Whole Blood Transcriptome Analysis in Children with Sickle Cell Anemia

Whole transcriptome RNA-sequencing was performed to quantify RNA expression changes in whole blood samples collected from steady state sickle cell anemia (SCA) and control subjects. Pediatric SCA and control subjects were recruited from Atlanta (GA)-based hospital(s) systems and consented for RNA sequencing. RNA sequencing was performed on an Ion Torrent S5 sequencer, using the Ion Total RNA-seq v2 protocol. Data were aligned to the hg19 reference genome and analyzed in the Partek Genomics studio package (v7.0). 223 genes were differentially expressed between SCA and controls (+/- 1.5 fold change FDR p < 0.001) and 441 genes show differential transcript expression (+/- 1.5 fold FDR p < 0.001). Differentially expressed RNA are enriched for hemoglobin associated genes and ubiquitin-proteasome pathway genes. Further analysis shows higher gamma globin gene expression in SCA (33-fold HBG1 and 49-fold HBG2, both FDR p < 0.05), which did not correlate with hemoglobin F protein levels. eQTL analysis identified SNPs in novel non-coding RNA RYR2 gene as having a potential regulatory role in HBG1 and HBG2 expression levels. Gene expression correlation identified JHDM1D-AS1(KDM7A-DT), a non-coding RNA associated with angiogenesis, enhanced GATA1 and decreased JAK-STAT signaling to correlate with HBG1 and HBG2 mRNA levels. These data suggest novel regulatory mechanisms for fetal hemoglobin regulation, which may offer innovative therapeutic approaches for SCA.

Automated summary

Whole transcriptome RNA-sequencing revealed differential expression of 223 genes and differential transcript expression of 441 genes in whole blood samples from sickle cell anemia (SCA) patients compared to controls. The differentially expressed RNA were enriched for genes associated with hemoglobin and ubiquitin-proteasome pathway. Further analysis showed higher expression of gamma globin genes in SCA patients, and identified non-coding RNAs associated with HBG1 and HBG2 mRNA levels. These findings suggest novel regulatory mechanisms for fetal hemoglobin regulation in SCA.