Figure 2 from Anti-EGFR Antibody–Drug Conjugate Carrying an Inhibitor Targeting CDK Restricts Triple-Negative Breast Cancer Growth

&lt;p&gt;Single-cell RNA sequencing and spatial transcriptomic analyses reveal cellular and spatial co-expression of EGFR with CDK2/cyclin E in TNBCs. &lt;b&gt;A,&lt;/b&gt; Dimensionality reduction &lt;i&gt;t&lt;/i&gt;-distributed stochastic neighbor embedding (&lt;i&gt;t&lt;/i&gt;-SNE) map of combined scRNA-seq transcriptomes of 150,290 cells from 27 untreated primary tumors (TNBC, &lt;i&gt;n&lt;/i&gt; = 8 samples, 54,819 cells; HER2+, &lt;i&gt;n&lt;/i&gt; = 6 samples, 31,917 cells; ER+, &lt;i&gt;n&lt;/i&gt; = 13 samples, 63,554 cells) colored by cell cluster (&lt;a href="#bib32" target="_blank"&gt;32&lt;/a&gt;). &lt;i&gt;EpCAM&lt;/i&gt; expression revealed two prominent &lt;i&gt;EpCAM&lt;/i&gt;+ tumor epithelial clusters in each cancer subtype (dotted lines). &lt;i&gt;t&lt;/i&gt;-SNE plots showing expression levels of &lt;i&gt;EGFR&lt;/i&gt;, &lt;i&gt;CCNE1&lt;/i&gt;, and &lt;i&gt;CDK2&lt;/i&gt; genes for the same clusters. Red: high expression, gray: not detected. Overall expression of &lt;i&gt;CCNA1&lt;/i&gt; was too low and was excluded from the analysis. &lt;b&gt;B,&lt;/b&gt; Analyses of the transcriptomic data were conducted to evaluate expression of &lt;i&gt;EGFR&lt;/i&gt;, &lt;i&gt;CCNE1&lt;/i&gt;, and &lt;i&gt;CDK2&lt;/i&gt; genes per patient and for each patient cohort (TNBC, HER2+, and ER+). Heatmap (top) with color boxes indicating normalized expression level; each column represents a patient tumor. Quantitative analysis (bottom) was calculated by the number of cells expressing &lt;i&gt;EGFR&lt;/i&gt;, &lt;i&gt;CCNE1&lt;/i&gt;, or &lt;i&gt;CDK2&lt;/i&gt;, in proportion to &lt;i&gt;EpCAM&lt;/i&gt;+ cells. &lt;b&gt;C,&lt;/b&gt; Same analysis was performed on &lt;i&gt;EpCAM&lt;/i&gt;+ &lt;i&gt;EGFR&lt;/i&gt;+ cells for the expression of &lt;i&gt;CCNE1&lt;/i&gt; and &lt;i&gt;CDK2&lt;/i&gt;. &lt;i&gt;P&lt;/i&gt; values determined by two-tailed unpaired &lt;i&gt;t&lt;/i&gt; test against TNBC subtype. &lt;b&gt;D,&lt;/b&gt; Spatial transcriptomic analysis of &lt;i&gt;EGFR&lt;/i&gt;,&lt;i&gt; CCNE1&lt;/i&gt;, and&lt;i&gt; CDK2 &lt;/i&gt;expression in &lt;i&gt;EpCAM&lt;/i&gt;+ cell clusters of 43 tumor sections from 22 patients with TNBC (&lt;a href="#bib33" target="_blank"&gt;33&lt;/a&gt;), where 26 sections were from 13 treatment-naïve patients and 17 sections were from nine residual TNBCs. Tissue architecture integrity in these sections was confirmed by hematoxylin and eosin staining (left). The color scale represents log-transformed normalized gene expression (red, highest; blue, lowest). Representative spatial mapping revealed a consistent pattern of &lt;i&gt;EGFR&lt;/i&gt; expression in chemo-naïve and post-NAC-resistant TNBCs, and its spatial relationships with &lt;i&gt;CCNE1&lt;/i&gt; and &lt;i&gt;CDK2&lt;/i&gt; co-expression in tumor sections. Venn diagrams illustrate quantitative analyses for the relationships among &lt;i&gt;EGFR&lt;/i&gt;, &lt;i&gt;CCNE1&lt;/i&gt;, and &lt;i&gt;CDK2&lt;/i&gt; co-expression (numbers in black represent the number of spatial clusters for all patients in the cohort, and % marked in red represent the proportion of these spatial clusters within all &lt;i&gt;EpCAM&lt;/i&gt;+ clusters).&lt;/p&gt;

Topic: Cancer Genomics and Diagnostics
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences