - Christina Biörserud
- Department of Gastrosurgical Research and Education, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Malin Ragnmark Ek
- Department of Gastrosurgical Research and Education, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Björklund
- Department of Gastrosurgical Research and Education, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marianne Quiding-Järbrink
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Fändriks
- Department of Gastrosurgical Research and Education, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Catherine Godson
- University College Dublin (UCD) Diabetes Complications Research Centre, UCD Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Kumar Sharma
- Centre for Renal Translational Medicine, Institute of Metabolomic Medicine, UC San Diego Health Sciences, San Diego VA HealthCare System, Stein Clinical Research Building, Room 406, mail code 0711, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Veteran's Affairs (VA), San Diego VA HealthCare System, Veterans Medical Research Foundation, San Diego, CA, USA.
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18
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Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D'Agati V, Beyret E, Belmonte JCI, Anders HJ, Sharma K. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight 2016; 1:e87877. [PMID: 27777973 DOI: 10.1172/jci.insight.87877] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To derive new insights in diabetic complications, we integrated publicly available human protein-protein interaction (PPI) networks with global metabolic networks using metabolomic data from patients with diabetic nephropathy. We focused on the participating proteins in the network that were computationally predicted to connect the urine metabolites. MDM2 had the highest significant number of PPI connections. As validation, significant downregulation of MDM2 gene expression was found in both glomerular and tubulointerstitial compartments of kidney biopsy tissue from 2 independent cohorts of patients with diabetic nephropathy. In diabetic mice, chemical inhibition of MDM2 with Nutlin-3a led to reduction in the number of podocytes, increased blood urea nitrogen, and increased mortality. Addition of Nutlin-3a decreased WT1+ cells in embryonic kidneys. Both podocyte- and tubule-specific MDM2-knockout mice exhibited severe glomerular and tubular dysfunction, respectively. Interestingly, the only 2 metabolites that were reduced in both podocyte and tubule-specific MDM2-knockout mice were 3-methylcrotonylglycine and uracil, both of which were also reduced in human diabetic kidney disease. Thus, our bioinformatics tool combined with multi-omics studies identified an important functional role for MDM2 in glomeruli and tubules of the diabetic nephropathic kidney and links MDM2 to a reduction in 2 key metabolite biomarkers.
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Affiliation(s)
- Rintaro Saito
- Institute of Metabolomic Medicine.,Center for Renal Translational Medicine, Division of Nephrology-Hypertension.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Anaïs Rocanin-Arjo
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU Munich, Munich, Germany
| | - Young-Hyun You
- Center for Renal Translational Medicine, Division of Nephrology-Hypertension.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Manjula Darshi
- Institute of Metabolomic Medicine.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Benjamin Van Espen
- Institute of Metabolomic Medicine.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Satoshi Miyamoto
- Center for Renal Translational Medicine, Division of Nephrology-Hypertension.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Jessica Pham
- Center for Renal Translational Medicine, Division of Nephrology-Hypertension.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Minya Pu
- Institute of Metabolomic Medicine.,Department of Family Medicine and Epidemiology, UCSD, San Diego, California, USA
| | - Simone Romoli
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU Munich, Munich, Germany
| | - Loki Natarajan
- Institute of Metabolomic Medicine.,Department of Family Medicine and Epidemiology, UCSD, San Diego, California, USA
| | - Wenjun Ju
- Department of Internal Medicine, Nephrology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Nephrology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Keiichiro Ono
- Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Dana Thomasova
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU Munich, Munich, Germany
| | - Shrikant R Mulay
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU Munich, Munich, Germany
| | - Trey Ideker
- Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA
| | - Vivette D'Agati
- Renal Pathology Laboratory, Columbia University, College of Physicians and Surgeons, Department of Pathology, New York, New York, USA
| | - Ergin Beyret
- Salk Institute for Biological Studies, San Diego, California, USA
| | | | - Hans Joachim Anders
