Extended Data Fig. 1: HNRNPC target mRNAs are translationally repressed in highly metastatic breast cancer cells and PDXs.

(a) Length distribution of ribosome protected footprints (RPFs) as determined by Ribo-seq. A representative data sample is shown. (b) Distribution of RPFs, aligned on an inferred ribosome P-site, on a metagene, centered around translation start (left) or stop (right) site. A representative data sample is shown. (c) Volcano plot illustrating the changes in protein abundance in MDA-LM2 compared to MDA-MB-231 cells, as determined by TMT-MS analysis. The data points are colored according to thresholds in effect size (logFC ± 0.33) and significance (p < 0.05, two-tailed t-test). (d) The distribution of changes in TEs (as determined by Ribo-seq) and in protein abundance (as determined by TMT-MS and normalized by RNA expression obtained from RNA-seq), in MDA-LM2 compared to MDA-MB-231 cells. Pearson R and associated p-value are shown. (e) The comparison of the metastatic capacity of breast cancer PDXs used in this study. (f) Representative images (n = 4-13 mice per cohort, as in (e)) of H&E stained mouse lung sections transplanted with breast cancer PDXs. The metastatic foci are indicated by black arrows. Scale bar = 100 µm. (g) Mutual information (MI) values and associated z-scores from the DeepBind algorithm, showing the prediction of poly(U) binding protein targets among translationally repressed mRNAs in MDA-LM2 compared to MDA-MB-231 cells. (h) Upset plot showing the distribution and overlap of HNRNPC peaks within genomic features, as determined by CLIP-seq. (i) Cumulative density plot of translation efficiency ratios (TER) comparing MDA-LM2 to MDA-MB-231 cells, for HNRNPC 3′ UTR target and non-target mRNAs. (j) Cumulative density plot of translation efficiency ratios (TER) comparing highly and poorly metastatic breast cancer PDXs, for HNRNPC 3′ UTR target and non-target mRNAs. Median difference (∆M) and p-value (calculated using two-tailed Mann-Whitney U-test) are shown. (k) Cumulative density plot of translation efficiency ratios (TER) comparing MDA-LM2 to MDA-MB-231 cells, for HNRNPC, ELAVL1 and TIA1 3′ UTR target mRNAs, as determined by CLIP-seq.