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Chella Krishnan K, El Hachem EJ, Keller MP, Patel SG, Carroll L, Vegas AD, Gerdes Gyuricza I, Light C, Cao Y, Pan C, Kaczor-Urbanowicz KE, Shravah V, Anum D, Pellegrini M, Lee CF, Seldin MM, Rosenthal NA, Churchill GA, Attie AD, Parker B, James DE, Lusis AJ. Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy. eLife 2023; 12:e82619. [PMID: 37276142 PMCID: PMC10241513 DOI: 10.7554/elife.82619] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Mitochondria play an important role in both normal heart function and disease etiology. We report analysis of common genetic variations contributing to mitochondrial and heart functions using an integrative proteomics approach in a panel of inbred mouse strains called the Hybrid Mouse Diversity Panel (HMDP). We performed a whole heart proteome study in the HMDP (72 strains, n=2-3 mice) and retrieved 848 mitochondrial proteins (quantified in ≥50 strains). High-resolution association mapping on their relative abundance levels revealed three trans-acting genetic loci on chromosomes (chr) 7, 13 and 17 that regulate distinct classes of mitochondrial proteins as well as cardiac hypertrophy. DAVID enrichment analyses of genes regulated by each of the loci revealed that the chr13 locus was highly enriched for complex-I proteins (24 proteins, P=2.2E-61), the chr17 locus for mitochondrial ribonucleoprotein complex (17 proteins, P=3.1E-25) and the chr7 locus for ubiquinone biosynthesis (3 proteins, P=6.9E-05). Follow-up high resolution regional mapping identified NDUFS4, LRPPRC and COQ7 as the candidate genes for chr13, chr17 and chr7 loci, respectively, and both experimental and statistical analyses supported their causal roles. Furthermore, a large cohort of Diversity Outbred mice was used to corroborate Lrpprc gene as a driver of mitochondrial DNA (mtDNA)-encoded gene regulation, and to show that the chr17 locus is specific to heart. Variations in all three loci were associated with heart mass in at least one of two independent heart stress models, namely, isoproterenol-induced heart failure and diet-induced obesity. These findings suggest that common variations in certain mitochondrial proteins can act in trans to influence tissue-specific mitochondrial functions and contribute to heart hypertrophy, elucidating mechanisms that may underlie genetic susceptibility to heart failure in human populations.
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Affiliation(s)
- Karthickeyan Chella Krishnan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Elie-Julien El Hachem
- Department of Integrative Biology and Physiology, Field Systems Biology, Sciences Sorbonne UniversitéParisFrance
| | - Mark P Keller
- Biochemistry Department, University of Wisconsin-MadisonMadisonUnited States
| | - Sanjeet G Patel
- Department of Surgery/Division of Cardiac Surgery, University of Southern California Keck School of MedicineLos AngelesUnited States
| | - Luke Carroll
- Metabolic Systems Biology Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Alexis Diaz Vegas
- Metabolic Systems Biology Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | | | - Christine Light
- Cardiovascular Biology Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
| | - Yang Cao
- Department of Medicine/Division of Cardiology, University of California, Los AngelesLos AngelesUnited States
| | - Calvin Pan
- Department of Medicine/Division of Cardiology, University of California, Los AngelesLos AngelesUnited States
| | - Karolina Elżbieta Kaczor-Urbanowicz
- Division of Oral Biology and Medicine, UCLA School of DentistryLos AngelesUnited States
- UCLA Institute for Quantitative and Computational BiosciencesLos AngelesUnited States
| | - Varun Shravah
- Department of Chemistry, University of CaliforniaLos AngelesUnited States
| | - Diana Anum
- Department of Integrative Biology and Physiology, University of CaliforniaLos AngelesUnited States
| | - Matteo Pellegrini
- UCLA Institute for Quantitative and Computational BiosciencesLos AngelesUnited States
| | - Chi Fung Lee
- Cardiovascular Biology Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
- Department of Physiology, University of Oklahoma Health Sciences CenterOklahoma CityUnited States
| | - Marcus M Seldin
- Center for Epigenetics and MetabolismIrvineUnited States
- Department of Biological Chemistry, University of CaliforniaIrvineUnited States
| | | | | | - Alan D Attie
- Biochemistry Department, University of Wisconsin-MadisonMadisonUnited States
| | - Benjamin Parker
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia
| | - David E James
- Metabolic Systems Biology Laboratory, Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, University of California, Los AngelesLos AngelesUnited States
- Department of Human Genetics, University of CaliforniaLos AngelesUnited States
- Department of Microbiology, Immunology and Molecular Genetics, University of CaliforniaLos AngelesUnited States
