Fig. 4: Clonal and molecular characterization of dysplasia and its similarity to esophageal adenocarcinoma.

a UMAP of scRNA-seq of a single Barrett’s esophagus biopsy from Patient 6 containing Barrett’s esophagus and dysplastic cells. b Heatmap showing mitochondrial DNA variant allele frequencies across cells, with hierarchical clustering revealing clonal structure. Cell types are color-coded (BE = Barrett’s esophagus, DYSP = dysplasia). Dysplastic cells are subsampled down to 25% of cells for visualization. c Gene expression heatmap of differentially expressed genes between dysplasia origin clone (containing 15153 G > A mutation) and other BE cells. d UMAPs from (A) featuring the expression of LGR5 and NOTUM. e RNA FISH HCR probing for LGR5 and NOTUM performed once on a fresh frozen tissue sections of a Barrett’s esophagus biopsy from Patient 6. f) Schematic illustrating the sequencing workflow for the cells isolated from a single Barrett’s esophagus biopsy taken from Patient 6. g Copy number analysis from whole-exome sequencing of the same cell population from Patient 6 that underwent scRNA-seq; featured is chromosome 9, highlighting the loss of CKDN2A. h Schematics of mutations detected in TP53⁶³ and APC⁶⁴ proteins by whole-exome sequencing. i Analysis of the contribution of mRNA signals from Barrett’s esophagus and dysplastic cell states to the bulk transcriptomes of esophageal adenocarcinoma tumors from TCGA. Dysp_1-Dysp_3 correspond to gene signatures specific to the dysplastic cells from Patient 6. j Heatmap shows genes differentially expressed within the dysplastic cells from Patient 6 grouped by clusters corresponding to the gene signatures in (i).