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Shah, A.

Publications and source records attributed to Shah, A..

At least 91 records · Page 5Linked to original sources
bioRxiv2021

Functional insights of two MATE transporters from Vibrio fluvialis

Functional characterization of H- and D-MATE (Multidrug and Toxin Extrusion) transporters from clinical isolates of Vibrio fluvialis revealed H-type conferred resistance to fluoroquinolones, ethidium bromide and safranin whereas D-type exhibited marginal resistance towards ethidium bromide only. Both H-/D-type transporters were inhibited by reserpine resulting in increased intracellular norfloxacin concentration. The efflux was facilitated by both Na+/K+ ions, suggesting that these efflux pumps were ion-dependent. In presence of various classes of EPIs, there was decrease in MIC exhibited by H-/D-type efflux pumps towards norfloxacin which didnt translate into transport inhibition. But reserpine presented a conclusive pattern with decrease in MIC towards norfloxacin and increased norfloxacin accumulation inferring maximum inhibition. Substrate binding and electrostatic charge distribution of both the transporters was similar to other known MATE transporters. The H-type exhibited 10 transmembranes and D-type exhibited 11 TMs which was different from other MATE transporters known to have 12 TMs (Transmembranes). Data derived from molecular docking and ion binding studies revealed that Aspartic Acid residue in 1st TM acts as ion binding site with transport mechanism similar to NorM. Electrostatic potential map of both the transporters revealed that there is a cavity formation within the transporters surrounded by charged electronegative amino acid residues. Interestingly, surface models of both transporters revealed that 1st TM forms covalent bond with 7th TM towards extracellular space. Docking studies also revealed that reserpine covalently binds to central pocket of both transporters and serves as excellent EPI against these transporters as evidenced by MIC and drug accumulation assays.

microbiology↗
bioRxiv2020

Clinical positioning of the IAP antagonist tolinapant (ASTX660) in colorectal cancer

Cancer cells frequently express elevated levels of Inhibitor of Apoptosis Proteins (IAPs): cIAPI, cIAP2 and XIAP. Elevated expression of cIAP1 and cIAP2 (but not XIAP) significantly correlated with poor prognosis in microsatellite stable (MSS) stage-III colorectal cancer (CRC) patients treated with adjuvant chemotherapy, suggesting their involvement in promoting resistance. Preclinical analysis of the IAP inhibitor tolinapant in CRC cell lines demonstrated robust on-target effects and caspase-8-dependent apoptosis that was inhibited by the caspase-8 paralogs FLIP and, unexpectedly, caspase-10. Importantly, tolinipant-induced apoptosis was augmented by standard-of-care chemotherapy (FOLFOX) in CRC disease models, due (at least in part) to FOLFOX-induced downregulation of Class-I histone deacetylases, leading to acetylation of the FLIP-binding partner Ku70 and downregulation of FLIP. Moreover, this effect could be phenocopied using a Class-I HDAC inhibitor. Further analyses revealed that caspase-8-knockout RIPK3-positive CRC models were sensitive to tolinostat-induced necroptosis, an effect that could be exploited with the FDA-approved caspase inhibitor emricasan. Our study provides evidence for immediate clinical exploration of tolinapant in combination with FOLFOX chemotherapy in poor prognosis MSS CRC with elevated cIAP1/2 expression.

cancer biology↗
bioRxiv2020

Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells

Changes in gene regulation and expression govern orderly transitions from hematopoietic stem cells to terminally differentiated blood cell types. These transitions are disrupted during leukemic transformation but knowledge of the gene regulatory changes underpinning this process is elusive. We hypothesised that identifying core gene regulatory networks in healthy hematopoietic and leukemic cells could provide insights into network alterations that perturb cell state transitions. A heptad of transcription factors (LYL1, TAL1, LMO2, FLI1, ERG, GATA2, RUNX1) bind key hematopoietic genes in human CD34+ haematopoietic stem and progenitor cells (HSPCs) and have prognostic significance in acute myeloid leukemia (AML). These factors also form a densely interconnected circuit by binding combinatorially at their own, and each others, regulatory elements. However, their mutual regulation during normal haematopoiesis and in AML cells, and how perturbation of their expression levels influences cell fate decisions remains unclear. Here, we integrated bulk and single cell data and found that the fully connected heptad circuit identified in healthy HSPCs persists with only minor alterations in AML, and that chromatin accessibility at key heptad regulatory elements was predictive of cell identity in both healthy progenitors and in leukemic cells. The heptad factors GATA2, TAL1 and ERG formed an integrated sub-circuit that regulates stem cell to erythroid transition in both healthy and leukemic cells. Components of this triad could be manipulated to facilitate erythroid transition providing a proof of concept that such regulatory circuits could be harnessed to promote specific cell type transitions and overcome dysregulated haematopoiesis.

