Ribosome changes reprogram translation for chemosurvival in G0 leukemic cells

Quiescent leukemic cells survive chemotherapy, with translation changes. Our data reveal that FXR1, a protein amplified in several aggressive cancers, is elevated in quiescent and chemo-treated leukemic cells and promotes chemosurvival. This suggests undiscovered roles for this RNA- and ribosome-associated protein in chemosurvival. We find that FXR1 depletion reduces translation, with altered rRNAs, snoRNAs, and ribosomal proteins (RPs). FXR1 regulates factors that promote transcription and processing of ribosomal genes and snoRNAs. Ribosome changes in FXR1-overexpressing cells, including RPLP0/uL10 levels, activate eIF2α kinases. Accordingly, phospho-eIF2α increases, enabling selective translation of survival and immune regulators in FXR1-overexpressing cells. Overriding these genes or phospho-eIF2α with inhibitors reduces chemosurvival. Thus, elevated FXR1 in quiescent or chemo-treated leukemic cells alters ribosomes that trigger stress signals to redirect translation for chemosurvival.

B cells support the repair of injured tissues by adopting MyD88-dependent regulatory functions and phenotype

Exogenously applied mature naïve B220+ /CD19+ /IgM+ /IgD+ B cells are strongly protective in the context of tissue injury. However, the mechanisms by which B cells detect tissue injury and aid repair remain elusive. Here, we show in distinct models of skin and brain injury that MyD88-dependent toll-like receptor (TLR) signaling through TLR2/6 and TLR4 is essential for the protective benefit of B cells in vivo, while B cell-specific deletion of MyD88 abrogated this effect. The B cell response to injury was multi-modal with simultaneous production of both regulatory cytokines, such as IL-10, IL-35, and transforming growth factor beta (TGFβ), and inflammatory cytokines, such as tumor necrosis factor alpha (TNFα), IL-6, and interferon gamma. Cytometry analysis showed that this response was time and environment-dependent in vivo, with 20%-30% of applied B cells adopting an immune modulatory phenotype with high co-expression of anti- and pro-inflammatory cytokines after 18-48 h at the injury site. B cell treatment reduced the expression of TNFα and increased IL-10 and TGFβ in infiltrating immune cells and fibroblasts at the injury site. Proteomic analysis further showed that B cells have a complex time-dependent homeostatic effect on the injured microenvironment, reducing the expression of inflammation-associated proteins, and increasing proteins associated with proliferation, tissue remodeling, and protection from oxidative stress. These findings chart and validate a first mechanistic understanding of the effects of B cells as an immunomodulatory cell therapy in the context of tissue injury.

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses

Inactivation of RB is one of the hallmarks of cancer, however gaps remain in our understanding of how RB-loss changes human cells. Here we show that pRB-depletion results in cellular reprogramming, we quantitatively measured how RB-depletion altered the transcriptional, proteomic and metabolic output of non-tumorigenic RPE1 human cells. These profiles identified widespread changes in metabolic and cell stress response factors previously linked to E2F function. In addition, we find a number of additional pathways that are sensitive to RB-depletion that are not E2F-regulated that may represent compensatory mechanisms to support the growth of RB-depleted cells. To determine whether these molecular changes are also present in RB1^-/- tumors, we compared these results to Retinoblastoma and Small Cell Lung Cancer data, and identified widespread conservation of alterations found in RPE1 cells. To define which of these changes contribute to the growth of cells with de-regulated E2F activity, we assayed how inhibiting or depleting these proteins affected the growth of RB1^-/- cells and of Drosophila E2f1-RNAi models in vivo. From this analysis, we identify key metabolic pathways that are essential for the growth of pRB-deleted human cells.

E2F/Dp inactivation in fat body cells triggers systemic metabolic changes

The E2F transcription factors play a critical role in controlling cell fate. In Drosophila, the inactivation of E2F in either muscle or fat body results in lethality, suggesting an essential function for E2F in these tissues. However, the cellular and organismal consequences of inactivating E2F in these tissues are not fully understood. Here, we show that the E2F loss exerts both tissue-intrinsic and systemic effects. The proteomic profiling of E2F-deficient muscle and fat body revealed that E2F regulates carbohydrate metabolism, a conclusion further supported by metabolomic profiling. Intriguingly, animals with E2F-deficient fat body had a lower level of circulating trehalose and reduced storage of fat. Strikingly, a sugar supplement was sufficient to restore both trehalose and fat levels, and subsequently rescued animal lethality. Collectively, our data highlight the unexpected complexity of E2F mutant phenotype, which is a result of combining both tissue-specific and systemic changes that contribute to animal development.

