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 shows the allele frequencies of mtDNA mutations within the Barrett’s esophagus cells in the adjacent UMAP. (C) Heatmap shows the allele frequencies of mtDNA mutations within the dysplastic cells in the adjacent UMAP; UMAPs of the Barrett’s esophagus and dysplastic cells in (A) colored by the allele frequencies of the dysplastic mtDNA mutations. (D) UMAPs from (A) featuring the expression of LGR5 and NOTUM. (E) RNA FISH HCR probing for LGR5 and NOTUM in 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 TP53⁵⁴ and APC⁵⁵ 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 is the set of mRNA signals from the dysplastic cells in (A); Dysp_2-Dysp_4 correspond to mRNA signals specific to the remaining three dysplastic biopsies. (J) There were three cell states (or subclusters) within the dysplastic tissue from patient 6. For the cases where at least 3/10 of the bulk transcriptome was contributed by mRNA signals from the dysplastic tissue from patient 6, highlighted is the fraction of that dysplastic signal that each of three cell states accounted for. The heatmap shows genes that were differentially expressed within the three cell states.