Abstract / Summary
Background: Aplastic anaemia (AA) is an immune-mediated bone marrow (BM) failure disorder characterized by haematopoietic stem and progenitor cell (HSPC) depletion. The post-transcriptional features in the case of HSPCs remain unexplored. Methods: We performed a secondary analysis of publicly available datasets in Gene Expression Omnibus (GEO) to get insights into the bone marrow environment. Bulk RNA-seq of lineage-negative CD34 + (Lin - CD34 + ) HSPCs (GSE165870) from 6 non-severe AA cases and 3 healthy subjects (HS) was analysed with DESeq2. NanoString nCounter miRNA profiling of whole BM specimens (GSE242216) from 85 AA and 10 HS was analysed with limma. Differentially expressed genes (DEGs) were designated with adj. p < 0.05 and |log2 fold change| ≥2. Cell-type composition of the bulk transcriptome data was imputed via CIBERSORTx. Hub genes were identified based on STRING and CytoScape. Predicted miRNA-target interactions were retrieved through the multiMiR package, and hybridization energetics were calculated using ViennaRNA cofold and IntaRNA. Results: Eighty-one differentially expressed genes (DEGs) were identified in CD34 + cells. We identified 10 hub genes ( GYPA, CA1, ALAS2, DMTN, OSBP2, SNCA, TRIM58, SLC4A1, BPGM , and EPB42 ) mostly associated with erythroid maturation and functions. CIBERSORTx indicated a directional reduction in the imputed HSC fraction in NSAA compared to controls; however, it did not remain significant after multiple testing corrections (adj. p = 0.311). MicroRNA profiling identified some candidate miRNAs such as hsa-miR-126-3p and hsa-miR-130a-3p to be significantly downregulated, which requires further validation in larger datasets. Target predictions identified nine candidate miRNA-mRNA pairs, all of which were thermodynamically favourable. Conclusion: The HSPC population in NSAA exhibits a directional shift in transcriptional state. The miR-126-3p and miR-130a-3p emerge as candidate markers for further validation. The miRNA-mRNA candidate pairs remain energetically favourable, which warrants further functional validation.