Integrative transcriptomic profiling reveals convergent coding and non-coding signatures in pediatric bone marrow failure syndromes
- 1Department of Laboratory Medicine, College of Medicine, Incheon St. Mary’s Hospital, The Catholic University of Korea
- 2Department of Pediatrics, Catholic Hematology Hospital, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea
- 3Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea
Abstract
Pediatric bone marrow failure (BMF) comprises heterogeneous inherited and immune-mediated disorders, yet many cases remain genetically unclassified despite comprehensive genomic evaluation. To identify shared transcriptional features beyond protein-coding variants, we performed total RNA sequencing on bone marrow samples from pediatric patients with BMF (n=12) and controls (n=2). Based on whole-genome sequencing, patients were stratified into genetically defined BMF (g-BMF, n=4) and genetically undefined BMF (u-BMF, n=8). Comparative transcriptomic analyses revealed minimal differences in protein-coding genes and long non-coding RNAs (lncRNAs) between g-BMF and u-BMF, indicating strong transcriptional concordance. Compared with controls, 55.2% of differentially expressed protein-coding genes were shared between g-BMF and u-BMF and were predominantly upregulated. Pathway enrichment analyses consistently identified immune activation and cellular stress-response pathways, suggesting a shared inflammatory transcriptional state across pediatric BMF irrespective of genetic classification. lncRNA profiling showed that 69.6% of differentially expressed lncRNAs were common to both BMF groups. ATP1A1-AS1, USP3-AS1, and SNHG32 were reproducibly overexpressed and validated by real-time quantitative polymerase chain reaction. Correlation-based pathway analyses associated ATP1A1-AS1 and USP3-AS1 with immune-related and biosynthetic programs, whereas SNHG32 showed a distinct co-expression pattern. Collectively, these findings suggest shared coding and non-coding transcriptomic patterns in pediatric BMF that appear largely independent of genetic classification within this cohort.
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BibTeX
@article{yoo2026integrative,
title = {{Integrative transcriptomic profiling reveals convergent coding and non-coding signatures in pediatric bone marrow failure syndromes}},
author = {Jaeeun Yoo and Jae Wook Lee and Nack-Gyun Chung and Jae Won Yoo and Yonggoo Kim and Myungshin Kim and Hyunjoo Bae and Jong-Mi Lee},
journal = {Scientific Reports},
year = {2026},
month = aug,
doi = {10.1038/s41598-026-68248-5},
url = {https://doi.org/10.1038/s41598-026-68248-5},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrative transcriptomic profiling reveals convergent coding and non-coding signatures in pediatric bone marrow failure syndromes
AU - Jaeeun Yoo
AU - Jae Wook Lee
AU - Nack-Gyun Chung
AU - Jae Won Yoo
AU - Yonggoo Kim
AU - Myungshin Kim
AU - Hyunjoo Bae
AU - Jong-Mi Lee
PY - 2026
DA - 2026/08/01
JO - Scientific Reports
DO - 10.1038/s41598-026-68248-5
UR - https://doi.org/10.1038/s41598-026-68248-5
AB - Pediatric bone marrow failure (BMF) comprises heterogeneous inherited and immune-mediated disorders, yet many cases remain genetically unclassified despite comprehensive genomic evaluation. To identify shared transcriptional features beyond protein-coding variants, we performed total RNA sequencing on bone marrow samples from pediatric patients with BMF (n=12) and controls (n=2). Based on whole-genome sequencing, patients were stratified into genetically defined BMF (g-BMF, n=4) and genetically undefined BMF (u-BMF, n=8). Comparative transcriptomic analyses revealed minimal differences in protein-coding genes and long non-coding RNAs (lncRNAs) between g-BMF and u-BMF, indicating strong transcriptional concordance. Compared with controls, 55.2% of differentially expressed protein-coding genes were shared between g-BMF and u-BMF and were predominantly upregulated. Pathway enrichment analyses consistently identified immune activation and cellular stress-response pathways, suggesting a shared inflammatory transcriptional state across pediatric BMF irrespective of genetic classification. lncRNA profiling showed that 69.6% of differentially expressed lncRNAs were common to both BMF groups. ATP1A1-AS1, USP3-AS1, and SNHG32 were reproducibly overexpressed and validated by real-time quantitative polymerase chain reaction. Correlation-based pathway analyses associated ATP1A1-AS1 and USP3-AS1 with immune-related and biosynthetic programs, whereas SNHG32 showed a distinct co-expression pattern. Collectively, these findings suggest shared coding and non-coding transcriptomic patterns in pediatric BMF that appear largely independent of genetic classification within this cohort.
SN - 2045-2322
ER -