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| Status |
Public on Apr 21, 2022 |
| Title |
Single-cell transcriptomic profiling provides insights into disease-related processes in human hypertrophic cardiomyopathy |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background – Hypertrophic cardiomyopathy (HCM) is a common genetic cardiac disorder that is characterized by the presence of left ventricular hypertrophy with histological evidence of myocyte disarray and fibrosis. Pathologic DNA variants in sarcomeric genes are seen in 50–60% of families, but the mechanistic origins of hypertrophy and disarray remain poorly understood. More molecular insights could contribute to a better understanding of these origins and improve therapeutic strategies for HCM.
Methods – To identify gene expression patterns relevant to HCM pathology, we quantified intercellular heterogeneity in cardiomyocyte gene expression by performing single-cell RNA sequencing (scRNA-seq) on myectomy tissue from HCM patients.
Results – Septal myectomy samples provide a unique opportunity to access diseased human heart tissue for scRNA-seq. We analysed gene expression of individual cardiomyocytes for three HCM patients, who each showed a similar presence of cardiomyocyte subpopulations. This similarity indicated these subpopulations emerge from biological processes, and not from experimental variability. Moreover, our data revealed functional links between genes important to HCM. A subpopulation characterized by elevated titin (TTN) expression showed increased expression of genes involved in muscle contraction and development. A subpopulation of Natriuretic Peptide A (NPPA)-enriched cells showed elevated expression of Natriuretic Peptide B (NPPB). Further analysis of gene co-expression revealed five groups of genes with tightly correlated expression (regulons), one consisting of mostly sarcomeric genes and another containing some well-known stress markers. These correlations were confirmed in 97 additional HCM myectomy samples and allowed us to de novo identify transcription factors related to sarcomeric gene expression and stress. Finally, using forward scatter, we charted functional implications of regulon expression and showed a link between the stress-marker regulon and cell size. Histology samples independently confirmed that regulon member skeletal alpha actin (ACTA1) correlates with cell size.
Conclusion – We have shown that single-cell sequencing on myectomy samples from HCM patients identified new functional links between genes, transcription factors, and a functional link between genes and cell size. This highlights the relevance of cardiomyocyte heterogeneity, and additionally provides a wealth of novel insights into molecular events at the base of HCM, which potentially contribute to understanding disease progression.
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| Overall design |
Single-cell RNA-sequencing on 5 septal myectomy samples from patients with hypertrophic cardiomyopathy
FACS sorting index data are not available for patients 1-3.
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| Contributor(s) |
Eding JE, de Leeuw AE, Wright Clark M, Wehrens M, Boogerd CJ, Molenaar B, van der Kraak PH, Kuster DW, van der Velden J, Michels M, Vink A, van Rooij E |
| Citation missing |
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| Submission date |
Oct 01, 2019 |
| Last update date |
Apr 23, 2022 |
| Contact name |
Eva van Rooij |
| E-mail(s) |
E.vanrooij@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA575238 |
| SRA |
SRP223884 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138262_RAW.tar |
24.7 Mb |
(http)(custom) |
TAR (of CSV, TSV) |
| GSE138262_readme_demultiplexing_Cel-seq2_data.pdf |
811.8 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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