Abstract B32: A specialized post-transcriptional program in chemoresistant, quiescent cancer cells

Quiescent (G0) cells are a clinically relevant fraction in cancers, which include dormant cancer stem cells, and resist clinical therapy. G0 cells reveal extensive changes in gene expression at the protein and translation levels. We previously identified that the translation mechanism is altered in G0 cancer cells. MicroRNAs, noncoding RNAs that target distinct mRNAs to alter gene expression, were found to associate with a key RNA-binding protein and enable specialized functions in G0, where they recruit noncanonical translation factors to regulate specific mRNA translation. We find that G0 leukemic cells show similar proteome and translatome to cells isolated post-chemotherapy. These data suggest that specialized post-transcriptional mechanisms in G0 leukemic cells regulate a distinct translatome to mediate chemoresistance. To understand the role of post-transcriptional regulation in chemoresistance, we compared global transcriptome, translatome and proteome profiling in chemoresistant G0 acute monocytic leukemic (AML) cells. We find that chemotherapy or G0 induction leads to DNA damage responsive ATM and stress signaling, which alter post-transcriptional and translational mechanisms. ATM and stress-activated p38 MAPK/MK2 increase AU-rich-element (ARE) bearing proinflammatory cytokine and immune gene mRNAs, by regulating a key ARE RNA binding protein and modifying canonical translation. AREs are present on 3'UTRs of tightly regulated oncogenes and cytokines, to post-transcriptionally control their expression. Both rate-limiting steps—mRNA cap recognition and tRNA recruitment—in canonical translation are altered. These signaling pathways lead to low mTOR activity in G0, which activates the cap complex inhibitor, eIF4EBP to impair canonical translation, leading to noncanonical translation of specific mRNAs with specialized cap binding and ribosome recruitment factors. In addition, stress and STAT1/interferon signaling are activated to reduce the canonical tRNA recruitment mechanism, enabling noncanonical translation of specific mRNAs. These changes permit translation of ARE bearing proinflammatory cytokine TNFa, and immune and cell-migration modulators that promote survival. Co-inhibiting p38 MAPK and TNFa that promote antiapoptosis—prior to or along with chemotherapy—decreases chemoresistance in AML cells, in vivo, and in patient samples without affecting normal cells. Our studies reveal a proinflammatory subpopulation in AML that mediates resistance, enabled by DNA damage- and stress-regulated post-transcriptional and translational mechanisms that are mediated by AU-rich-elements and a critical ARE RNA binding protein. Disrupting ARE regulation reduces TNFα and chemoresistance, revealing AREs, an important ARE RNA binding protein and noncanonical translation as regulators of chemoresistance. These studies reveal the significance of post-transcriptional regulation of proinflammatory and immune gene-mediated chemoresistance.

Citation Format: Sooncheol Lee, Syed I.A. Bukhari, Samuel S. Truesdell, Swapna Kollu, Richard D. Mortensen, Myriam Boukhali, Esha Jain, Dongjun Lee, Maria Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas Haradhwala, Akiko Yanagiya, Michael Lawrence, Roopali Gandhi, Ruslan Sadreyev, David Sweetser, Wilhelm Haas, Shobha Vasudevan. A specialized post-transcriptional program in chemoresistant, quiescent cancer cells [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B32.

Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover

How allelic asymmetry is generated remains a major unsolved problem in epigenetics. Here we model the problem using X-chromosome inactivation by developing "BioRBP", an enzymatic RNA-proteomic method that enables probing of low-abundance interactions and an allelic RNA-depletion and -tagging system. We identify messenger RNA-decapping enzyme 1A (DCP1A) as a key regulator of Tsix, a noncoding RNA implicated in allelic choice through X-chromosome pairing. DCP1A controls Tsix half-life and transcription elongation. Depleting DCP1A causes accumulation of X-X pairs and perturbs the transition to monoallelic Tsix expression required for Xist upregulation. While ablating DCP1A causes hyperpairing, forcing Tsix degradation resolves pairing and enables Xist upregulation. We link pairing to allelic partitioning of CCCTC-binding factor (CTCF) and show that tethering DCP1A to one Tsix allele is sufficient to drive monoallelic Xist expression. Thus, DCP1A flips a bistable switch for the mutually exclusive determination of active and inactive Xs.

Obtusaquinone: A Cysteine-Modifying Compound That Targets Keap1 for Degradation

We have previously identified the natural product obtusaquinone (OBT) as a potent antineoplastic agent with promising in vivo activity in glioblastoma and breast cancer through the activation of oxidative stress; however, the molecular properties of this compound remained elusive. We used a multidisciplinary approach comprising medicinal chemistry, quantitative mass spectrometry-based proteomics, functional studies in cancer cells, and pharmacokinetic analysis, as well as mouse xenograft models to develop and validate novel OBT analogs and characterize the molecular mechanism of action of OBT. We show here that OBT binds to cysteine residues with a particular affinity to cysteine-rich Keap1, a member of the CUL3 ubiquitin ligase complex. This binding promotes an overall stress response and results in ubiquitination and proteasomal degradation of Keap1 and downstream activation of the Nrf2 pathway. Using positron emission tomography (PET) imaging with the PET-tracer 2-[¹⁸F]fluoro-2-deoxy-d-glucose (FDG), we confirm that OBT is able to penetrate the brain and functionally target brain tumors. Finally, we show that an OBT analog with improved pharmacological properties, including enhanced potency, stability, and solubility, retains the antineoplastic properties in a xenograft mouse model.

