A functional network of gastric-cancer-associated splicing events controlled by dysregulated splicing factors

Abstract

Comprehensive understanding of aberrant splicing in gastric cancer is lacking. We RNA-sequenced 19 gastric tumor–normal pairs and identified 118 high-confidence tumor-associated (TA) alternative splicing events (ASEs) based on high-coverage sequencing and stringent filtering, and also identified 8 differentially expressed splicing factors (SFs). The TA ASEs occurred in genes primarily involved in cytoskeletal organization. We constructed a correlative network between TA ASE splicing ratios and SF expression, replicated it in independent gastric cancer data from The Cancer Genome Atlas and experimentally validated it by knockdown of the nodal SFs (PTBP1, ESRP2 and MBNL1). Each SF knockdown drove splicing alterations in several corresponding TA ASEs and led to alterations in cellular migration consistent with the role of TA ASEs in cytoskeletal organization. We have therefore established a robust network of dysregulated splicing associated with tumor invasion in gastric cancer. Our work is a resource for identifying oncogenic splice forms, SFs and splicing-generated tumor antigens as biomarkers and therapeutic targets.

Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial–Mesenchymal Transition Subtypes Associated with Survival

“…Spliced genes were associated with cell adhesion and the cytoskeleton (e.g., SMTN, TPM1, PDLIM7, ADAM15), translational control (e.g., RPS24), cell proliferation (e.g., PDGFA, KRAS), cell metabolism (e.g., AFMID, ECHDC2, INOE80, GPT), or immune cell signaling (e.g., CD47). Our analysis also detected a skipped exon in the KRAS oncogene that was previously identified in a smaller cohort of gastric cancer patients (30), as well as mutually exclusive exons in AFMID detected in hepatocellular carcinoma (31).…”

“…Although AS is a key regulatory mechanism that impacts virtually all cellular processes, few studies have explored the role of AS in gastric cancer (30,(40)(41)(42), and even fewer studies have investigated the utility of AS-based patient classification (11). Given this, we i) systematically profiled the AS landscape in gastric cancer, ii) identified RBPs that regulate tumor subtype-specific AS events, and iii) devised a patient classification scheme based on variable AS events or their regulatory RBPs.…”

A tumor-associated splice-isoform of MAP2K7 drives dedifferentiation in MBNL1-low cancers via JNK activation

“…Gene Ontology (GO) term analysis of MBNL1 correlated TA-ASEs in MBNL1-low cancers from Sebestyén et al ( 20 ) showed the enrichment of “actin cytoskeleton organization” GO: 0030036 ( P value = 4.38 × 10 −06 ) as the key biological process enriched. Our previous work also showed that MBNL1 is one of the key splice factors that regulate an AS program in gastric cancer involved in actin cytoskeleton reorganization associated with invasive/metastatic properties of cancer ( 28 ). Together, this suggests that MBNL1 down-regulation-mediated AS affects important cellular processes involved in cancer.…”

“…Corollary to this analysis, we compared the high-confidence ASEs with MBNL1 correlated tumor-associated (TA)-ASEs computed by Sebestyén et al and Cheng et al ( 20 , 28 ). We found 17 overlapping ASEs between our high-confidence ASEs and MBNL1-correlated TA-ASEs from the above studies ( Dataset S1, Table S6 ).…”

Tumorigenic de-differentiation: the alternative splicing way

“…Transcriptomic studies have established cancer-associated splicing as a common feature of cancer. 1 , 9 However, how individual splicing alterations impact protein function in order to contribute to tumorigenesis is largely understudied. In our work, we discovered that a discrete set of 12 ‘Embryonic stem cell (ESC)-differential’ splice isoforms (described in 10 ) are upregulated in MBNL1-low cancers.…”