U2‐related proteins CHERP and SR140 contribute to colorectal tumorigenesis via alternative splicing regulation

Abstract

Dysregulation of calcium homeostasis endoplasmic reticulum protein (CHERP) has been implicated in several cancers, but it remains elusive how CHERP contributes to cancer cell proliferation and cancer development. Here, we observed that CHERP and its binding partner SR140 are significantly upregulated in human clinical colorectal cancer tissues (CRC). CHERP and SR140 could form a protein complex to stabilize each other. Knockdown of CHERP or SR140 triggers double‐stranded DNA breaks and cell death. Furthermore, UPF3A, the RNA surveillance factor, was identified as a splicing target of CHERP and SR140, which bind specifically to the regulated exon4 and modulate UPF3A splicing. UPF3A knockdown recapitulates CHERP/SR140 depletion both in vitro and in mice. Importantly, overexpression of UPF3A significantly rescues proliferation defect of CHERP/SR140‐depleted cells. These results confirmed that the effect of CHERP/SR140 in promoting tumorigenesis was partially mediated by UPF3A. Extending these results, upregulation of CHERP/SR140 observed in CRC remarkably parallels increased inclusion of UPF3A exon4. Together, our study clarifies how CHERP/SR140 exert an oncogenic role in CRC development partially through regulating expression of UPF3A variants.

STRAP regulates alternative splicing fidelity during lineage commitment of mouse embryonic stem cells

“…7g ). To test whether certain splicing variants could be regulated by the WD-40 domain(s) of STRAP, we performed gain-of-function assays in MEF cells using a mini-gene splicing tool, which contains UPF3A exon 4 in a SR140-dependent manner 49 . Compared to WT MEFs, the usage of exon 4 was significantly reduced in STRAP KO MEFs and could be partially rescued by overexpression of STRAP-Flag, STRAP (1–4)-Flag, and STRAP (3–4)-Flag mutants (Fig.…”

“…The primers used for subcloning are listed in Supplementary Table 10 . Plasmid SR140-HA was a gift from Dr. Ying Feng (Chinese Academy of Sciences, China) 49 . For co-IP assays, HEK293T cells were transfected with various plasmids using Lipofectamine3000 (Thermo Fisher Scientific), and lysates were subjected to co-immunoprecipitation with an anti-HA antibody (3 μg/mg lysates, Bethyl, A190-208A) and probed with either an antibody for anti-Flag (at the dilution of 1:15,000, Sigma, F3165) or anti-HA (at the dilution of 1:1000, Bethyl, A190-208A).…”

“…The primers used for subcloning are listed in Supplementary Table 10 . The UPF3A mini-gene with exons 3–5 was kindly provided by Dr. Ying Feng 49 . Mini-gene vector and STRAP truncating variants were co-transfected into MEF cell lines using Lipofectamine3000 reagent and the cells were cultured for a further 48 h until RNA isolation.…”

Molecular Characterization and Clinical Relevance of RNA Binding Proteins in Colorectal Cancer

“…*p < 0.05, **p < 0.01. endometrial carcinoma (Xing et al, 2020). UPF3A partially contributes to the effect of calcium homeostasis endoplasmic reticulum protein (CHERP) in promoting tumorigenesis in CRC (Wang Q. et al, 2019). UPF3B and other UPframeshift proteins can be interacted (Raimondeau et al, 2018).…”

Signature of gene aberrant alternative splicing events in pancreatic adenocarcinoma prognosis

“…For example, SRSF1 can direct the MYO1B gene to produce AS, which increases the tumourigenic potential of glioma cells via the PDK1 / AKT and PAK / LIMK pathways [9]. CHERP and SR140 regulate the expression of UPF3A splices in CRC by forming protein complexes [10]. In addition, the relevant alternative splicing event can even occur at the lncRNA level, and the lncRNA-PXN-AS1 splicing factor MBNL3 can produce different alternative splicing variants lncRNA-PXN-AS1-L and lncRNA-PXN-AS1-S, which bind to different parts of PXN mRNA, regulate PXN from two different directions and exert different biological functions [11].…”