Substrate-based kinase activity inference identifies MK2 as driver of colitis

Inflammatory bowel disease (IBD) is a chronic and debilitating disorder that has few treatment options due to a lack of comprehensive understanding of its molecular pathogenesis. We used multiplexed mass spectrometry to collect high-content information on protein phosphorylation in two different mouse models of IBD. Because the biological function of the vast majority of phosphorylation sites remains unknown, we developed Substrate-based Kinase Activity Inference (SKAI), a methodology to infer kinase activity from phosphoproteomic data. This approach draws upon prior knowledge of kinase-substrate interactions to construct custom lists of kinases and their respective substrate sites, termed kinase-substrate sets that employ prior knowledge across organisms. This expansion as much as triples the amount of prior knowledge available. We then used these sets within the Gene Set Enrichment Analysis framework to infer kinase activity based on increased or decreased phosphorylation of its substrates in a dataset. When applied to the phosphoproteomic datasets from the two mouse models, SKAI predicted largely non-overlapping kinase activation profiles. These results suggest that chronic inflammation may arise through activation of largely divergent signaling networks. However, the one kinase inferred to be activated in both mouse models was mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2 or MK2), a serine/threonine kinase that functions downstream of p38 stress-activated mitogen-activated protein kinase. Treatment of mice with active colitis with ATI450, an orally bioavailable small molecule inhibitor of the MK2 pathway, reduced inflammatory signaling in the colon and alleviated the clinical and histological features of inflammation. These studies establish MK2 as a therapeutic target in IBD and identify ATI450 as a potential therapy for the disease.

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

BACKGROUND

Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown.

RESULTS

We induce chemoresistant and G0 leukemic cells by serum starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the upregulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, Tristetraprolin (TTP) in G0. This permits expression of ARE mRNAs that promote chemoresistance. Conversely, inhibition of TTP phosphorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE-bearing TNFα and DUSP1 mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα prior to or along with chemotherapy substantially reduces chemoresistance in primary leukemic cells ex vivo and in vivo.

CONCLUSIONS

These studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE-bearing mRNAs that promote chemoresistance. By disrupting this pathway, we develop an effective combination therapy against chemosurvival.

Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex

Although the microcrustacean Daphnia is becoming an organism of choice for proteomic studies, protein expression across its life cycle have not been fully characterized. Proteomes of adult females, juveniles, asexually produced embryos, and the ephippia-resting stages containing sexually produced diapausing freezing- and desiccation-resistant embryos are analyzed. Overall, proteins with known molecular functions are more likely to be detected than proteins with no detectable orthology. Similarly, proteins with stronger gene model support in two independent genome assemblies can be detected, than those without such support. This suggests that the proteomics pipeline can be applied to verify hypothesized proteins, even given questionable reference gene models. In particular, upregulation of vitellogenins and downregulation of actins and myosins in embryos of both types, relative to juveniles and adults, and overrepresentation of cell-cycle related proteins in the developing embryos, relative to diapausing embryos and adults, are observed. Upregulation of small heat-shock proteins and peroxidases, as well as overrepresentation of stress-response proteins in the ephippium relative to the asexually produced non-diapausing embryos, is found. The ephippium also shows upregulation of three trehalose-synthesis proteins and downregulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Single-cell technologies have described heterogeneity across tissues, but the spatial distribution and forces that drive single-cell phenotypes have not been well defined. Combining single-cell RNA and protein analytics in studying the role of stromal cancer-associated fibroblasts (CAFs) in modulating heterogeneity in pancreatic cancer (pancreatic ductal adenocarcinoma [PDAC]) model systems, we have identified significant single-cell population shifts toward invasive epithelial-to-mesenchymal transition (EMT) and proliferative (PRO) phenotypes linked with mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription 3 (STAT3) signaling. Using high-content digital imaging of RNA in situ hybridization in 195 PDAC tumors, we quantified these EMT and PRO subpopulations in 319,626 individual cancer cells that can be classified within the context of distinct tumor gland "units." Tumor gland typing provided an additional layer of intratumoral heterogeneity that was associated with differences in stromal abundance and clinical outcomes. This demonstrates the impact of the stroma in shaping tumor architecture by altering inherent patterns of tumor glands in human PDAC.

A Code of Mono-phosphorylation Modulates the Function of RB

Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here, we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB's interactions and confer functional specificity. All 14 mP-RBs interact with E2F/DP proteins, but they provide different shades of E2F regulation. RB mono-phosphorylation at S811, for example, alters RB transcriptional activity by promoting its association with NuRD complexes. The greatest functional differences between mP-RBs are evident beyond the cell cycle machinery. RB mono-phosphorylation at S811 or T826 stimulates the expression of oxidative phosphorylation genes, increasing cellular oxygen consumption. These results indicate that RB activation signals are integrated in a phosphorylation code that determines the diversity of RB activity.

