Exon Skipping in the RET Gene Encodes Novel Isoforms That Differentially Regulate RET Protein Signal Transduction

Abstract

Rearranged during transfection (RET), a receptor tyrosine kinase that is activated by the glial cell line-derived neurotrophic factor family ligands (GFLs), plays a crucial role in the development and function of the nervous system and additionally is required for kidney development and spermatogenesis. RET encodes a transmembrane receptor that is 20 exons long and produces two known protein isoforms differing in C-terminal amino acid composition, referred to as RET9 and RET51. Studies of human pheochromocytomas identified two additional novel transcripts involving the skipping of exon 3 or exons 3, 4, and 5 and are referred to as RET ⌬E3 and RET ⌬E345 , respec- higher baseline autophosphorylation, specifically on the catalytic tyrosine, Tyr 905 , and also on one of the most important signaling residues, Tyr 1062 . These data provide the first evidence for a physiologic role of these isoforms in RET pathway function.RET is a receptor tyrosine kinase that is critical for kidney morphogenesis, spermatogenesis, and development of the nervous system (1-4). RET is activated by a family of four growth factors known as the glial cell line-derived neurotrophic factor (GDNF) 2 family ligands (GFLs), which includes GDNF, neurturin, artemin, and persephin (1). Each GFL binds to one of four cognate glycosylphosphatidylinositol-anchored co-receptors known as the GDNF family receptor ␣s (GFR␣s) (2, 5). The GFL-GFR␣ complex binds to RET, inducing RET dimerization and subsequent autophosphorylation on multiple tyrosine residues within the intracellular tyrosine kinase domain. This enhances tyrosine kinase activity and initiates the association of adaptor proteins and enzymes that trigger multiple second messenger cascades (6). The presence of two major Ret isoforms, RET9 and RET51, has been extensively described in the literature, and a third isoform, RET43, has also been observed in humans (7-9). Ret is 20 exons long, and Ret9 and Ret51 transcripts differ in alternative splicing of intron 19. Intron 19 in the Ret51 transcript is excised properly, whereas, in the Ret9 transcript, the intron is retained, changing the reading frame and inserting a premature stop codon into the amino acid sequence. This creates a unique nine-amino acid C-terminal sequence for RET9 and a unique 51-amino acid C-terminal sequence for RET51. Interestingly, these two different isoforms display marked differences in their degradation and function (7, 10, 11).Three additional Ret transcripts have been reported in various tumor sources as well as adult human tissues (12). These novel transcripts are a product of exon skipping in the 5Ј region of RET, which encodes for the extracellular domain of the protein. Skipping of exons 3 (RET ⌬E3 ) or exons 3, 4 and 5 (RET ⌬E345) gives rise to transcripts that encode for full-length Ret proteins but with deletions in the extracellular domain, specifically cadherin-like domain 1 (CLD1) or CLD1-3, respectively. These deletions are hypothesized to change the extracellular domain structure as well as binding to GFL-GFR...

Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice

“…In addition, cell membrane and receptor were also enriched in Figure 3B . For instance, Ret is a crucial gene that plays an important role in the development and function of the nervous system ( Gabreski et al, 2016 ), as well as driving HSCs survival. Ablation of Ret cannot only impair the number of HSCs but also influences its normal differentiation potential ( Fonseca-Pereira et al, 2014 ).…”

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data

“…Others attempt to estimate junctions de novo from short reads ( Trapnell et al 2009 ; Dobin et al 2013 ; Kim et al 2013a ). The literature indicates that the vast majority of novel isoforms are assembled from currently annotated exons ( Booms et al 1999 ; Hide et al 2001 ; Zhou et al 2010 ; Lim et al 2011 ; Eswaran et al 2013 ; Kim et al 2013b ; Gabreski et al 2016 ; Nellore et al 2016 ; Tardaguila et al 2018 ). By designing a junction catalog that includes junctions created from all possible logical combinations of existing exons, and mapping to that catalog more true novel junctions are mapped than by mapping to the genome with a splice aware aligner.…”

“…Nellore et al ( Nellore et al 2016 ) studied more than 20,000 human RNA-seq samples derived from multiple cell types and found that that only 3.5% of junctions are not derivable in from existing genome annotations in some form, and that 81.4% are from already annotated transcripts. We also note that in the literature, there are examples of identified novel transcripts of several genes that are comprised of new combinations of known splice sites, frequently those that are the result of a variant inducing an exon-skipping event ( Booms et al 1999 ; Hide et al 2001 ; Zhou et al 2010 ; Lim et al 2011 ; Eswaran et al 2013 ; Kim et al 2013b ; Gabreski et al 2016 ). This suggests that an augmented reference consisting of probable new events based on the set of existing transcripts can be developed.…”

Artemin and an Artemin-Derived Peptide, Artefin, Induce Neuronal Survival, and Differentiation Through Ret and NCAM

“…The third isoform of RET, RET43, was described in humans (Carter et al, 2001). Recently, two additional functional isoforms of RET that lack either exon 3 or exons 3–5 were described in CNS (Gabreski et al, 2016).…”