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Updated: Jun 10, 2025
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Analysis of SLC genes alternative splicing identifies the SLC7A6 RI isoform as a therapeutic target for colorectal
Chao Sun1,2, Boning Zeng1,2, Jilong Zhou1
1Department of Pharmacy, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China.
Abstract:
Alternative splicing (AS), a crucial mechanism in post-transcriptional regulation, has been implicated in diverse cancer processes. Several splicing variants of solute carrier (SLC) transporters reportedly play pivotal roles in tumorigenesis and tumor development. However, an in-depth analysis of AS landscapes of SLCs in colon adenocarcinoma (COAD) is lacking. Herein, we analyzed data from The Cancer Genome Atlas and identified 1215 AS events across 243 SLC genes, including 109 differentially expressed AS (DEAS) events involving 62 SLC genes in COAD. Differentially spliced SLCs were enriched in biological processes, including transmembrane transporter activity, transporter activity, ferroptosis, and choline metabolism. In patients with COAD, tumor tissues exhibited higher expression of longer mitochondrial carrier SLC25A16 isoforms than adjacent normal tissues, consistent with bioinformatics analysis. Protein-coding sequences and transmembrane helices of survival-related DEAS were predicted, revealing that shifts in splicing sites altered the number and structure of their transmembrane proteins. We developed a prognostic risk model based on the screened 6-SLC-AS (SLC7A6_RI_37208 (SLC7A6-RI), SLC11A2_AP_21724, SLC2A8_ES_87631, SLC35B1_AA_42317, SLC39A11_AD_43204, and SLC7A8_AP_26712). Knockdown of the intronic region of SLC7A6-RI isoform enhanced colon cancer cell proliferation. In vivo, knockdown of the intronic region of SLC7A6-RI isoform enhanced tumor growth in colon cancer. Mechanistically, si-SLC7A6-RI isoform exerted oncogenic effects by activating the PI3K-Akt-mTOR signaling pathway and promoting cell proliferation, evidenced by increased expression of key regulators Phosphorylated Mammalian Target of Rapamycin (p-mTOR) and a cell proliferation marker Proliferating Cell Nuclear Antigen (PCNA) using western blotting. Our study elucidated SLC-AS in COAD, highlighting its potential as a prognostic and therapeutic target and emphasizing the suppressive influence of SLC7A6-RI in colon cancer progression.
Insights
Alternative splicing in solute carrier (SLC) transporters impacts colon cancer. A new study reveals SLC7A6-RI isoform suppresses colon cancer progression by inhibiting PI3K-Akt-mTOR signaling.
Area of Science:
- Genomics and Molecular Biology
- Cancer Research
- Biochemistry
Background:
- Alternative splicing (AS) is a key post-transcriptional regulation mechanism involved in various cancer processes.
- Splicing variants of solute carrier (SLC) transporters are implicated in tumorigenesis, but their role in colon adenocarcinoma (COAD) remains underexplored.
Purpose of the Study:
- To comprehensively analyze the alternative splicing landscape of SLC genes in colon adenocarcinoma (COAD).
- To identify differentially expressed AS events and their associated biological processes in COAD.
- To develop a prognostic model and investigate the functional role of specific SLC AS events in colon cancer progression.
Main Methods:
- Analysis of The Cancer Genome Atlas (TCGA) data for AS events in 243 SLC genes in COAD.
- Bioinformatic prediction of protein-coding sequences and transmembrane helices for survival-related DEAS.
- Development of a prognostic risk model based on 6 key SLC-AS events.
- In vitro and in vivo experiments involving knockdown of SLC7A6-RI isoform.
- Western blotting to analyze PI3K-Akt-mTOR pathway activation and cell proliferation markers.
Main Results:
- Identified 1215 AS events and 109 differentially expressed AS (DEAS) events involving 62 SLC genes in COAD.
- Differentially spliced SLCs were enriched in transmembrane transporter activity, ferroptosis, and choline metabolism.
- A 6-SLC-AS prognostic model was developed.
- Knockdown of SLC7A6-RI isoform promoted colon cancer cell proliferation and tumor growth in vivo.
- SLC7A6-RI isoform activated the PI3K-Akt-mTOR pathway, increasing p-mTOR and PCNA expression.
Conclusions:
- Alternative splicing of SLC transporters plays a significant role in COAD.
- The identified SLC-AS events and the prognostic model offer potential for COAD diagnosis and prognosis.
- SLC7A6-RI isoform acts as a tumor suppressor in colon cancer, suggesting its therapeutic potential.
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