cancer biology↗
bioRxiv2020

A roadmap for the characterization of energy metabolism in human cardiomyocytes derived from induced pluripotent stem cells

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are an increasingly employed model in cardiac research and drug discovery. A significant limitation with respect to clinical translation is their immature structural and functional phenotype. Cellular metabolism plays an integral role in determining phenotype but the metabolic profile of hiPSC-CM during maturation is poorly characterized. In this study we employ a combination of methods including extracellular flux and 13C-glucose flux analyses to study the metabolic profile of hiPSC-CM over a 12 week maturation period. Results show a progressive remodeling of pathways involved in energy metabolism and substrate utilization. The oxidative capacity of hiPSC-CM and particularly their ability to utilize fatty acids increased with time. In parallel, relative glucose oxidation was reduced while glutamine oxidation was maintained at similar levels. Anaerobic glycolysis as assessed by lactate production was maintained throughout the 12 week period but with significant alterations in proximal glycolytic enzymes such as hexokinase and phosphofructokinase. We also observed a progressive maturation of mitochondrial oxidative capacity at comparable levels of mitochondrial content between timepoints. The time-dependent restructuring of the hiPSC-CM metabolic profile indicates their potential to overcome the lack of full maturation previously reported and enhance their applicability for pharmacological studies and cardiac disease modeling.

cell biology↗
bioRxiv2020

Mantis shrimp rank the shape of an object over its color during recognition

Mantis shrimp are predatory crustaceans that commonly occupy burrows in shallow, tropical waters worldwide. Most of these animals inhabit structurally complex, benthic environments with an abundance of visual features that are regularly observed, including conspecifics, predators, prey, and landmarks for use in navigation. While these animals are capable of learning and discriminating color and polarization, it is unknown what specific attributes of a visual object are important for its recognition. Here we show that mantis shrimp of the species Neogonodactylus oerstedii can learn the shape of a trained target. Furthermore, when the shape and color of a target which they had been trained to identify were placed in conflict, N. oerstedii significantly chose the target of the trained shape over the target of the trained color. Thus, we conclude that the shape of a target is more important than its color for its recognition by N. oerstedii. Our findings suggest that the shapes of learned structures, such as landmarks or other animals, are important for N. oerstedii during object recognition.

animal behavior and cognition↗
bioRxiv2020

Elucidating the mechanism of cyclodextrins in the treatment of Niemann-Pick Disease Type C using crosslinked 2-hydroxypropyl-β-cyclodextrin

Niemann-Pick Disease Type C (NPC) is a severe neurovisceral disorder that is pathophysiologically characterized by intracellular transport abnormalities leading to cytoplasmic accumulation of lipids such as cholesterol and multiple sphingolipids, including sphingosine. The compound 2-hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) is a compound with high cholesterol complexation capacity and is currently under clinical investigation for the treatment of NPC. However, due to its short blood half-life, high doses are required to produce a therapeutic effect. It has been reported in mice that HP{beta}CDs circulation time and efficacy can be improved by increasing its size via polymerization, but the biodegradable nature of these systems did not allow the contribution of the macromolecule to the activity to be determined. In this work, stable forms of polymerized HP{beta}CD were generated (via epichlorohydrin crosslinking) to investigate their in vitro mechanisms of action and in vivo effects. Crosslinked CDs (8-312 kDa) displayed a 10-fold greater complexation capacity towards cholesterol than monomeric HP{beta}CD but were taken up by cells to a lower extent (in a size-dependent fashion), resulting in an overall comparable in vitro effect on intracellular cholesterol accumulation that was dependent on cholesterol complexation. When tested in vivo, the crosslinked 19.3 kDa HP{beta}CD exhibited a longer terminal half-life than the monomeric HP{beta}CD. However, it did not increase the life span of Npc1 mice, possibly due to reduced organ penetration and brain diffusion consequence of its large molecular weight. This could be circumvented by the application of magnetic resonance imaging-guided low intensity-pulsed focused ultrasound (MRIg-FUS), which increased the brain penetration of the CD. In conclusion, stable forms of polymerized HP{beta}CD constitute valuable tools to elucidate CDs mechanism of action. Moreover, the use of MRIg-FUS to maximize CDs tissue penetration warrants further investigation, as it may be key to harnessing CDs full therapeutic potential in the treatment of NPC. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/230136v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@3dbaf1org.highwire.dtl.DTLVardef@bc255dorg.highwire.dtl.DTLVardef@390e7borg.highwire.dtl.DTLVardef@1e5e5c5_HPS_FORMAT_FIGEXP M_FIG C_FIG The 2-hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) is a well-established pharmaceutical excipient that can complex cholesterol and is currently under clinical investigation to treat Niemann-Pick Disease Type C (NPC). However, high doses of the drug are needed to achieve a therapeutic effect. Using stable and long circulating crosslinked HP{beta}CDs, this study attempts to further understand the mechanisms behind CDs activity.