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU Munich, Munich, Germany
| | - Kumar Sharma
- Institute of Metabolomic Medicine.,Center for Renal Translational Medicine, Division of Nephrology-Hypertension.,Division of Medical Genetics, Department of Medicine, UCSD, San Diego, California, USA.,Veterans Affairs Health Systems, San Diego, California, USA
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19
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Sas KM, Kayampilly P, Byun J, Nair V, Hinder LM, Hur J, Zhang H, Lin C, Qi NR, Michailidis G, Groop PH, Nelson RG, Darshi M, Sharma K, Schelling JR, Sedor JR, Pop-Busui R, Weinberg JM, Soleimanpour SA, Abcouwer SF, Gardner TW, Burant CF, Feldman EL, Kretzler M, Brosius FC, Pennathur S. Tissue-specific metabolic reprogramming drives nutrient flux in diabetic complications. JCI Insight 2016; 1:e86976. [PMID: 27699244 PMCID: PMC5033761 DOI: 10.1172/jci.insight.86976] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022] Open
Abstract
Diabetes is associated with altered cellular metabolism, but how altered metabolism contributes to the development of diabetic complications is unknown. We used the BKS db/db diabetic mouse model to investigate changes in carbohydrate and lipid metabolism in kidney cortex, peripheral nerve, and retina. A systems approach using transcriptomics, metabolomics, and metabolic flux analysis identified tissue-specific differences, with increased glucose and fatty acid metabolism in the kidney, a moderate increase in the retina, and a decrease in the nerve. In the kidney, increased metabolism was associated with enhanced protein acetylation and mitochondrial dysfunction. To confirm these findings in human disease, we analyzed diabetic kidney transcriptomic data and urinary metabolites from a cohort of Southwestern American Indians. The urinary findings were replicated in 2 independent patient cohorts, the Finnish Diabetic Nephropathy and the Family Investigation of Nephropathy and Diabetes studies. Increased concentrations of TCA cycle metabolites in urine, but not in plasma, predicted progression of diabetic kidney disease, and there was an enrichment of pathways involved in glycolysis and fatty acid and amino acid metabolism. Our findings highlight tissue-specific changes in metabolism in complication-prone tissues in diabetes and suggest that urinary TCA cycle intermediates are potential prognostic biomarkers of diabetic kidney disease progression.
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Affiliation(s)
| | | | | | - Viji Nair
- Department of Internal Medicine
- Department of Computational Medicine and Bioinformatics
| | - Lucy M. Hinder
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | | | | | | | - George Michailidis
- Department of Statistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Robert G. Nelson
- Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, USA
| | - Manjula Darshi
- Institute of Metabolomic Medicine and Center for Renal Translational Medicine, Department of Medicine, University of California San Diego, and Veterans Administration San Diego Healthcare System, La Jolla, California, USA
| | - Kumar Sharma
- Institute of Metabolomic Medicine and Center for Renal Translational Medicine, Department of Medicine, University of California San Diego, and Veterans Administration San Diego Healthcare System, La Jolla, California, USA
| | | | - John R. Sedor
- Department of Medicine
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | | | | | | | - Charles F. Burant
- Department of Internal Medicine
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Eva L. Feldman
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine
- Department of Computational Medicine and Bioinformatics
| | - Frank C. Brosius
- Department of Internal Medicine
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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20
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Abstract
The development of new therapies for chronic diseases, such as diabetic kidney disease (DKD), will continue to be hampered by lack of sufficient biomarkers that will provide insights and will be responsive to treatment interventions. The recent application of metabolomic technologies, such as nuclear magnetic resonance and mass spectroscopy, has allowed large-scale analysis of small molecules to be interrogated in a targeted or untargeted manner. Recent advances from both human and animal studies that have arisen from metabolomic analysis have recognized that mitochondrial function and fatty acid oxidation play key roles in the development and progression of DKD. Although many challenges in the technology for clinical chronic kidney disease (CKD) are yet to be validated, there will very likely be ongoing major contributions of metabolomics to develop new biochemical understanding for diabetic and CKD. The clinical application of metabolomics and accompanying bioinformatic tools will likely be a cornerstone of personalized medicine triumphs for CKD.
