Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer

Abstract

Many mammalian genes contain overlapping antisense RNAs, but the functions and mechanisms of action of these transcripts are mostly unknown. WT1 is a well-characterized developmental gene that is mutated in Wilms' tumor (WT) and acute myeloid leukaemia (AML) and has an antisense transcript (WT1-AS), which we have previously found to regulate WT1 protein levels. In this study, we show that WT1-AS is present in multiple spliceoforms that are usually expressed in parallel with WT1 RNA in human and mouse tissues. We demonstrate that the expression of WT1-AS correlates with methylation of the antisense regulatory region (ARR) in WT1 intron 1, displaying imprinted monoallelic expression in normal kidney and loss of imprinting in WT. However, we find no evidence for imprinting of mouse Wt1-as. WT1-AS transcripts are exported into the cytoplasm and form heteroduplexes with WT1 mRNA in the overlapping region in WT1 exon 1. In AML, there is often abnormal splicing of WT1-AS, which may play a role in the development of this malignancy. These results show that WT1 encodes conserved antisense RNAs that may have an important regulatory role in WT1 expression via RNA:RNA interactions, and which can become deregulated by a variety of mechanisms in cancer.

Expression and prognostic impact of lncRNAs in acute myeloid leukemia

“…The fact that lncRNA profiles were "mutually exclusive" with these mutations is suggestive of a shared effect within the epigenetic pathway. The association of the WT1-AS lncRNA with FLT3-ITD is interesting because the expression of the near WT1 protein-coding gene is also increased in this molecular subtype of CN-AML, and splicing alterations have been described for WT1-AS (41,42). It remains to be investigated whether this event represents just a coexpression phenomenon or has a truly functional role.…”

“…Alternative splicing of WT1-AS has been found in AML. Whereas the functional significance of this finding is unknown, aberrations in alternative splicing have been suggested as contributing factors in the development of various diseases including cancer (42).…”

Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value

“…WT1 is an extensively studied transcription factor essential for normal development of the urogenital system and deregulated across many cancer types 31 . In breast cancer, high mRNA levels of WT1 were reported to be associated with poor patient survival 53 and positive modulation of expression of WT1 by its antisense transcript WT1-AS 54,55 . Our observed patterns of methylation and survival support an extensive body of evidence on the tight epigenetic transcriptional regulation of WT1 and its role in breast cancer prognosis.…”

Frequency and Timing of Loss of Imprinting at 11p13 and 11p15 in Wilms' Tumor Development

“…The functions of the imprinted WT1 transcripts are still being investigated, but WT1-AS seems to stabilize WT1 coding transcripts via RNA-RNA interactions (37) and AWT1 retains transcriptional regulatory activity but with different effects on some target genes and has paradoxical growth-promoting activity compared with the canonical WT1 proteins (38). Thus, overexpression of these novel WT1 transcripts could contribute to the development of WT and may be caused by somatic genetic defects (11p13 LOH), somatic epigenetic alterations (WT1 ARR hypomethylation), or germ-line genetic defects (paternal uniparental disomy in Beckwith-Wiedemann syndrome).…”