Single-cell multi-omics in the study of digestive system cancers

Shuang Zhou; Nanfei Lin; Liying Yu; Xiaoshan Su; Zhenlong Liu; Xiaowan Yu; Hongzhi Gao; Shu Lin; Yiming Zeng

doi:10.1016/j.csbj.2023.12.007

Single-cell multi-omics in the study of digestive system cancers

Comput Struct Biotechnol J. 2023 Dec 12:23:431-445. doi: 10.1016/j.csbj.2023.12.007. eCollection 2024 Dec.

Authors

Shuang Zhou^{1

2}, Nanfei Lin², Liying Yu², Xiaoshan Su³, Zhenlong Liu⁴, Xiaowan Yu⁵, Hongzhi Gao², Shu Lin^{6

7}, Yiming Zeng^{3

8

9}

Affiliations

¹ The Second Clinical Medical School of Fujian Medical University, Quanzhou, Fujian Province, China.
² The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
³ Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China.
⁴ Lady Davis Institute for Medical Research, Jewish General Hospital, & Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada.
⁵ Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
⁶ Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
⁷ Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.
⁸ Fujian Provincial Key Laboratory of Lung Stem Cells, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
⁹ Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, China.

Abstract

Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.

Keywords: Digestive system cancer; Heterogeneity; Single-cell omics; Single-cell sequencing (SCS); Single-cell transcriptomics (ST); Tumor microenvironment (TME).

Publication types

Review