Exploring the role of pyroptosis in shaping the tumor microenvironment of colorectal cancer by bulk and single-cell RNA sequencing

Chengsheng Ding; Xiao Yang; Shuchun Li; Enkui Zhang; Xiaodong Fan; Ling Huang; Zirui He; Jing Sun; Junjun Ma; Lu Zang; Minhua Zheng

doi:10.1186/s12935-023-02897-8

Exploring the role of pyroptosis in shaping the tumor microenvironment of colorectal cancer by bulk and single-cell RNA sequencing

Cancer Cell Int. 2023 May 18;23(1):95. doi: 10.1186/s12935-023-02897-8.

Authors

Chengsheng Ding^#^{1

2

3}, Xiao Yang^#^{1

2

3}, Shuchun Li^{1

2

3}, Enkui Zhang^{1

2

3}, Xiaodong Fan^{1

2

3}, Ling Huang^{1

2

3}, Zirui He^{1

2

3}, Jing Sun^{4

5

6}, Junjun Ma^{7

8

9}, Lu Zang^{10

11

12}, Minhua Zheng^{13

14

15}

Affiliations

¹ Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
² Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
³ Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China.
⁴ Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China. sj11788@rjh.com.cn.
⁵ Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. sj11788@rjh.com.cn.
⁶ Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China. sj11788@rjh.com.cn.
⁷ Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China. marsnew1997@163.com.
⁸ Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. marsnew1997@163.com.
⁹ Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China. marsnew1997@163.com.
¹⁰ Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China. zanglu@yeah.net.
¹¹ Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. zanglu@yeah.net.
¹² Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China. zanglu@yeah.net.
¹³ Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China. zhengmhrjhospital@163.com.
¹⁴ Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. zhengmhrjhospital@163.com.
¹⁵ Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China. zhengmhrjhospital@163.com.

^# Contributed equally.

Abstract

Background: Emerging studies have shown that pyroptosis plays a non-negligible role in the development and treatment of tumors. However, the mechanism of pyroptosis in colorectal cancer (CRC) remains still unclear. Therefore, this study investigated the role of pyroptosis in CRC.

Methods: A pyroptosis-related risk model was developed using univariate Cox regression and LASSO Cox regression analyses. Based on this model, pyroptosis-related risk scores (PRS) of CRC samples with OS time > 0 from Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database were calculated. The abundance of immune cells in CRC tumor microenvironment (TME) was predicted by single-sample gene-set enrichment analysis (ssGSEA). Then, the responses to chemotherapy and immunotherapy were predicted by pRRophetic algorithm, the tumor immune dysfunction and exclusion (TIDE) and SubMap algorithms, respectively. Moreover, the Cancer Therapeutics Response Portal (CTRP) and PRISM Repurposing dataset (PRISM) were used to explore novel drug treatment strategies of CRC. Finally, we investigated pyroptosis-related genes in the level of single-cell and validated the expression levels of these genes between normal and CRC cell lines by RT-qPCR.

Results: Survival analysis showed that CRC samples with low PRS had better overall survival (OS) and progression-free survival (PFS). CRC samples with low PRS had higher immune-related gene expression and immune cell infiltration than those with high PRS. Besides, CRC samples with low PRS were more likely to benefit from 5-fluorouracil based chemotherapy and anti-PD-1 immunotherapy. In novel drug prediction, some compounds such as C6-ceramide and noretynodrel, were inferred as potential drugs for CRC with different PRS. Single-cell analysis revealed pyroptosis-related genes were highly expressed in tumor cells. RT-qPCR also demonstrated different expression levels of these genes between normal and CRC cell lines.

Conclusions: Taken together, this study provides a comprehensive investigation of the role of pyroptosis in CRC at the bulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) levels, advances our understanding of CRC characteristics, and guides more effective treatment regimens.

Keywords: Colorectal cancer; Immunotherapy; Pyroptosis; Single-cell analysis; Tumor microenvironments.

Abstract

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