Gastrointestinal (GI) cancers account for 26% of the global cancer incidence and 35% of all cancer-related deaths. Although the top 5 cancers in this group (i.e., colorectum, stomach, liver, esophagus, and pancreas) are diverse in specific function and etiology, they are linked through the same system and the majority of them stem from epithelial cells. The genetic and phenotypic heterogeneity among cancer cells and the interplay between them and the tumor microenvironment are two fundamental elements at play in cancer initiation, progression and response to therapy. We are now able to study them at unprecedented scales thanks to the development of technologies able to capture expression levels and chromatin status at the single cell level, even alongside spatial annotations. It is now possible to elucidate the functional impacts of gene expression changes in the context of tumor development, progression, and response to treatment both within and between cell types.This collection aims to bring together current research that exploits single cell technologies in the context of GI cancers; to offer an integrated view that could help identify mechanisms specific to single tumor types or recurring among them.The aim of this Research Topic is to highlight what is currently known about the single cell RNA expression and DNA accessibility landscapes in GI cancer based on different omic and multi-omic technologies. Both systematic reviews and original research, alongside re-analyses of already published datasets with new computational approaches will be welcomed in this collection. Specific topics that are of interest included, but are not limited to:• single cell RNA-seq studies in GI cancer• spatial transcriptomic studies in GI cancer• single cell ATAC-seq in GI cancer• comparisons between gene expression in tumor microenvironment and cancer cells• single cell gene expression changes throughout disease progression and in response to treatment• CITE-seq for detailed characterization of tumor heterogeneity and the tumor microenvironment• REAP-seq for simultaneous measurement of RNA and protein levels for understanding diverse cellular responses to treatments• single cell proteomics to provide insights into functional states and potential therapeutic targets• single cell metabolomics for the understanding of tumor metabolism and potential metabolic vulnerabilities• G&T-seq for providing insights into how genetic mutations influence gene expression patterns• single cell multi-omics to integrate various single cell technologies for unraveling complex biological processes and disease mechanisms
Gastrointestinal (GI) cancers account for 26% of the global cancer incidence and 35% of all cancer-related deaths. Although the top 5 cancers in this group (i.e., colorectum, stomach, liver, esophagus, and pancreas) are diverse in specific function and etiology, they are linked through the same system and the majority of them stem from epithelial cells. The genetic and phenotypic heterogeneity among cancer cells and the interplay between them and the tumor microenvironment are two fundamental elements at play in cancer initiation, progression and response to therapy. We are now able to study them at unprecedented scales thanks to the development of technologies able to capture expression levels and chromatin status at the single cell level, even alongside spatial annotations. It is now possible to elucidate the functional impacts of gene expression changes in the context of tumor development, progression, and response to treatment both within and between cell types.This collection aims to bring together current research that exploits single cell technologies in the context of GI cancers; to offer an integrated view that could help identify mechanisms specific to single tumor types or recurring among them.The aim of this Research Topic is to highlight what is currently known about the single cell RNA expression and DNA accessibility landscapes in GI cancer based on different omic and multi-omic technologies. Both systematic reviews and original research, alongside re-analyses of already published datasets with new computational approaches will be welcomed in this collection. Specific topics that are of interest included, but are not limited to:• single cell RNA-seq studies in GI cancer• spatial transcriptomic studies in GI cancer• single cell ATAC-seq in GI cancer• comparisons between gene expression in tumor microenvironment and cancer cells• single cell gene expression changes throughout disease progression and in response to treatment• CITE-seq for detailed characterization of tumor heterogeneity and the tumor microenvironment• REAP-seq for simultaneous measurement of RNA and protein levels for understanding diverse cellular responses to treatments• single cell proteomics to provide insights into functional states and potential therapeutic targets• single cell metabolomics for the understanding of tumor metabolism and potential metabolic vulnerabilities• G&T-seq for providing insights into how genetic mutations influence gene expression patterns• single cell multi-omics to integrate various single cell technologies for unraveling complex biological processes and disease mechanisms