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Affiliation(s)
- Manjula Darshi
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, Calif., USA
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21
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Miyamoto S, Hsu CC, Hamm G, Darshi M, Diamond-Stanic M, Declèves AE, Slater L, Pennathur S, Stauber J, Dorrestein PC, Sharma K. Mass Spectrometry Imaging Reveals Elevated Glomerular ATP/AMP in Diabetes/obesity and Identifies Sphingomyelin as a Possible Mediator. EBioMedicine 2016; 7:121-34. [PMID: 27322466 PMCID: PMC4909366 DOI: 10.1016/j.ebiom.2016.03.033] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
AMP-activated protein kinase (AMPK) is suppressed in diabetes and may be due to a high ATP/AMP ratio, however the quantitation of nucleotides in vivo has been extremely difficult. Via matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to localize renal nucleotides we found that the diabetic kidney had a significant increase in glomerular ATP/AMP ratio. Untargeted MALDI-MSI analysis revealed that a specific sphingomyelin species (SM(d18:1/16:0)) accumulated in the glomeruli of diabetic and high-fat diet-fed mice compared with wild-type controls. In vitro studies in mesangial cells revealed that exogenous addition of SM(d18:1/16:0) significantly elevated ATP via increased glucose consumption and lactate production with a consequent reduction of AMPK and PGC1α. Furthermore, inhibition of sphingomyelin synthases reversed these effects. Our findings suggest that AMPK is reduced in the diabetic kidney due to an increase in the ATP/AMP ratio and that SM(d18:1/16:0) could be responsible for the enhanced ATP production via activation of the glycolytic pathway. MALDI-MSI revealed an increase in glomerular ATP/AMP ratio in the diabetic kidney. SM(d18:1/16:0) is increased in the glomeruli of diabetic and high-fat diet-fed mice. SM(d18:1/16:0) stimulated ATP production via enhanced aerobic glycolysis and reduced AMPK activity in mesangial cells. AMPK is known to be suppressed in states of high ATP/AMP ratio but the measurement of nucleotides in vivo has been difficult. Miyamoto et al. utilize matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate the distribution of nucleotides and find an increase in glomerular ATP/AMP ratio in the diabetic kidney. Untargeted MALDI-MSI revealed that sphingomyelin(d18:1/16:0) is accumulated in the glomeruli of diabetic and high-fat diet-fed mice compared with controls. Sphingomyelin(d18:1/16:0) promotes ATP production in mesangial cells via activation of the glycolytic pathway. The inhibition of sphingomyelin(d18:1/16:0) synthesis may lead to novel therapeutic targets for the treatment of caloric-induced CKD.
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Affiliation(s)
- Satoshi Miyamoto
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA; Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, CA 92093, USA; Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA; Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Gregory Hamm
- ImaBiotech, MS Imaging Department, Lille 59120, France
| | - Manjula Darshi
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA
| | - Maggie Diamond-Stanic
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA; Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, CA 92093, USA
| | - Anne-Emilie Declèves
- Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA
| | - Larkin Slater
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA; Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, CA 92093, USA
| | | | | | - Pieter C Dorrestein
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kumar Sharma
- Institute of Metabolomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; Center for Renal Translational Medicine, Division of Nephrology-Hypertension, University of California San Diego, La Jolla, CA 92093, USA; Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, CA 92093, USA.
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Pfanner N, van der Laan M, Amati P, Capaldi RA, Caudy AA, Chacinska A, Darshi M, Deckers M, Hoppins S, Icho T, Jakobs S, Ji J, Kozjak-Pavlovic V, Meisinger C, Odgren PR, Park SK, Rehling P, Reichert AS, Sheikh MS, Taylor SS, Tsuchida N, van der Bliek AM, van der Klei IJ, Weissman JS, Westermann B, Zha J, Neupert W, Nunnari J. Uniform nomenclature for the mitochondrial contact site and cristae organizing system. ACTA ACUST UNITED AC 2014; 204:1083-6. [PMID: 24687277 PMCID: PMC3971754 DOI: 10.1083/jcb.201401006] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mitochondrial inner membrane contains a large protein complex that functions in inner membrane organization and formation of membrane contact sites. The complex was variably named the mitochondrial contact site complex, mitochondrial inner membrane organizing system, mitochondrial organizing structure, or Mitofilin/Fcj1 complex. To facilitate future studies, we propose to unify the nomenclature and term the complex “mitochondrial contact site and cristae organizing system” and its subunits Mic10 to Mic60.