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El Hachem EJ, Sokolovska N, Soula H. Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework. BMC Bioinformatics 2023; 24:61. [PMID: 36823548 PMCID: PMC9948385 DOI: 10.1186/s12859-023-05177-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Current clinical routines rely more and more on "omics" data such as flow cytometry data from host and microbiota. Cohorts variability in addition to patients' heterogeneity and huge dimensions make it difficult to understand underlying structure of the data and decipher pathologies. Patients stratification and diagnostics from such complex data are extremely challenging. There is an acute need to develop novel statistical machine learning methods that are robust with respect to the data heterogeneity, efficient from the computational viewpoint, and can be understood by human experts. RESULTS We propose a novel approach to stratify cell-based observations within a single probabilistic framework, i.e., to extract meaningful phenotypes from both patients and cells data simultaneously. We define this problem as a double clustering problem that we tackle with the proposed approach. Our method is a practical extension of the Latent Dirichlet Allocation and is used for the Double Clustering task (LDA-DC). We first validate the method on artificial datasets, then we apply our method to two real problems of patients stratification based on cytometry and microbiota data. We observe that the LDA-DC returns clusters of patients and also clusters of cells related to patients' conditions. We also construct a graphical representation of the results that can be easily understood by humans and are, therefore, of a big help for experts involved in pre-clinical research.
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Affiliation(s)
- Elie-Julien El Hachem
- Sorbonne University, INSERM, Nutrition and Obesities: Systemic Approaches, NutriOmique, 91 Boulevard de l'hôpital, 75013, Paris, France.
| | - Nataliya Sokolovska
- Sorbonne University, INSERM, Nutrition and Obesities: Systemic Approaches, NutriOmique, 91 Boulevard de l'hôpital, 75013, Paris, France
| | - Hedi Soula
- Sorbonne University, INSERM, Nutrition and Obesities: Systemic Approaches, NutriOmique, 91 Boulevard de l'hôpital, 75013, Paris, France
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Lecoutre S, Merabtene F, El Hachem EJ, Gamblin C, Rouault C, Sokolovska N, Soula H, Lai WS, Blackshear PJ, Clément K, Dugail I. Beta-hydroxybutyrate dampens adipose progenitors' profibrotic activation through canonical Tgfβ signaling and non-canonical ZFP36-dependent mechanisms. Mol Metab 2022; 61:101512. [PMID: 35550189 PMCID: PMC9123279 DOI: 10.1016/j.molmet.2022.101512] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND/PURPOSE Adipose tissue contains progenitor cells that contribute to beneficial tissue expansion when needed by de novo adipocyte formation (classical white or beige fat cells with thermogenic potential). However, in chronic obesity, they can exhibit an activated pro-fibrotic, extracellular matrix (ECM)-depositing phenotype that highly aggravates obesity-related adipose tissue dysfunction. METHODS Given that progenitors' fibrotic activation and fat cell browning appear to be antagonistic cell fates, we have examined the anti-fibrotic potential of pro-browning agents in an obesogenic condition. RESULTS In obese mice fed a high fat diet, thermoneutral housing, which induces brown fat cell dormancy, increases the expression of ECM gene programs compared to conventionally raised animals, indicating aggravation of obesity-related tissue fibrosis at thermoneutrality. In a model of primary cultured murine adipose progenitors, we found that exposure to β-hydroxybutyrate selectively reduced Tgfβ-dependent profibrotic responses of ECM genes like Ctgf, Loxl2 and Fn1. This effect is observed in both subcutaneous and visceral-derived adipose progenitors, as well as in 3T3-L1 fibroblasts. In 30 patients with obesity eligible for bariatric surgery, those with higher circulating β-hydroxybutyrate levels have lower subcutaneous adipose tissue fibrotic scores. Mechanistically, β-hydroxybutyrate limits Tgfβ-dependent collagen accumulation and reduces Smad2-3 protein expression and phosphorylation in visceral progenitors. Moreover, β-hydroxybutyrate induces the expression of the ZFP36 gene, encoding a post-transcriptional regulator that promotes the degradation of mRNA by binding to AU-rich sites within 3'UTRs. Importantly, complete ZFP36 deficiency in a mouse embryonic fibroblast line from null mice, or siRNA knock-down in primary progenitors, indicate that ZFP36 is required for β-hydroxybutyrate anti-fibrotic effects. CONCLUSION These data unravel the potential of β-hydroxybutyrate to limit adipose tissue matrix deposition, a finding that might exploited in an obesogenic context.
