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Kattih B, Boeckling F, Shumliakivska M, Tombor L, Rasper T, Schmitz K, Hoffmann J, Nicin L, Abplanalp WT, Carstens DC, Arsalan M, Emrich F, Holubec T, Walther T, Puntmann VO, Nagel E, John D, Zeiher AM, Dimmeler S. Single-nuclear transcriptome profiling identifies persistent fibroblast activation in hypertrophic and failing human hearts of patients with longstanding disease. Cardiovasc Res 2023; 119:2550-2562. [PMID: 37648651 DOI: 10.1093/cvr/cvad140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/19/2022] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 09/01/2023] Open
Abstract
AIMS Cardiac fibrosis drives the progression of heart failure in ischaemic and hypertrophic cardiomyopathy. Therefore, the development of specific anti-fibrotic treatment regimens to counteract cardiac fibrosis is of high clinical relevance. Hence, this study examined the presence of persistent fibroblast activation during longstanding human heart disease at a single-cell resolution to identify putative therapeutic targets to counteract pathological cardiac fibrosis in patients. METHODS AND RESULTS We used single-nuclei RNA sequencing with human tissues from two samples of one healthy donor, and five hypertrophic and two failing hearts. Unsupervised sub-clustering of 7110 nuclei led to the identification of 7 distinct fibroblast clusters. De-convolution of cardiac fibroblast heterogeneity revealed a distinct population of human cardiac fibroblasts with a molecular signature of persistent fibroblast activation and a transcriptional switch towards a pro-fibrotic extra-cellular matrix composition in patients with established cardiac hypertrophy and heart failure. This sub-cluster was characterized by high expression of POSTN, RUNX1, CILP, and a target gene adipocyte enhancer-binding protein 1 (AEBP1) (all P < 0.001). Strikingly, elevated circulating AEBP1 blood level were also detected in a validation cohort of patients with confirmed cardiac fibrosis and hypertrophic cardiomyopathy by cardiac magnetic resonance imaging (P < 0.01). Since endogenous AEBP1 expression was increased in patients with established cardiac hypertrophy and heart failure, we assessed the functional consequence of siRNA-mediated AEBP1 silencing in human cardiac fibroblasts. Indeed, AEBP1 silencing reduced proliferation, migration, and fibroblast contractile capacity and α-SMA gene expression, which is a hallmark of fibroblast activation (all P < 0.05). Mechanistically, the anti-fibrotic effects of AEBP1 silencing were linked to transforming growth factor-beta pathway modulation. CONCLUSION Together, this study identifies persistent fibroblast activation in patients with longstanding heart disease, which might be detected by circulating AEBP1 and therapeutically modulated by its targeted silencing in human cardiac fibroblasts.
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Affiliation(s)
- Badder Kattih
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Cardiology, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Felicitas Boeckling
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Cardiology, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Mariana Shumliakivska
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Lukas Tombor
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Tina Rasper
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Katja Schmitz
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Jedrzej Hoffmann
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Centre for Cardiovascular Imaging, Institute of Experimental and Translational Cardiovascular Imaging, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Luka Nicin
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Wesley T Abplanalp
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Daniel C Carstens
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Mani Arsalan
- Goethe University Frankfurt, University Hospital, Department of Cardiovascular Surgery, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
| | - Fabian Emrich
- Goethe University Frankfurt, University Hospital, Department of Cardiovascular Surgery, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
| | - Tomas Holubec
- Goethe University Frankfurt, University Hospital, Department of Cardiovascular Surgery, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
| | - Thomas Walther
- Goethe University Frankfurt, University Hospital, Department of Cardiovascular Surgery, Theodor-Stern-Kai 7, Frankfurt 60590, Germany
| | - Valentina O Puntmann
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Centre for Cardiovascular Imaging, Institute of Experimental and Translational Cardiovascular Imaging, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Eike Nagel
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Centre for Cardiovascular Imaging, Institute of Experimental and Translational Cardiovascular Imaging, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - David John
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Andreas M Zeiher
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
| | - Stefanie Dimmeler
- Goethe University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Centre for Cardiovascular Research, Partner Site Rhine-Main, 60590 Frankfurt am Main, Germany
