Elizabeth Donato

Colorectal cancer develops through a normal-adenoma-carcinoma sequence, yet only 5-10% of adenomas progress to malignancy, and the cellular programs governing that sequence remain poorly defined. Here we generate a spatial multi-omics atlas of human colon adenomas, combining Visium CytAssist and protein co-detection across 24 nonadvanced and advanced tubular adenomas with single-cell resolution Xenium Prime 5K profiling of 101 patient-matched normal, adenoma, and carcinoma cores from 16 patients. Integrating whole-transcriptome and 31-plex protein data identifies nine spatial clusters and two dysplastic epithelial populations that co-express stemness, proliferation, and senescence programs. These programs occupy a shared, spatially confined epithelial niche that expands from adenoma to carcinoma. Spatial analysis revealed GDF15, a senescence-associated secretory factor, mediated the coupling between senescence and stemness in advanced adenomas, and that GDF15-high epithelium locally excludes CD8+ T cells in adenoma and, more broadly, in carcinoma. These findings position senescence as a spatially instructive rather than merely tumor-suppressive program during colorectal carcinogenesis and suggest GDF15 might be a potential candidate target for cancer prevention and interception in the colon. Statement of Significance: Spatial multi-omics identifies spatially co-localized senescence and stemness programs in dysplastic epithelium during colorectal tumorigenesis and links GDF15-associated niches to CD8-positive T-cell exclusion, nominating GDF15 for colorectal cancer prevention and interception strategies. Conflicts of interests: The authors declare the following competing interests: W.M.G.: Consulting for Guardant Health, Research support from Lucid Diagnostics; E.W.N.: Co-founder, advisor, and shareholder of ImmunoScape. All the other authors declare no competing interests.

Supplemental Table 2 Shows a summary of Translational Research Program in Colorectal Cancer Disparities physical repository of colorectal cancer patients stratified by case-control status

Supplemental Figure 1. Shows the process for requesting data from Alaska Native peoples from the Alaska Native Tribal Health Consortium and accessible via the NIH dbGaP data repository.

Supplemental Table 1 shows a Summary of Translational Research Program in Colorectal Cancer Disparities virtual repository of colorectal cancer patients.

Background: Cancer incidence and mortality vary substantially across populations. The Translational Research Program in Cancer Differences across Populations (TRPCDP) was established in 2020 to address differences in cancer incidence and mortality rates within the United States, with a particular focus on colorectal cancer. Methods: The TRPCDP centralized data acquisition and harmonization across three sites in the United States to create a well-annotated resource of colorectal cancer tumors across four populations: African American/Black, Alaska Native, Hispanic/Latino/Latina, and non-Hispanic White. Using a case–control framework, patients with lethal colorectal cancer were matched to two controls with nonlethal colorectal cancer. Formalin-fixed, paraffin-embedded tumor and normal tissue were retrieved and sent for centralized pathology review, followed by DNA and RNA extraction and tissue microarray development. Multiomics and spatial profiling are underway to evaluate the transcriptome, proteome, and microbiome. Patient demographic and clinical data were obtained by medical record review, patient self-report, or linkage to cancer registries. Additional health-related factors were assessed using geospatial linkage. Results: The virtual biorepository includes 7,181 patients [African American (n = 1,345), Alaska Native (n = 1,640), Hispanic (n = 1,659), and non-Hispanic White (n = 2,537)]. Tissue blocks (1,594 tumor and 728 normal colon samples) were selected for 938 patients. To date, DNA and RNA have been extracted (n = 831), and tissue microarrays have been constructed (n = 414). Transcriptomic analysis, spatial tumor profiling (multiplex immunofluorescence, PhenoCycler, and GeoMx), and microbiome data (16S rRNA sequencing and digital droplet PCR) are available. Conclusions: The TRPCDP has developed a clinically annotated biorepository for future molecular epidemiology studies. Impact: The TRPCDP is a unique program that supports collaborative research, community engagement, and pipeline development for the next generation of scientists.

