Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach

• Published in: Cell reports (Cambridge) 2023-10, Vol.42 (10), p.113236-113236, Article 113236
• Main Authors: Tsubosaka, Ayumu, Komura, Daisuke, Kakiuchi, Miwako, Katoh, Hiroto, Onoyama, Takumi, Yamamoto, Asami, Abe, Hiroyuki, Seto, Yasuyuki, Ushiku, Tetsuo, Ishikawa, Shumpei
• Format: Article
• Language: English
• Subjects: CP: Genomics; intestinal metaplasia; scRNA-seq; spatial transcriptome; stem cell; stomach
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.113236

The stomach is an important digestive organ with various biological functions. However, because of the complexity of its cellular and glandular composition, its precise cellular biology has yet to be elucidated. In this study, we conducted single-cell RNA sequencing (scRNA-seq) and subcellular-level spatial transcriptomics analysis of the human stomach and constructed the largest dataset to date: a stomach encyclopedia. This dataset consists of approximately 380,000 cells from scRNA-seq and the spatial transcriptome, enabling integrated analyses of transcriptional and spatial information of gastric and metaplastic cells. This analysis identified LEFTY1 as an uncharacterized stem cell marker, which was confirmed through lineage tracing analysis. A wide variety of cell-cell interactions between epithelial and stromal cells, including PDGFRA+BMP4+WNT5A+ fibroblasts, was highlighted in the developmental switch of intestinal metaplasia. Our extensive dataset will function as a fundamental resource in investigations of the stomach, including studies of development, aging, and carcinogenesis. [Display omitted] •Stomach cell atlas by integrated single-cell and spatial transcriptomics•LEFTY1 was shown to be a novel stem cell marker in the gastric mucosa•Signal interactions found between metaplastic epithelium and fibroblast subclass Ayumu Tsubosaka et al. develop a “stomach encyclopedia” using integrated single-cell and spatial transcriptomics. Their analyses propose LEFTY1 as a previously unidentified stem cell marker and point out diverse cell-to-cell interactions in a spatial context, especially highlighting the role of PDGFRA+BMP4+WNT5A+ fibroblasts in metaplastic processes.