Fig 2: Intratumoral heterogeneity observed across organ-derived cell lines. Bulk RNA analysis of the organ-derived cell lines revealed distinct expression patterns relevant to A cellular metabolism, B extracellular remodeling of the microenvironment, C stem cell signatures, and D cellular dormancy among the cell lines. Clusters were assigned based on CD44 expression and the metastatic origin of each cell line as shown in the lower right

Fig 3: CD44 expression correlates with different transcriptome patterns in organ-derived cell lines. Differentially expressed genes for A CD44high (red) and CD44low (blue) EpCAMhigh cells (across all samples) were used to generate GO terms. CD44low cells exhibited high levels of expression for genes relevant to tumor microenvironment remodeling and tumor dormancy markers. CD44high cells exhibited higher levels of gene expression associated with GO terms related to cellular proliferation, tumor aggression, and EMT. Differentially expressed genes and associated GO terms for CD44high/low EpCAMhigh cells from B lymph nodes and C lungs are also shown. For A–C, the − log(P value) scale applies to both the CD44high (red) and CD44low (blue) samples

Fig 4: The identification of a de novo TNBC‐CTC transcriptomic signature (A) Graph displaying pattern of up‐ and downregulated genes of TNBC patient‐isolated de novo CTCs (CD45−/CD34−/CD73−/CD90−/CD105− but CK+/CD44+/CD24− cells) (GSE99394, n = 4) vs pTNBCs (GSE76250, n = 31); (B) scatter plot showing global gene expression changes in TNBC‐isolated de novo CTCs; (C) hierarchical clustering showing distinct transcriptomic signature of TNBC de novo CTCs vs pTNBCs (FC = 8; P‐value = 005) Two‐way ANOVA test was performed to calculate FC and P‐value; (D‐F) table displaying significantly altered top (D) canonical pathways, (E) functional annotation, and (F) upstream transcription regulators of de novo CTCs vs pTNBCs.

Fig 5: Deletion of genes in naive T cells with minimal off-target editing using CHIME. a Quantification of thymic subsets (CD4– CD8–, CD4– CD8+, CD4+ CD8–, CD4+ CD8+) from WT or Cas9 + control sgRNA chimeric mice. b Representative flow cytometry plots of CD44, CD62L, and c CD69 from splenic CD8+ T cells. d Quantification of naïve status of CD8+ T cells in (b, c). e Flow cytometry plots of PD-1 expression in CD4+ T cells (top panel) and CD8+ T cells (bottom panel) from representative non-targeting control sgRNA or Pdcd1 sgRNA chimeras following αCD3/CD28 stimulation. f Quantification of PD-1 expression for two control and three Pdcd1 sgRNAs from (e). g TIDE assay on naïve CD4+ and CD8+ T cells for three Pdcd1 targeting sgRNAs. h, i TIDE assay on naïve (h) CD4+ and (i) CD8+ T cells designed to detect the top three predicted off-target sites (1st, 2nd, 3rd) for three Pdcd1 targeting sgRNAs. Dashed line represents the aberrant sequence (%) when comparing two non-targeting control sgRNAs (background aberrant sequence). All experiments had at least three biological replicate animals per group and are representative of two independent experiments. Bar graphs represent mean and error bars represent standard deviation. Statistical significance was assessed among the replicate bone marrow chimeras by one-way ANOVA (a, d, f) (*p < .05, **p < .01, ***p < .001, ****p < .0001). See also Supplementary Fig. 2. Source data are provided as a source data file