Mutant GNAS drives pancreatic tumourigenesis by inducing PKA-mediated SIK suppression and reprogramming lipid metabolism

G protein αs (GNAS) mediates receptor-stimulated cAMP signalling, which integrates diverse environmental cues with intracellular responses. GNAS is mutationally activated in multiple tumour types, although its oncogenic mechanisms remain elusive. We explored this question in pancreatic tumourigenesis where concurrent GNAS and KRAS mutations characterize pancreatic ductal adenocarcinomas (PDAs) arising from intraductal papillary mucinous neoplasms (IPMNs). By developing genetically engineered mouse models, we show that GnasR201C cooperates with KrasG12D to promote initiation of IPMN, which progress to invasive PDA following Tp53 loss. Mutant Gnas remains critical for tumour maintenance in vivo. This is driven by protein-kinase-A-mediated suppression of salt-inducible kinases (Sik1-3), associated with induction of lipid remodelling and fatty acid oxidation. Comparison of Kras-mutant pancreatic cancer cells with and without Gnas mutations reveals striking differences in the functions of this network. Thus, we uncover Gnas-driven oncogenic mechanisms, identify Siks as potent tumour suppressors, and demonstrate unanticipated metabolic heterogeneity among Kras-mutant pancreatic neoplasms.

Abstract 4443: A post-transcriptional program of chemoresistance regulators in quiescent cancer cells

Quiescent (G0) cells are a clinically relevant fraction in several cancers, which include dormant cancer stem cells, and resist clinical therapy. G0 cells reveal extensive changes in gene expression at the protein and translation levels. We previously identified that the translation mechanism is altered in G0 cancer cells. MicroRNAs, noncoding RNAs that target distinct mRNAs to alter gene expression—were found to associate with an important RNA-binding protein, and enable specialized functions in G0—where they recruit non-canonical translation factors to regulate specific mRNA translation. We find that G0 leukemic cells show similar proteome and translatome to cells isolated post-chemotherapy. These data suggest that specialized post-transcriptional and translational mechanisms in G0 leukemic cells regulate a distinct translatome to mediate chemoresistance.

To understand the role of post-transcriptional and translational regulation in chemoresistance, we compared global RNA, translational and proteome profiling in chemoresistant G0 acute monocytic leukemic (AML) cells. We find that chemotherapy or G0 induction leads to DNA damage responsive ATM and stress signaling, which alter post-transcriptional and translational mechanisms. ATM and stress activated p38 MAPK/MK2 increase AU-rich-element (ARE) bearing pro-inflammatory cytokine and immune gene mRNAs by regulating a key ARE RNA binding protein, and by activating STAT1/interferon pathway to alter canonical translation. AREs are present on 3'UTRs of critical, tightly regulated oncogenes and cytokines to post-transcriptionally control their expression. These changes permit translation of ARE bearing pro-inflammatory cytokine TNFα, and immune and cell-migration modulators that promote survival. Co-inhibiting p38 MAPK and TNFα that promote anti-apoptosis—prior to or alongwith chemotherapy—decreases chemoresistance in AML cell lines, in vivo, and in patient samples, without affecting normal cells. These studies reveal a pro-inflammatory subpopulation in AML that mediates chemoresistance, enabled by DNA damage- and stress-regulated post-transcriptional and translational mechanisms that are mediated by AU-rich-elements and a critical ARE RNA binding protein. Disrupting ARE regulation reduces TNFα and chemoresistance, revealing AREs and an important ARE RNA binding protein as key regulators of inflammation-mediated chemoresistance. These studies reveal the significance of post-transcriptional regulation of inflammation/immune gene-mediated chemoresistance.

Correspondence: vasudevan.shobha@mgh.harvard.edu

Citation Format: Sooncheol Lee, Samuel S. Truesdell, Syed I. Bukhari, Myriam Boukhali, Dongjun Lee, Maria A. Mazzola, Radhika Raheja, Adam Langenbucher, Nicholas J. Haradhvala, Michael Lawrence, Roopali Gandhi, David A. Sweetser, Wilhelm Haas, Shobha Vasudevan. A post-transcriptional program of chemoresistance regulators in quiescent cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4443.

Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.

E2F/DP Prevents Cell-Cycle Progression in Endocycling Fat Body Cells by Suppressing dATM Expression

To understand the consequences of the complete elimination of E2F regulation, we profiled the proteome of Drosophila dDP mutants that lack functional E2F/DP complexes. The results uncovered changes in the larval fat body, a differentiated tissue that grows via endocycles. We report an unexpected mechanism of E2F/DP action that promotes quiescence in this tissue. In the fat body, dE2F/dDP limits cell-cycle progression by suppressing DNA damage responses. Loss of dDP upregulates dATM, allowing cells to sense and repair DNA damage and increasing replication of loci that are normally under-replicated in wild-type tissues. Genetic experiments show that ectopic dATM is sufficient to promote DNA synthesis in wild-type fat body cells. Strikingly, reducing dATM levels in dDP-deficient fat bodies restores cell-cycle control, improves tissue morphology, and extends animal development. These results show that, in some cellular contexts, dE2F/dDP-dependent suppression of DNA damage signaling is key for cell-cycle control and needed for normal development.

TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes. Using a transgenic screen in zebrafish, thymocyte selection-associated high mobility group box protein (TOX) was uncovered as a collaborating oncogenic driver that accelerated T-ALL onset by expanding the initiating pool of transformed clones and elevating genomic instability. TOX is highly expressed in a majority of human T-ALL and is required for proliferation and continued xenograft growth in mice. Using a wide array of functional analyses, we uncovered that TOX binds directly to KU70/80 and suppresses recruitment of this complex to DNA breaks to inhibit nonhomologous end joining (NHEJ) repair. Impaired NHEJ is well known to cause genomic instability, including development of T-cell malignancies in KU70- and KU80-deficient mice. Collectively, our work has uncovered important roles for TOX in regulating NHEJ by elevating genomic instability during leukemia initiation and sustaining leukemic cell proliferation following transformation.Significance: TOX is an HMG box-containing protein that has important roles in T-ALL initiation and maintenance. TOX inhibits the recruitment of KU70/KU80 to DNA breaks, thereby inhibiting NHEJ repair. Thus, TOX is likely a dominant oncogenic driver in a large fraction of human T-ALL and enhances genomic instability. Cancer Discov; 7(11); 1336-53. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1201.

Abstract 4997: Specialized microRNP and translation mechanisms in quiescent cancer cells

Quiescence (G0) represents an assortment of reversible, cell cycle-arrested states that are resistant to unfavorable conditions and associated with cancer persistence. G0 involves regulated gene expression with selective mRNA expression and decreased canonical translation. Low mTOR activity in G0 activates the cap complex inhibitor, eIF4EBP, and impairs canonical translation. The alternative translation mechanisms in G0 remain to be uncovered. Our data show that microRNAs, regulatory, non-coding RNAs that target distinct mRNAs to alter gene expression, can associate with alternative complexes and translation factors to regulate specific mRNA translation in G0. One subset of transcripts expressed in G0 includes specific mRNAs recruited by an FXR1a-associated microRNP (microRNA-protein complex) for translation activation in G0 mammalian cells. MicroRNPs predominantly mediate repression and downregulation; however, FXR1a-microRNP lacks conventional microRNP repressors, and instead, contains a specific RNA binding protein isoform, FXR1a. FXR1a promotes translation and is overexpressed and associated with poor prognosis in several cancers. Our data reveal that microRNA-mediated activation requires target mRNAs with unadenylated/ shortened poly(A) tails to avoid the roles of PABP in enhancing microRNA-mediated downregulation and in canonical translation that is impaired in G0. Instead of canonical translation factors that are inhibited by eIF4EBP in G0, we find alternative translation factors—a non-canonical 5’cap binding factor and an eIF4G homolog that interacts with the ribosome—are recruited by the 3’-UTR binding FXR1a-microRNP, and promote specific mRNA translation. Our data show that G0 leukemic cells are chemoresistant and their translation profile is similar to surviving leukemic cells that are isolated after clinical therapy. We find expression of critical cytokines and immune regulators in G0. Significantly, inhibiting these immune regulators in resistant G0 cancer cells reduces their survival and chemoresistance. These data reveal a specialized translation mechanism in G0 cancer cells that promotes specific mRNA translation in these conditions of reduced canonical translation, and is important for chemoresistance.

Citation Format: Syed I. Bukhari, Samuel S. Truesdell, Sooncheol Lee, Swapna Kollu, Anthony Classon, Myriam Boukhali, Esha Jain, Richard D. Mortensen, Akiko Yanagiya, Ruslan Sadreyev, Wilhelm Haas, Shobha Vasudevan. Specialized microRNP and translation mechanisms in quiescent cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4997. doi:10.1158/1538-7445.AM2017-4997

Negative regulation of EGFR signalling by the human folliculin tumour suppressor protein

Germline mutations in the Folliculin (FLCN) tumour suppressor gene result in fibrofolliculomas, lung cysts and renal cancers, but the precise mechanisms of tumour suppression by FLCN remain elusive. Here we identify Rab7A, a small GTPase important for endocytic trafficking, as a novel FLCN interacting protein and demonstrate that FLCN acts as a Rab7A GTPase-activating protein. FLCN^−/− cells display slower trafficking of epidermal growth factor receptors (EGFR) from early to late endosomes and enhanced activation of EGFR signalling upon ligand stimulation. Reintroduction of wild-type FLCN, but not tumour-associated FLCN mutants, suppresses EGFR signalling in a Rab7A-dependent manner. EGFR signalling is elevated in FLCN^−/− tumours and the EGFR inhibitor afatinib suppresses the growth of human FLCN^−/− cells as tumour xenografts. The functional interaction between FLCN and Rab7A appears conserved across species. Our work highlights a mechanism explaining, at least in part, the tumour suppressor function of FLCN.

Folliculin is a known tumour suppressor but the molecular mechanisms behind this function are unclear. Here the authors show that Folliculin regulates EGFR signalling by modulating its Rab7a-dependent trafficking.

