Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer

Genome Med. 2023 Sep 21;15(1):76. doi: 10.1186/s13073-023-01226-y.

Qiang Sun ^# ¹ ² ³ ⁴, Ye Han ^# ⁵, Jianxing He ^# ¹, Jie Wang ¹, Xuejie Ma ¹, Qianqian Ning ¹, Qing Zhao ¹, Qian Jin ¹, Lili Yang ¹, Shuang Li ⁴, Yang Li ⁶, Qiaoming Zhi ⁷, Junnian Zheng ⁸ ⁹, Dong Dong ¹⁰ ¹¹ ¹²

Affiliations

1 Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China.
2 Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China.
3 Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China.
4 Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
5 Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
6 International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
7 Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China. strexboy@163.com.
8 Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China. jnzheng@xzhmu.edu.cn.
9 Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China. jnzheng@xzhmu.edu.cn.
10 Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China. ddong@xzhmu.edu.cn.
11 Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China. ddong@xzhmu.edu.cn.
12 Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China. ddong@xzhmu.edu.cn.
# Contributed equally.

PMID: 37735421 DOI: 10.1186/s13073-023-01226-y

Abstract

Background: Alternative splicing complexity plays a vital role in carcinogenesis and Cancer progression. Improved understanding of novel splicing events and the underlying regulatory mechanisms may contribute new insights into developing new therapeutic strategies for colorectal Cancer (CRC).

Methods: Here, we combined long-read Sequencing technology with short-read RNA-seq methods to investigate the transcriptome complexity in CRC. By using experiment assays, we explored the function of newly identified splicing isoform TIMP1 Δ4-5. Moreover, a CRISPR/dCasRx-based strategy to induce the TIMP1 exon 4-5 exclusion was introduced to inhibit neoplasm growth.

Results: A total of 90,703 transcripts were identified, of which > 62% were novel compared with current transcriptome annotations. These novel transcripts were more likely to be sample specific, expressed at relatively lower levels with more exons, and oncogenes displayed a characteristic to generate more transcripts in CRC. Clinical outcome data analysis showed that 1472 differentially expressed alternative splicing events (DEAS) were tightly associated with CRC patients' prognosis, and many novel isoforms were likely to be important determinants for patient survival. Among these, newly identified splicing isoform TIMP1 Δ4-5 was significantly downregulated in CRC. Further in vitro and in vivo assays demonstrated that ectopic expression of TIMP1 Δ4-5 significantly suppresses tumor cell growth and metastasis. Serine/arginine-rich splicing factor 1 (SRSF1) acts as a onco-splicing regulator through sustaining the inclusion of TIMP1 exon 4-5. Furthermore, CRISPR/dCasRx-based strategies designed to induce TIMP1 exon 4-5 exclusion have the potential to restrain the CRC growth.

Conclusions: This data provides a rich resource for deeper studies of gastrointestinal malignancies. Newly identified splicing isoform TIMP1 Δ4-5 plays an important role in mediating CRC progression and may be a potential therapy target in CRC.

Keywords

Alternative splicing; Colorectal cancer; Long-read sequencing; TIMP1 Δ4-5.

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