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FPKM levels below 1. 0 were set to 1. 0. Both RNA Seq and Ribo Seq FPKM measurements were highly reproducible, both showing correlation above 0. 95 for biological replicates sequenced on the same sequencer run. The correlation between biological repli cates processed on different Ribo Seq runs was lower but still very high. Transcript TE was calculated per condition as the ratio between transcript translation and expression levels. RNA Seq and Ribo Seq data from the study of Hsieh et al. that examined responses to mTOR inhibi tion were downloaded from GEO and analyzed in the same way. To detect the major response patterns in our dataset, we first searched for transcripts that showed either differential expression or differential TE in the examined conditions relative to the control proliferating samples.

Since we observed a sequencer run batch effect, we compared each test condition to the control sample profiled in the same run. As variation is larger among lowly expressed transcripts, we set a dynamic cut off depending on expression level or translation levels. A total of approximately 2,800 tran scripts passed the cut off and were subjected to clustering. Clustering and GO enrichment analyses were done using the EXPANDER package. De novo motif analysis was done using AMADEUS. All other statistical analyses were done in R. Isolation of polysome associated mRNA Cells were lysed in buffer A containing 1 U of Rnase OUT. Lysate was homogenized using a 26 G needle, and the cytosolic extract was obtained by centrifugation at 1,300 g for 10 min. The extract was overlaid on a 7% to 47% linear sucrose gradient and centrifuged in a SW41Ti rotor at 36,000 rpm for 2 h at 4 C. Twelve fractions were collected from the gra dients and RNA was isolated from each using Trizol reagent. Reverse transcription was performed using GoScript Reverse Transcription System following the manufacturers instructions.

Introduction Triple negative breast cancers are defined by the lack of expression of the estrogen receptor, proges terone receptor and human epidermal growth factor receptor 2. TNBC has distinct clinical and pathological characteristics and occurs at higher rates in younger women and in women of African American descent. Advanced TNBC confer an aggressive clin ical course with a poor prognosis compared with other breast cancer subtypes. Most notably, patients who present with TNBC have a median survival of 7 to 13 months following recurrence, compared with greater than 20 months for patients with non TNBC. It is now recognized that TNBC is molecularly heteroge neous and there are ongoing efforts to define appropriate targets for directed therapy. With no confirmed single oncogenic driver, TNBC is not amenable to treatment with currently approved targeted approaches, such as trastuzumab or endocrine therapy, making chemotherapy treatment the main systemic treatment option.