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Affiliation(s)
- Simon Lecoutre
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Fatiha Merabtene
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Elie-Julien El Hachem
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Camille Gamblin
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Christine Rouault
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Nataliya Sokolovska
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | - Hedi Soula
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France
| | | | | | - Karine Clément
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France,Assistance Publique-Hôpitaux de Paris, Nutrition Department, Pitié-Salpêtrière Hospital, Paris 75013. France
| | - Isabelle Dugail
- Sorbonne Université, INSERM, Nutrition and obesities: systemic approach research group, Nutriomics, Paris F-75013. France,Corresponding author.
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Chella Krishnan K, El Hachem EJ, Light C, Shravah V, Anum D, Seldin MM, Lee CF, Parker BL, James DE, Lusis AJ. Abstract MP252: Genetic Architecture Of Heart Mitochondrial Proteome Influencing Cardiac Hypertrophy. Circ Res 2021. [DOI: 10.1161/res.129.suppl_1.mp252] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/16/2022]
Abstract
Our lab studies how natural genetic variations affect common diseases using a mouse population called hybrid mouse diversity panel (HMDP). In this study, we have explored the genetic regulation of mitochondrial pathways and their contribution to heart function using an integrative proteomics approach. We first performed a whole heart proteomic analysis in the HMDP (72 strains, n=2-3 mice) and surveyed mitochondrial localization using MitoCarta2.0. We retrieved 840 of these proteins (quantified in ≥50 strains) and performed high-resolution association mapping on their respective abundance levels to the HMDP genotypes. Our analyses identified three genetic loci, located on chromosome (chr) 7, chr13 and chr17, that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Follow-up high resolution regional mapping identified NDUFS4, LRPPRC and COQ7 as the candidate genes for chr13, chr17 and chr7 loci, respectively. All three are associated with heart mass in two independent heart stress models, namely, isoproterenol (ISO)-induced heart failure and diet-induced obesity (DIO) models. Next, to identify the aspects of mitochondrial metabolism regulated by these loci, we constructed co-expression protein networks using weighted gene co-expression network analysis (WGCNA) and identified five modules. Eigengenes, representing the first principal component of two of these modules (Brown and Green), mapped to the same regions as the chr13 and chr17 loci, respectively. DAVID enrichment analyses revealed that the Brown module (72 proteins, 96% overlap with chr13) was highly enriched for complex-I proteins (35 proteins, P = 8.8E-74) and the Green module (44 proteins, 73% overlap with chr17) for mitochondrial ribosomal proteins (25 proteins, P = 1.3E-53). The proteins in the chr7 locus were found primarily in the Turquoise module (393 proteins, 81% overlap) but this module was not enriched for any single mitochondrial protein complex. In summary, we now report the identification of three genetic loci that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Our results provide strong support for a role of the mitochondrial proteome in heart pathophysiology.
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Affiliation(s)
| | | | | | | | - Diana Anum
- Univ of California Los Angeles, Los Angeles, CA
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