Novel RBPJ transcripts identified in human amniotic fluid cells

Rheumatoid arthritis-associated RBPJ polymorphism alters memory CD4+ T cells

Notch signaling has recently emerged as an important regulator of immune responses in autoimmune diseases. The recombination signal-binding protein for immunoglobulin kappa J region (RBPJ) is a transcriptional repressor, but converts into a transcriptional activator upon activation of the canonical Notch pathway. Genome-wide association studies of rheumatoid arthritis (RA) identified a susceptibility locus, rs874040(CC), which implicated the RBPJ gene. Here, chromatin state mapping generated using the chromHMM algorithm reveals strong enhancer regions containing DNase I hypersensitive sites overlapping the rs874040 linkage disequilibrium block in human memory, but not in naïve CD4(+) T cells. The rs874040 overlapping this chromatin state was associated with increased RBPJ expression in stimulated memory CD4(+) T cells from healthy subjects homozygous for the risk allele (CC) compared with memory CD4(+) T cells bearing the protective allele (GG). Transcriptomic analysis of rs874040(CC) memory T cells showed a repression of canonical Notch target genes IL (interleukin)-9, IL-17 and interferon (IFN)γ in the basal state. Interestingly, activation of the Notch pathway using soluble Notch ligand, Jagged2-Fc, induced IL-9 and IL-17A while delta-like 4Fc, another Notch ligand, induced higher IFNγ expression in the rs874040(CC) memory CD4(+) T cells compared with their rs874040(GG) counterparts. In RA, RBPJ expression is elevated in memory T cells from RA patients compared with control subjects, and this was associated with induced inflammatory cytokines IL-9, IL-17A and IFNγ in response to Notch ligation in vitro. These findings demonstrate that the rs874040(CC) allele skews memory T cells toward a pro-inflammatory phenotype involving Notch signaling, thus increasing the susceptibility to develop RA.

RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome

OBJECTIVE

The aim of this study was to compare the complexity of the amniotic fluid supernatant cell-free fetal transcriptome as described by RNA Sequencing (RNA-Seq) and gene expression microarrays.

METHODS

Cell-free fetal RNA from the amniotic fluid supernatant of five euploid mid-trimester samples was divided and prepared in tandem for analysis by either the Affymetrix HG-U133 Plus 2.0 Gene Chip microarray or Illumina HiSeq. Transcriptomes were assembled and compared on the basis of the presence of signal, rank-order gene expression, and pathway enrichment using Ingenuity Pathway Analysis (IPA). RNA-Seq data were also examined for evidence of alternative splicing.

RESULTS

Within individual samples, gene expression was strongly correlated (R = 0.43-0.57). Fewer expressed genes were observed using RNA-Seq than gene expression microarrays (4158 vs 8842). Most of the top pathways in the 'Physiological Systems Development and Function' IPA category were shared between platforms, although RNA-Seq yielded more significant p-values. Using RNA-Seq, examples of known alternative splicing were detected in several genes including H19 and IGF2.

CONCLUSIONS

In this pilot study, we found that expression microarrays gave a broader view of overall gene expression, while RNA-Seq demonstrated alternative splicing and specific pathways relevant to the developing fetus. The degraded nature of cell-free fetal RNA presented technical challenges for the RNA-Seq approach.