Abstract
Background
MicroRNAs (miRNAs) are short single-stranded nucleotides that can regulate gene expression. Although we previously evaluated the expression of miRNAs in pediatric dilated cardiomyopathy (DCM) by miRNA array, pathway prediction based on changes in mRNA expression has not been previously analyzed in this population. The current study aimed to determine the regulation of miRNA expression by miRNA-sequencing (miRNA-seq) and, through miRNA-sequencing (mRNA-seq), analyze their putative target genes and altered pathways in pediatric DCM hearts.
Methods
miRNA expression was determined by miRNA-seq [n = 10 non-failing (NF), n = 20 DCM]. Expression of a subset of miRNAs was evaluated in adult DCM patients (n = 11 NF, n = 13 DCM). miRNA–mRNA prediction analysis was performed using mRNA-seq data (n = 7 NF, n = 7 DCM) from matched samples.
Results
Expression of 393 miRNAs was significantly different (p < 0.05) in pediatric DCM patients compared to NF controls. TargetScan-based miRNA–mRNA analysis revealed 808 significantly inversely expressed genes. Functional analysis suggests upregulated pathways related to the regulation of stem cell differentiation and cardiac muscle contraction, and downregulated pathways related to the regulation of protein phosphorylation, signal transduction, and cell communication.
Conclusions
Our results demonstrated a unique age-dependent regulation of miRNAs and their putative target genes, which may contribute to distinctive phenotypic characteristics of DCM in children.
Impact
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This is the first study to compare miRNA expression in the heart of pediatric DCM patients to age-matched healthy controls by RNA sequencing.
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Expression of a subset of miRNAs is uniquely dysregulated in children.
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Using mRNA-seq and miRNA-seq from matched samples, target prediction was performed.
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This study underscores the importance of pediatric-focused studies.
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Acknowledgements
We would like to acknowledge the Children’s Hospital Colorado (CHCO) and University of Colorado Hospital (UCH) Cardiothoracic surgical teams including Drs. David Campbell, M.D., Max Mitchell, M.D., James Jaggers, M.D., and Matthew Stone, M.D. (CHCO), and David Fullerton, M.D., and Bret Reece, M.D. (UCH) for the procurement of heart tissue. We would also like to acknowledge Drs. Peter Buttrick, M.D. and Amrut Ambardekar, M.D. for maintenance of the adult tissue bank, and Jacqueline Holstein (CHCO) for patient recruitment and assistance with collection of historical clinical data of pediatric patients. This work was supported by the National Institutes of Health Grants (3R01 HL139968-01S1 to F.T.H., K24 HL150630 to C.C.S., R01 HL1399683 to C.C.S. and S.D.M., R01 HL107715-01A1S1 and R01 HL107715 to B.L.S.), the Jack Cooper Millisor Chair in Pediatric Heart Disease, the Rose Community Foundation, and the Colorado CTSA Grant [UL1 TR002535].
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Substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data: F.T.H., A.K.-F., L.S.T., B.L.S., and C.C.S. Drafting the article or revising it critically for important intellectual content: F.T.H., A.K.F., L.S.T., M.R.B., S.D.M., B.L.S., and C.C.S. Final approval of the version to be published: F.T.H., A.K.-F., L.S.T., M.R.B., S.D.M., B.L.S., and C.C.S.
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C.C.S. and M.R.B.: scientific founder and shareholder at miRagen Inc. C.C.S., S.D.M., and B.L.S.: scientific founders and shareholders at CoramiR Inc. The authors declare no competing interests.
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All subjects gave informed consent and donated their hearts to the institutional review board-approved Investigations of Pediatric or Adult heart tissue bank at the University of Colorado, Denver.
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Hailu, F.T., Karimpour-Fard, A., Toni, L.S. et al. Integrated analysis of miRNA–mRNA interaction in pediatric dilated cardiomyopathy. Pediatr Res 92, 98–108 (2022). https://doi.org/10.1038/s41390-021-01548-w
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DOI: https://doi.org/10.1038/s41390-021-01548-w
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