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Affiliation(s)
- Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, Zentrum für Biochemie und Molekulare Zellforschung, and 2 BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
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Guo Y, Darshi M, Ma Y, Perkins GA, Shen Z, Haushalter KJ, Saito R, Chen A, Lee YS, Patel HH, Briggs SP, Ellisman MH, Olefsky JM, Taylor SS. Quantitative proteomic and functional analysis of liver mitochondria from high fat diet (HFD) diabetic mice. Mol Cell Proteomics 2013; 12:3744-58. [PMID: 24030101 DOI: 10.1074/mcp.m113.027441] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Insulin resistance plays a major role in the development of type 2 diabetes and obesity and affects a number of biological processes such as mitochondrial biogenesis. Though mitochondrial dysfunction has been linked to the development of insulin resistance and pathogenesis of type 2 diabetes, the precise mechanism linking the two is not well understood. We used high fat diet (HFD)-induced obesity dependent diabetes mouse models to gain insight into the potential pathways altered with metabolic disease, and carried out quantitative proteomic analysis of liver mitochondria. As previously reported, proteins involved in fatty acid oxidation, branched chain amino acid degradation, tricarboxylic acid cycle, and oxidative phosphorylation were uniformly up-regulated in the liver of HFD fed mice compared with that of normal diet. Further, our studies revealed that retinol metabolism is distinctly down-regulated and the mitochondrial structural proteins-components of mitochondrial inter-membrane space bridging (MIB) complex (Mitofilin, Sam50, and ChChd3), and Tim proteins-essential for protein import, are significantly up-regulated in HFD fed mice. Structural and functional studies on HFD and normal diet liver mitochondria revealed remodeling of HFD mitochondria to a more condensed form with increased respiratory capacity and higher ATP levels compared with normal diet mitochondria. Thus, it is likely that the structural remodeling is essential to accommodate the increased protein content in presence of HFD: the mechanism could be through the MIB complex promoting contact site and crista junction formation and in turn facilitating the lipid and protein uptake.
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Darshi M, Trinh KN, Murphy AN, Taylor SS. Targeting and import mechanism of coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial intermembrane space. J Biol Chem 2012; 287:39480-91. [PMID: 23019327 PMCID: PMC3501047 DOI: 10.1074/jbc.m112.387696] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) is a mitochondrial inner membrane (IM) protein facing toward the intermembrane space (IMS). In the IMS, ChChd3 complexes with multiple proteins at the crista junctions and contact sites and plays a key role in maintaining crista integrity. ChChd3 is myristoylated at the N terminus and has a CHCH domain with twin CX9C motifs at its C terminus. The CHCH domain proteins are traditionally imported and trapped in the IMS by using a disulfide relay system mediated by Mia40 and Erv1. In this study, we systematically analyzed the role of the myristoylation and the CHCH domain in the import and mitochondrial localization of ChChd3. Based on our results, we predict that myristoylation promotes binding of ChChd3 to the outer membrane and that the CHCH domain translocates the protein across the outer membrane. By analysis of the CHCH domain cysteine mutants, we further show that they have distinct roles in binding to Mia40 in the IMS and proper folding of the protein. The transient disulfide-bonded intermediate with Mia40 is formed preferentially between the second cysteine in helix 1, Cys193, and the active site cysteine in Mia40, Cys55. Although each of the four cysteines is essential for folding of the protein and binding to mitofilin and Sam50, they are not involved in import. Together our results indicate that both the myristoylation and the CHCH domain are essential for the import and mitochondrial localization of ChChd3. Once imported, ChChd3 binds to Mia40 for further folding and assembly into macromolecular complexes.