Abstract NTOC-110: UNEXPECTED ROLES FOR KDM4A: PROTEIN SYNTHESIS AND MTOR INHIBITOR SENSITIVITY

Single nucleotide polymorphisms (SNPs) occur within chromatin-modulating factors; however, little is known about how these variants within the coding sequence impact cancer progression or treatment. Therefore, there is a need to establish their biochemical and/or molecular contribution, their use in sub-classifying patients and their impact on therapeutic response. We demonstrate that coding SNP-A482 within the lysine tri-demethylase KDM4A/JMJD2A associates with differential outcome in cancer patients and promotes KDM4A protein turnover. Interestingly, homozygous SNP-482 cells have increased mTOR inhibitor sensitivity. mTOR inhibitors significantly reduce SNP-A482 protein levels, which parallels the increased drug sensitivity observed with KDM4A depletion. Furthermore, we demonstrate that KDM4A interacts with the translation initiation complex and impacts the distribution of translation initiation factors within polysome fractions. Upon KDM4A depletion, protein synthesis was reduced and there was enhanced protein synthesis suppression with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Lastly, we demonstrate that JIB-04, a JmjC demethylases inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected role for KDM4A in regulating protein synthesis, in modulating mTOR inhibitor sensitivity and suggest potential novel therapeutic applications for this class of enzyme.

Citation Format: Capucine Van Rechem, Joshua C. Black, Patricia Greninger, Yang Zhao, Myriam Boukhali, Carlos Donado, Martin J. Aryee, Paul d. Burrowes, Brendon Ladd, Susanne Gräslund, Wilhelm Haas, David C. Christiani, Cyril H. Benes and Johnathan R. Whetstine. UNEXPECTED ROLES FOR KDM4A: PROTEIN SYNTHESIS AND MTOR INHIBITOR SENSITIVITY [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr NTOC-110.

Interaction of p190A RhoGAP with eIF3A and Other Translation Preinitiation Factors Suggests a Role in Protein Biosynthesis

The negative regulator of Rho family GTPases, p190A RhoGAP, is one of six mammalian proteins harboring so-called FF motifs. To explore the function of these and other p190A segments, we identified interacting proteins by tandem mass spectrometry. Here we report that endogenous human p190A, but not its 50% identical p190B paralog, associates with all 13 eIF3 subunits and several other translational preinitiation factors. The interaction involves the first FF motif of p190A and the winged helix/PCI domain of eIF3A, is enhanced by serum stimulation and reduced by phosphatase treatment. The p190A/eIF3A interaction is unaffected by mutating phosphorylated p190A-Tyr³⁰⁸, but disrupted by a S296A mutation, targeting the only other known phosphorylated residue in the first FF domain. The p190A-eIF3 complex is distinct from eIF3 complexes containing S6K1 or mammalian target of rapamycin (mTOR), and appears to represent an incomplete preinitiation complex lacking several subunits. Based on these findings we propose that p190A may affect protein translation by controlling the assembly of functional preinitiation complexes. Whether such a role helps to explain why, unique among the large family of RhoGAPs, p190A exhibits a significantly increased mutation rate in cancer remains to be determined.

Genomic Instability Is Induced by Persistent Proliferation of Cells Undergoing Epithelial-to-Mesenchymal Transition

TGF-β secreted by tumor stroma induces epithelial-to-mesenchymal transition (EMT) in cancer cells, a reversible phenotype linked to cancer progression and drug resistance. However, exposure to stromal signals may also lead to heritable changes in cancer cells, which are poorly understood. We show that epithelial cells failing to undergo proliferation arrest during TGF-β-induced EMT sustain mitotic abnormalities due to failed cytokinesis, resulting in aneuploidy. This genomic instability is associated with the suppression of multiple nuclear envelope proteins implicated in mitotic regulation and is phenocopied by modulating the expression of LaminB1. While TGF-β-induced mitotic defects in proliferating cells are reversible upon its withdrawal, the acquired genomic abnormalities persist, leading to increased tumorigenic phenotypes. In metastatic breast cancer patients, increased mesenchymal marker expression within single circulating tumor cells is correlated with genomic instability. These observations identify a mechanism whereby microenvironment-derived signals trigger heritable genetic changes within cancer cells, contributing to tumor evolution.

A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence

MicroRNAs predominantly decrease gene expression; however, specific mRNAs are translationally upregulated in quiescent (G0) mammalian cells and immature Xenopus laevis oocytes by an FXR1a-associated microRNA-protein complex (microRNP) that lacks the microRNP repressor, GW182. Their mechanism in these conditions of decreased mTOR signaling, and therefore reduced canonical (cap-and-poly(A)-tail-mediated) translation, remains undiscovered. Our data reveal that mTOR inhibition in human THP1 cells enables microRNA-mediated activation. Activation requires shortened/no poly(A)-tail targets; polyadenylated mRNAs are partially activated upon PAIP2 overexpression, which interferes with poly(A)-bound PABP, precluding PABP-enhanced microRNA-mediated inhibition and canonical translation. Consistently, inhibition of PARN deadenylase prevents activation. P97/DAP5, a homolog of canonical translation factor, eIF4G, which lacks PABP- and cap binding complex-interacting domains, is required for activation, and thereby for the oocyte immature state. P97 interacts with 3' UTR-binding FXR1a-associated microRNPs and with PARN, which binds mRNA 5' caps, forming a specialized complex to translate recruited mRNAs in these altered canonical translation conditions.

AKT Inhibition Promotes Nonautonomous Cancer Cell Survival

Small molecule inhibitors of AKT (v-akt murine thymoma viral oncogene homolog) 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 subtherapeutic 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, multiscale, molecular snapshot of this "AKT(low)" 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 upregulate a host of other proteins and metabolites posttranscriptionally, 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.

