AKT Inhibition Promotes Nonautonomous Cancer Cell Survival

Abstract

Small-molecule inhibitors of AKT signaling are being evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication.

A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

“…Quiescent (G0) cells are an assortment of reversibly arrested cells, including dormant stem cells, which are found as a clinically relevant subpopulation in cancers [1][2][3][4]. Such cells are anti-proliferative, anti-differentiation, and anti-apoptotic and show distinct properties including resistance to harsh conditions [1,2,[5][6][7][8][9][10]. G0 cells show specific gene expression that may underlie their resistance and other properties [1,2,[8][9][10].…”

“…Such cells are anti-proliferative, anti-differentiation, and anti-apoptotic and show distinct properties including resistance to harsh conditions [1,2,[5][6][7][8][9][10]. G0 cells show specific gene expression that may underlie their resistance and other properties [1,2,[8][9][10]. Analyses from multiple groups revealed some genes upregulated at the transcriptional level [1,8,11].…”

“…G0 cells show specific gene expression that may underlie their resistance and other properties [1,2,[8][9][10]. Analyses from multiple groups revealed some genes upregulated at the transcriptional level [1,8,11]. Altered polyadenylation site selection on mRNAs produces longer 3′-untranslated regions (3′UTRs) in G0 compared to proliferating cells-which increases 3′UTR elements that can mediate post-transcriptional gene expression regulation [12].…”

Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies

“…For one of the GRO-seq datasets (GSE71898: SRR2153508), we found 230 protein-coding genes where the unfiltered dataset showed at least 2-fold difference in PI values compared to the filtered dataset ( Fig. 5C, D) [24]. These proteincoding genes include cases where mispriming leads to higher PI (indicating promoterproximal pausing) and some that show lower PI (indicating higher elongation rates).…”

“…In several GRO-seq datasets we were able to identify 10,000 -50,000 mispriming sites accounting for millions of reads in some datasets ( Table 2, Fig. 5A-B and Figure S5) [23,24]. Since GRO-seq utilizes the position-specific count of cDNA reads to detect RNA polymerase pausing, we suspected that artefactual fluctuations in read densities as a result of mispriming could lead to mis-identification of pause sites.…”