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Affiliation(s)
- Manjula Darshi
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0654, USA
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25
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Taylor SS, Ilouz R, Darshi M, Sarma G, Kornev A, Zhang P. PKA: assembly of dynamic macromolecular signaling. BMC Pharmacol 2011. [PMCID: PMC3363169 DOI: 10.1186/1471-2210-11-s1-o12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Darshi M, Mendiola VL, Mackey MR, Murphy AN, Koller A, Perkins GA, Ellisman MH, Taylor SS. ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function. J Biol Chem 2010; 286:2918-32. [PMID: 21081504 PMCID: PMC3024787 DOI: 10.1074/jbc.m110.171975] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial inner membrane (IM) serves as the site for ATP production by hosting the oxidative phosphorylation complex machinery most notably on the crista membranes. Disruption of the crista structure has been implicated in a variety of cardiovascular and neurodegenerative diseases. Here, we characterize ChChd3, a previously identified PKA substrate of unknown function (Schauble, S., King, C. C., Darshi, M., Koller, A., Shah, K., and Taylor, S. S. (2007) J. Biol. Chem. 282, 14952-14959), and show that it is essential for maintaining crista integrity and mitochondrial function. In the mitochondria, ChChd3 is a peripheral protein of the IM facing the intermembrane space. RNAi knockdown of ChChd3 in HeLa cells resulted in fragmented mitochondria, reduced OPA1 protein levels and impaired fusion, and clustering of the mitochondria around the nucleus along with reduced growth rate. Both the oxygen consumption and glycolytic rates were severely restricted. Ultrastructural analysis of these cells revealed aberrant mitochondrial IM structures with fragmented and tubular cristae or loss of cristae, and reduced crista membrane. Additionally, the crista junction opening diameter was reduced to 50% suggesting remodeling of cristae in the absence of ChChd3. Analysis of the ChChd3-binding proteins revealed that ChChd3 interacts with the IM proteins mitofilin and OPA1, which regulate crista morphology, and the outer membrane protein Sam50, which regulates import and assembly of β-barrel proteins on the outer membrane. Knockdown of ChChd3 led to almost complete loss of both mitofilin and Sam50 proteins and alterations in several mitochondrial proteins, suggesting that ChChd3 is a scaffolding protein that stabilizes protein complexes involved in maintaining crista architecture and protein import and is thus essential for maintaining mitochondrial structure and function.
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Affiliation(s)
- Manjula Darshi
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0654, USA
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Darshi M, Perkins GA, Mackey MR, Petrosyan S, Murphy AN, Ellisman MH, Taylor SS. ChChd3, an Inner Mitochondrial Membrane Protein is Essential for Maintaining Cristae Integrity and Mitochondrial Function. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.510.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Guy A Perkins
- Department of Neurosciences and National Center for Microscopy and Imaging Research
| | - Mason R Mackey
- Department of Neurosciences and National Center for Microscopy and Imaging Research
| | - Susanna Petrosyan
- Department of PharmacologyUniversity of California San DiegoLa JollaCA
| | - Anne N Murphy
- Department of PharmacologyUniversity of California San DiegoLa JollaCA
| | - Mark H Ellisman
- Department of Neurosciences and National Center for Microscopy and Imaging Research
| | - Susan S Taylor
- Howard Hughes Medical InstituteLa JollaCA
- Department of PharmacologyUniversity of California San DiegoLa JollaCA
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28
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Affiliation(s)
| | - Susan S Taylor
- Chemistry and BiochemistryUniversity of CaliforniaSan DiegoLa JollaCA
- Howard Hughes Medical InstituteLa JollaCA
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29
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Das SK, Darshi M, Cheley S, Wallace MI, Bayley H. Membrane protein stoichiometry determined from the step-wise photobleaching of dye-labelled subunits. Chembiochem 2007; 8:994-9. [PMID: 17503420 DOI: 10.1002/cbic.200600474] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Somes K Das
- Department of Molecular & Cellular Medicine, The Texas A&M University System Health Science Center, College Station, TX 77843-1114, USA
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Schauble S, King CC, Darshi M, Koller A, Shah K, Taylor SS. Identification of ChChd3 as a novel substrate of the cAMP-dependent protein kinase (PKA) using an analog-sensitive catalytic subunit. J Biol Chem 2007; 282:14952-9. [PMID: 17242405 DOI: 10.1074/jbc.m609221200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Due to the numerous kinases in the cell, many with overlapping substrates, it is difficult to find novel substrates for a specific kinase. To identify novel substrates of cAMP-dependent protein kinase (PKA), the PKA catalytic subunit was engineered to accept bulky N(6)-substituted ATP analogs, using a chemical genetics approach initially pioneered with v-Src (1). Methionine 120 was mutated to glycine in the ATP-binding pocket of the catalytic subunit. To express the stable mutant C-subunit in Escherichia coli required co-expression with PDK1. This mutant protein was active and fully phosphorylated on Thr(197) and Ser(338). Based on its kinetic properties, the engineered C-subunit preferred N(6)(benzyl)-ATP and N(6)(phenethyl)-ATP over other ATP analogs, but still retained a 30 microm K(m) for ATP. This mutant recombinant C-subunit was used to identify three novel PKA substrates. One protein, a novel mitochondrial ChChd protein, ChChd3, was identified, suggesting that PKA may regulate mitochondria proteins.