Mechanisms for Helicobacter pylori (Hp)-driven stomach cancer are not fully understood. In a transgenic mouse model of gastric preneoplasia, concomitant Hp infection and induction of constitutively active KRAS (Hp+KRAS+) alters metaplasia phenotypes and elicits greater inflammation than either perturbation alone. Gastric single-cell RNA sequencing showed that Hp+KRAS+ mice had a large population of metaplastic pit cells that expressed the intestinal mucin Muc4 and the growth factor amphiregulin. Flow cytometry and IHC-based immune profiling revealed that metaplastic pit cells were associated with macrophage and T-cell inflammation. Accordingly, expansion of metaplastic pit cells was prevented by gastric immunosuppression and reversed by antibiotic eradication of Hp. Finally, MUC4 expression was significantly associated with proliferation in human gastric cancer samples. These studies identify an Hp-associated metaplastic pit cell lineage, also found in human gastric cancer tissues, whose expansion is driven by Hp-dependent inflammation.Significance:Using a mouse model, we have delineated metaplastic pit cells as a precancerous cell type whose expansion requires Hp-driven inflammation. In humans, metaplastic pit cells show enhanced proliferation as well as enrichment in precancer and early cancer tissues, highlighting an early step in the gastric metaplasia to cancer cascade.

Mechanisms for Helicobacter pylori (Hp)-driven stomach cancer are not fully understood. In a transgenic mouse model of gastric preneoplasia, concomitant Hp infection and induction of constitutively active KRAS (Hp+KRAS+) alters metaplasia phenotypes and elicits greater inflammation than either perturbation alone. Gastric single-cell RNA sequencing showed that Hp+KRAS+ mice had a large population of metaplastic pit cells that expressed the intestinal mucin Muc4 and the growth factor amphiregulin. Flow cytometry and IHC-based immune profiling revealed that metaplastic pit cells were associated with macrophage and T-cell inflammation. Accordingly, expansion of metaplastic pit cells was prevented by gastric immunosuppression and reversed by antibiotic eradication of Hp. Finally, MUC4 expression was significantly associated with proliferation in human gastric cancer samples. These studies identify an Hp-associated metaplastic pit cell lineage, also found in human gastric cancer tissues, whose expansion is driven by Hp-dependent inflammation.Significance:Using a mouse model, we have delineated metaplastic pit cells as a precancerous cell type whose expansion requires Hp-driven inflammation. In humans, metaplastic pit cells show enhanced proliferation as well as enrichment in precancer and early cancer tissues, highlighting an early step in the gastric metaplasia to cancer cascade.

Mechanisms for Helicobacter pylori (Hp)-driven stomach cancer are not fully understood. In a transgenic mouse model of gastric preneoplasia, concomitant Hp infection and induction of constitutively active KRAS (Hp+KRAS+) alters metaplasia phenotypes and elicits greater inflammation than either perturbation alone. Gastric single-cell RNA sequencing showed that Hp+KRAS+ mice had a large population of metaplastic pit cells that expressed the intestinal mucin Muc4 and the growth factor amphiregulin. Flow cytometry and IHC-based immune profiling revealed that metaplastic pit cells were associated with macrophage and T-cell inflammation. Accordingly, expansion of metaplastic pit cells was prevented by gastric immunosuppression and reversed by antibiotic eradication of Hp. Finally, MUC4 expression was significantly associated with proliferation in human gastric cancer samples. These studies identify an Hp-associated metaplastic pit cell lineage, also found in human gastric cancer tissues, whose expansion is driven by Hp-dependent inflammation. Significance: Using a mouse model, we have delineated metaplastic pit cells as a precancerous cell type whose expansion requires Hp-driven inflammation. In humans, metaplastic pit cells show enhanced proliferation as well as enrichment in precancer and early cancer tissues, highlighting an early step in the gastric metaplasia to cancer cascade.

Genes driving the subclustering of the major gastric epithelial cell types.

Description of the mouse samples used for single-cell RNA-sequencing.