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O'Neill NK, Stein TD, Hu J, Rehman H, Campbell JD, Yajima M, Zhang X, Farrer LA. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. BMC Bioinformatics 2023; 24:349. [PMID: 37726653 PMCID: PMC10507917 DOI: 10.1186/s12859-023-05476-w] [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: 12/06/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA-seq) data to make these calculations. Single-nuclei RNA-sequencing (snRNA-seq) reference data can be used instead of scRNA-seq data for tissues such as human brain where single-cell data are difficult to obtain, but accuracy suffers due to sequencing differences between the technologies. RESULTS We propose a modification to MuSiC entitled 'DeTREM' which compensates for sequencing differences between the cell-type signature and bulk RNA-seq datasets in order to better predict cell-type fractions. We show DeTREM to be more accurate than MuSiC in simulated and real human brain bulk RNA-sequencing datasets with various cell-type abundance estimates. We also compare DeTREM to SCDC and CIBERSORTx, two recent deconvolution methods that use scRNA-seq cell-type signatures. We find that they perform well in simulated data but produce less accurate results than DeTREM when used to deconvolute human brain data. CONCLUSION DeTREM improves the deconvolution accuracy of MuSiC and outperforms other deconvolution methods when applied to snRNA-seq data. DeTREM enables accurate cell-type deconvolution in situations where scRNA-seq data are not available. This modification improves characterization cell-type specific effects in brain tissue and identification of cell-type abundance differences under various conditions.
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Affiliation(s)
- Nicholas K O'Neill
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Veterans Administration Medical Center, Bedford, MA, USA
| | - Junming Hu
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Habbiburr Rehman
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Joshua D Campbell
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Computational Biomedicine), Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA, USA
| | - Xiaoling Zhang
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| | - Lindsay A Farrer
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
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Cameron D, Mi D, Vinh NN, Webber C, Li M, Marín O, O'Donovan MC, Bray NJ. Single-Nuclei RNA Sequencing of 5 Regions of the Human Prenatal Brain Implicates Developing Neuron Populations in Genetic Risk for Schizophrenia. Biol Psychiatry 2023; 93:157-166. [PMID: 36150908 PMCID: PMC10804933 DOI: 10.1016/j.biopsych.2022.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 03/22/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND While a variety of evidence supports a prenatal component in schizophrenia, there are few data regarding the cell populations involved. We sought to identify cells of the human prenatal brain mediating genetic risk for schizophrenia by integrating cell-specific gene expression measures generated through single-nuclei RNA sequencing with recent large-scale genome-wide association study (GWAS) and exome sequencing data for the condition. METHODS Single-nuclei RNA sequencing was performed on 5 brain regions (frontal cortex, ganglionic eminence, hippocampus, thalamus, and cerebellum) from 3 fetuses from the second trimester of gestation. Enrichment of schizophrenia common variant genetic liability and rare damaging coding variation was assessed in relation to gene expression specificity within each identified cell population. RESULTS Common risk variants were prominently enriched within genes with high expression specificity for developing neuron populations within the frontal cortex, ganglionic eminence, and hippocampus. Enrichments were largely independent of genes expressed in neuronal populations of the adult brain that have been implicated in schizophrenia through the same methods. Genes containing an excess of rare damaging variants in schizophrenia had higher expression specificity for developing glutamatergic neurons of the frontal cortex and hippocampus that were also enriched for common variant liability. CONCLUSIONS We found evidence for a distinct contribution of prenatal neuronal development to genetic risk for schizophrenia, involving specific populations of developing neurons within the second-trimester fetal brain. Our study significantly advances the understanding of the neurodevelopmental origins of schizophrenia and provides a resource with which to investigate the prenatal antecedents of other psychiatric and neurologic disorders.
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Affiliation(s)
- Darren Cameron
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Da Mi
- Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ngoc-Nga Vinh
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Meng Li
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom; Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Oscar Marín
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom; Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom; Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.
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