Abstract NG08: Transcriptional mechanisms for autophagy regulation and metabolic reprogramming in pancreatic cancer

How do cancer cells escape tightly controlled regulatory circuits that link their growth to extracellular signaling cues? An emerging theme in cancer biology is how, in addition to genetic alterations in signaling pathways (eg. MAPK and PI3K), cancer cells can hijack normal stress response pathways to overcome reliance on external nutrients for growth. Pancreatic adenocarcinoma (PDA) is the quintessence of an aggressive malignancy that relies on constitutive activation of stress response pathways for growth and survival, with the tumors progressing rapidly in the context of extreme hypoxia, poor vascularity, and limited nutrient availability. As such, PDA employ profoundly altered networks of biosynthetic and catabolic pathways, including constitutive activation of autophagy (cellular self-catabolism) and macropinocytosis (bulk uptake of extracellular proteins), which are necessary to maintain metabolic homeostasis and drive tumorigenesis. While, these pathways are essential for tumor growth, the precise mechanism of autophagy-lysosome activation and how this organellar system contributes to metabolic reprogramming in PDA were unknown.

MiT/TFE TRANSCRIPTION FACTORS ARE OVEREXPRESSED IN PDA AND REGULATED THE EXPRESSION OF AUTOPAHGY-LYSOSOME GENES.

We now show that autophagy induction in PDA occurs as part of a broader transcriptional program that coordinates activation of lysosome biogenesis and function, and nutrient scavenging, mediated by the MiT/TFE family transcription factors; MITF, TFE3 and TFEB. These factors show increased expression in primary human PDA tumor datasets compared to matched normal tissue and correlate with expression of a coherent network of autophagy-lysosome genes, incorporating essential autophagy genes, structural lysosomal proteins, hydrolases, solute transporters and luminal enzymes. Importantly, autophagy-lysosome components also show elevated expression in human PDA samples and cell lines, which is dependent on MiT/TFE activity.

CONSTITUTIVE ACTIVITY OF MiT/TFE PROTEINS IS MEDIATED THROUGH ENHANCED NUCLEAR IMPORT.

In non-transformed cells, MiT/TFE factors are phosphorylated by mTORC1 and retained in the cytoplasm in an inactive state under nutrient replete conditions. However, in addition to increased expression, these factors show constitutive nuclear localization and activation in PDA. Mechanistically, we show that this occurs through increased binding to nuclear import factors (IPO) that mediates their escape from mTORC1 inhibition and efficient nuclear translocation in PDA cells. Importantly, IPO expression is up-regulated in PDA cells compared to non-transformed pancreatic epithelial cells and other types of pancreatic tumors (pancreatic neuroendocrine tumor; PNET). Moreover, loss of IPO inhibits nuclear localization of MiT/TFE factors specifically in PDA cells. Therefore this work uncovers novel mechanisms enabling sustained activation of catabolic processes in PDA cells, that are only transiently induced by stress in normal cells, which incorporate alterations in the expression of tumorigenic transcription factors that act in concert with elevated levels of nuclear import proteins.

MiT/TFE FACTORS FUNCTION TO MAINTAIN LYSOSOME INTEGRITY IN PDA CELLS.

Having clarified the mechanisms of their constitutive nuclear import, we turned to the functional roles of MiT/TFE factors in PDA. Our transcriptional data imply contributions of the activated MiT/TFE proteins to the integrity and function of the lysosomal system in PDA cells. To test this key point, we depleted MiT/TFE proteins in PDA cells and observed striking defects in lysosome morphology, degradation of cargo protein and maturation of autophagosomes. In addition, we found that loss of MiT/TFE factors in PDA cells led to a dramatic defect in lysosomal pH. Importantly, these parameters were not altered following knockdown of MiT/TFE proteins in non-transformed control cell lines. Reciprocally, MITF or TFE3 overexpression in HPDE, HPNE, or PDA cells induced autophagy-lysosomal gene expression, LC3B foci, and lipidated LC3-II that was further enhanced following treatment with chloroquine (CQ), an inhibitor of lysosome acidification, indicating a marked augmentation of autophagic flux. Collectively, these data show that MiT/TFE proteins govern both autophagic flux and lysosome activity in PDA cells. This integrated cellular clearance program appears to enable efficient processing of cargo from autophagy as well as macropinocytosis, providing PDA cells access to critical sources of both intracellular and extracellular nutrients.

AMINO ACIDS ARE THE PRIMARY METABOLITE POOL DERIVED FROM ENHANCED AUTOPHAGY-LYSSOOME ACTIVITY IN PDA.

