The introduction of RNA-DNA differences underlies interindividual variation in the human IL12RB1 mRNA repertoire

Abstract

Human interleukin 12 and interleukin 23 (IL12/23) influence susceptibility or resistance to multiple diseases. However, the reasons underlying individual differences in IL12/23 sensitivity remain poorly understood. Here we report that in human peripheral blood mononuclear cells (PBMCs) and inflamed lungs, the majority of interleukin-12 receptor β1 (IL12RB1) mRNAs contain a number of RNA-DNA differences (RDDs) that concentrate in sequences essential to IL12Rβ1's binding of IL12p40, the protein subunit common to both IL-12 and IL-23. IL12RB1 RDDs comprise multiple RDD types and are detectable by next-generation sequencing and classic Sanger sequencing. As a consequence of these RDDs, the resulting IL12Rβ1 proteins have an altered amino acid sequence that could not be predicted on the basis of genomic DNA sequencing alone. Importantly, the introduction of RDDs into IL12RB1 mRNAs negatively regulates IL12Rβ1's binding of IL12p40 and is sensitive to activation. Collectively, these results suggest that the introduction of RDDs into an individual's IL12RB1 mRNA repertoire is a novel determinant of IL12/23 sensitivity.IL12RB1 | IL-12 | IL-23 | RNA | RDD

Cancer-associated rs6983267 SNP and its accompanying long noncoding RNACCAT2induce myeloid malignancies via unique SNP-specific RNA mutations

“…However, with the advent of the Human Genome Project and the discovery of noncoding RNAs, this simplistic concept has been repeatedly challenged. DNA-RNA discrepancies have been previously reported: peripheral blood mononuclear cells (Ju et al 2011), immortalized B cells (Peng et al 2012), at the interleukin-12 receptor β1 (IL-12Rβ1) locus in peripheral blood mononuclear cells (Turner et al 2015), and at three specific loci in the human mitochondrial DNA from different cell types (Bar-Yaacov et al 2013). Notably, these DNA-RNA discrepancies have only been reported in normal tissues and their incidence in human diseases is still unknown.…”

Human IL12RB1 expression is allele-biased and produces a novel IL12 response regulator

“…To determine if IL12RB1 expression in the lungs is allele biased, we deep sequenced IL12RB1 gDNA and mRNA from human lung specimens, determined each donor genotype at eleven polymorphic positions in the IL12RB1 gene, and then used this information to educe the allelic origin of IL12RB1 mRNA in the same specimen. Deep sequencing was done using the Ion Torrent platform as previously described 43 ; the average IL12RB1 gDNA and mRNA read depths across all samples were 2907× and 13222×, respectively ( supplemental TABLE S2 ). To determine a donor’s genotype, we queried their gDNA sequence at eleven polymorphic sites in the IL12RB1 gene (chromosome 19 positions 18170384, 18170755, 18180413, 18180451, 18186575, 18186618, 18188408, 18191664, 18192977, 18194255 and 18197635), and whether they were heterozygous (i.e.…”

“…Genomic DNA (gDNA) and messenger RNA (mRNA) were extracted from human tissues and cell lines using the AllPrep DNA/RNA method (Qiagen, Germantown, MD). We performed PCR amplification and Ion Torrent sequencing of IL12RB1 gDNA/mRNA per our previously reported methods 43 . Single nucleotide polymorphisms (SNPs) in the donor IL12RB1 gDNA sequence were identified by comparing the donor gDNA sequence to the reference genome build Hg19.…”

RNA–DNA sequence differences in Saccharomyces cerevisiae

“…Recently, hundreds of thousands of ADAR-mediated editing sites have been identified in human cells (Kawahara et al 2004;Ju et al 2011;Alon et al 2012;Chen et al 2012;Peng et al 2012;Silberberg et al 2012;Vesely et al 2012;Chen 2013;Wang et al 2013;Bazak et al 2014). Furthermore, we and others have found that there are other types of RNA-DNA sequence differences (RDDs) that are unlikely to be mediated by these deaminases (Li et al 2011;Bahn et al 2012;Bar-Yaacov et al 2013;Rubio et al 2013;Turner et al 2015). These events are found in normal cells, and altered patterns of RDDs were found in neurologic diseases (van Leeuwen et al 1998;Silberberg et al 2012;Krestel et al 2013;Wang et al 2014) and in cancers (Klimek-Tomczak et al 2006;Martinez et al 2008;Lee et al 2013;Avesson and Barry 2014;Han et al 2014;Niavarani et al 2015).…”

“…The first published work we know of is a G-to-A site in WT1, Wilms tumor 1 (Sharma et al 1994). Subsequently RDD sites in brain tissues from Alzheimer's and Down syndrome patients (van Leeuwen et al 1998) and in other human cells were identified (Ju et al 2011;Bahn et al 2012;Silberberg et al 2012;Turner et al 2015;Zhang et al 2015). A recent paper suggests that APOBEC3A is the protein that mediates G-to-A RDD in WT1 (Niavarani et al 2015).…”