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Affiliation(s)
- Sharmin Schauble
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0654, USA
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Darshi M, Schauble S, Ma Y, Taylor SS. Characterization of chchd3; A novel cAMP dependent protein kinase A substrate in mitochondria. FASEB J 2007. [DOI: 10.1096/fasebj.21.6.a986-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Manjula Darshi
- Howard Hughes Medical InstituteUniversity Of California9500 Gilman DrSan DiegoCA92093
| | - Sharmin Schauble
- Department of Chemistry and BiochemistryUniversity of California, San Diego9500 Gilman DrSan DiegoCA92093
| | - Yuliang Ma
- Howard Hughes Medical InstituteUniversity Of California9500 Gilman DrSan DiegoCA92093
| | - Susan S Taylor
- Howard Hughes Medical InstituteUniversity Of California9500 Gilman DrSan DiegoCA92093
- Department of Chemistry and BiochemistryUniversity of California, San Diego9500 Gilman DrSan DiegoCA92093
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Singh AK, Darshi M. A fluorescence study of (4-{(1E,3E)-4-[4-(dimethylamino)phenyl]buta-1,3-dienyl}phenyl)methanol and its bioconjugates with bovine and human serum albumins. NEW J CHEM 2004. [DOI: 10.1039/b304951e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Singh AK, Darshi M. Fluorescence probe properties of intramolecular charge transfer diphenylbutadienes in micelles and vesicles. Biochim Biophys Acta 2002; 1563:35-44. [PMID: 12007623 DOI: 10.1016/s0005-2736(02)00372-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This paper reports absorption and fluorescence spectral studies of methyl 4-[(1E,3E)-4-phenylbuta-1,3-dienyl]benzoate (1), N,N-dimethyl-N-[4-[(1E,3E)-4-phenylbuta-1,3-dienyl]phenyl]amine (2), methyl 4-[(1E,3E)-4-[4-(dimethylamino)phenyl]buta-1,3-dienyl]benzoate (3) and 1-methyl-4-[(1E,3E)-4-[4-methoxyphenyl]buta-1,3-dienyl]benzoate (4) in homogeneous media of 1,4-dioxane and 1,4-dioxane-water binary mixtures, and in microheterogeneous media of cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS) and Triton-X-100 micelles, and dipalmotoyl phosphatidylcholine (DPPC) vesicles. The binding site of the diene probes in micelles and vesicles has been determined and it has been found that while in micelles dienes occupy the polar interfacial regions, in vesicles the probes are located deep inside the hydrophobic bilayer. The binding of dienes to the vesicles is stronger than their binding to the micelles as indicated by the binding constant values. The fluorescence emission of the probe dienes in micelles is from a conformationally relaxed intramolecular charge transfer excited state. However, in vesicles, since the excited state conformational motions are restricted due to the rigidity of the alkyl chain, the dienes fluoresce from their planar locally excited states.
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Affiliation(s)
- Anil K Singh
- Department of Chemistry, Indian Institute of Technology, Powai, Mumbai, 400 076 Bombay, India.
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Singh AK, Darshi M, Kanvah S. α,ω-Diphenylpolyenes Cabable of Exhibiting Twisted Intramolecular Charge Transfer Fluorescence: A Fluorescence and Fluorescence Probe Study of Nitro- and Nitrocyano-Substituted 1,4-Diphenylbutadienes. J Phys Chem A 1999. [DOI: 10.1021/jp992275a] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anil K. Singh
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
| | - Manjula Darshi
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
| | - Sriram Kanvah
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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Singh AK, Darshi M, Kanvah S. Twisted intramolecular charge transfer fluorescence in nitro-substituted α,ω-diphenylpolyene compounds. NEW J CHEM 1999. [DOI: 10.1039/a907329i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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