By degrading numerous cellular substrates, the lysosome generates metabolic intermediates that may feed into multiple pathways. We took advantage of the impaired autophagy-lysosome function caused by MiT/TFE inactivation to dissect the metabolic circuitry that sustains PDA growth. First, we conducted global metabolite profiling of PDA cells transfected with control or TFE3-targeted siRNAs. Dual gas chromatography and mass spectrometry (GC/MS) and liquid chromatography mass spectrometry (LC/MS) detected 347 known metabolites. Of these, 15.2% (53/347) showed a statistically significant change upon TFE3 inactivation in both cell lines (48/53 downregulated, 5/53 upregulated). Most prominently altered were amino acids (AA) and their breakdown products, with 31% (25/80) showing decreased abundance. No change in AA uptake was observed upon TFE3 silencing suggesting that in PDA the autophagy-lysosome system may supply a significant fraction of intracellular AA irrespective of external availability. Correspondingly, TFE3 inactivation or Bafilomycin A1 treatment (a specific inhibitor of the lysosomal V-H+ATPase), caused a significant decrease in intracellular AA levels in a multiple PDA cell lines, as did specific inactivation of autophagy by ATG5 knockdown. Importantly, these manipulations did not result in significant changes in AA levels in control non-PDA cells. Thus, the MiT/TFE factors and the autophagy-lysosome system are critical and specific regulators of intracellular AA abundance in PDA.

MiT/TFE FACTORS ARE REQUIRED FOR PDA GROWTH IN VITRO AND IN VIVO.

Consistent with their key roles in organelle function and metabolic regulation, the MiT/TFE proteins were central to PDA growth. PDA cell lines expressing high endogenous levels of MITF, TFE3, or TFEB were exceedingly sensitive to knockdown of that factor, displaying marked impairment in colony formation and reduction in proliferation, whereas non-PDA control cells were unaffected. Expression of shRNA-resistant cDNAs of MITF and TFE3 rescued proliferation in the knockdown setting, confirming the specificity of these experiments. Furthermore, PDA cells were broadly sensitive to chloroquine treatment (CQ; a well characterized autophagy inhibitor) as compared to non-PDA control cells.

Conversely, ectopic expression of MITF or TFE3 rendered control cells hypersensitive to CQ treatment, linking MiT/TFE-regulated clearance pathways to these growth phenotypes. We next sought to test the contributions of MiT/TFE to PDA tumorigenicity in vivo. Significantly, TFE3 or MITF knockdown virtually abolished xenograft tumor growth of PDA cells. In reciprocal gain-of-function studies, we investigated the impact of MITF overexpression on the tumorigenicity of primary KrasG12D-expressing mouse ductal epithelial cells. KrasG12D control cells formed only focal low-grade PanIN-like lesions by six weeks following orthotopic injection, whereas co-expression of MITF induced the expression of autophagy-lysosome genes and resulted in large orthotopic tumors in mice. In summary, our work places a new focus on lysosome regulation by MiT/TFE proteins as a nexus for metabolic reprogramming in PDA cells. Beyond serving a generic housekeeping role, lysosomes show increased activity in PDA and are critical integrators of major routes for nutrient scavenging and metabolic adaptation, providing an alternate pathway for maintaining intracellular AA stores. These studies also demonstrate activation of clearance pathways converging on the lysosome as a novel hallmark of aggressive malignancy.

Citation Format: Rushika M. Perera, Svetlana Stoykova, Brandon N. Nicolay, Kenneth N. Ross, Julien Fitamant, Myriam Boukhali, Vikram Deshpande, Martin K. Selig, Cristina R. Ferrone, Jeff Settleman, Gregory Stephanopoulos, Nicholas J. Dyson, Roberto Zoncu, Sridhar Ramaswamy, Wilhelm Haas, Nabeel M. Bardeesy. Transcriptional mechanisms for autophagy regulation and metabolic reprogramming in pancreatic cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr NG08. doi:10.1158/1538-7445.AM2015-NG08

Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform "identification of direct RNA interacting proteins" (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors-including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers, and modifiers-that synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. Although Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes.

Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis

Chromatin-modifying enzymes are predominantly nuclear; however, these factors are also localized to the cytoplasm, and very little is known about their role in this compartment. In this report, we reveal a non-chromatin-linked role for the lysine-specific demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation complex and affects the distribution of translation initiation factors within polysome fractions. Furthermore, KDM4A depletion reduced protein synthesis and enhanced the protein synthesis suppression observed with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Finally, we demonstrate that JIB-04, a JmjC demethylase inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected cytoplasmic role for KDM4A in regulating protein synthesis and suggest novel potential therapeutic applications for this class of enzyme.

SIGNIFICANCE

This report documents an unexpected cytoplasmic role for the lysine demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation machinery, regulates protein synthesis and, upon coinhibition with mTOR inhibitors, enhances the translation suppression and cell sensitivity to these therapeutics.

[Human retrovirus XMRV: The end of an exciting story?]

Viruses represent an important cause of cancer in humans: infections are estimated to account for close to one cancer case out of five.With the ongoing discovery of new infectious agents, this number should be raising in the near future. In 2006, the discovery of a new _-retrovirus in prostate cancer biopsies launched an intense research activity: could this new xenotropic MLV-related virus (XMRV) be the cause of prostate cancer? Five years later, the initial enthusiasm of retrovirologists has dramatically diminished. One by one, arguments favouring the hypothesis of human infection with XMRV are being refuted. The aim of this review article is to present the discovery of XMRV and to analyze recent data arguing against its existence in humans. A synthetic interpretation of XMRV literature will then be suggested.