pharmacology and toxicology↗
bioRxiv2020

IP6K1 upregulates the formation of processing bodies by promoting proteome remodeling on the mRNA cap

Inositol hexakisphosphate kinases (IP6Ks) are ubiquitously expressed small molecule kinases that catalyze the conversion of the inositol phosphate IP6 to 5-IP7. IP6Ks have been reported to influence cellular functions by protein-protein interactions independent of their enzymatic activity. Here, we show that IP6K1 regulates the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that serve as sites for storage of translationally repressed mRNA. Cells with reduced levels of IP6K1 display a dramatic reduction in the number of P-bodies, which can be restored by the expression of active or catalytically inactive IP6K1. IP6K1 does not localize to P-bodies, but instead facilitates the formation of P-bodies by promoting translation suppression. We demonstrate that IP6K1 is present on ribosomes, where it interacts with proteins that constitute the mRNA decapping complex - the scaffold protein EDC4, activator proteins DCP1A/B, and the decapping enzyme DCP2. IP6K1 also interacts with components of the eIF4F translation initiation complex - the scaffolding protein eIF4G1, the RNA helicase eIF4A2, and the cap binding protein eIF4E. The RNA helicase DDX6 and the eIF4E binding protein 4E-T are known to promote translation suppression to facilitate P-body formation. We show that IP6K1 binds to DDX6 and promotes the interaction of DDX6 and 4E-T with the cap binding protein eIF4E, and also enhances the binding between DDX6 and EDC4, thus acting to suppress mRNA translation and promote mRNA decapping. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translation repression over initiation, and thus leading to the formation of P-bodies.

cell biology↗
bioRxiv2020

Gatekeeper transcription factors regulate switch between lineage preservation and cell plasticity

Reprogramming somatic cells to pluripotency by repressing lineage-instructive transcription factors (TFs) alone has not been pursued because lineage specification is thought to be regulated by transcriptional regulatory networks (TRNs) comprising of multiple TFs rather than by single pivotal "gatekeeper" TFs. Utilizing an intra-species somatic cell hybrid model, we identified Snai2 and Prrx1 as the most critical determinants of mesenchymal commitment in rat embryonic fibroblasts (REFs) and demonstrate that siRNA-mediated knockdown of either of these master regulators is adequate to convert REFs into functional adipocytes, chondrocytes or osteocytes without requiring exogenous TFs or small molecule cocktails. Furthermore, knockdown of Snai2 alone proved sufficient to transform REFs to dedifferentiated pluripotent stem-like cells (dPSCs) that formed embryoid bodies capable of triple germ-layer differentiation. These findings suggest that inhibition of a single gatekeeper TF in a lineage committed cell is adequate for acquisition of cell plasticity and reprogramming without requiring permanent genetic modification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/999433v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1acdb83org.highwire.dtl.DTLVardef@17fb3ddorg.highwire.dtl.DTLVardef@f994c9org.highwire.dtl.DTLVardef@197541e_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic diagram depicting transdifferentiation of REFs into adipocytes, osteocytes, chondrocytes and dedifferentiation into MSCs on individual treatment with siSnai2 or siPrrx1. dPSCs were generated only in the siSnai2 group.

cell biology↗
bioRxiv2020

A pyro-phosphodegron controls MYC polyubiquitination to regulate cell survival

The transcription factor MYC regulates cell survival and growth, and its level is tightly controlled in normal cells. Here, we report that serine pyrophosphorylation - an enigmatic posttranslational modification triggered by inositol pyrophosphate signaling molecules - controls MYC levels via regulated protein degradation. We find that endogenous MYC is stabilized and less polyubiquitinated in cells with reduced inositol pyrophosphates. We show that the inositol pyrophosphate 5-IP7 transfers its high-energy beta phosphate moiety to pre-phosphorylated serine residues in the central PEST domain of MYC. Pyrophosphorylation of MYC promotes its interaction with the E3 ubiquitin ligase FBW7, thereby enhancing MYC polyubiquitination and degradation. FBW7 can bind directly to the PEST domain of MYC in a pyrophosphorylation-dependent manner. A stabilized, pyrophosphorylation-deficient form of MYC increases cell death during growth stress in untransformed cells, and promotes cell proliferation in response to mitogens. Thus, control of MYC stability through a novel pyro-phosphodegron provides unexpected insight into the regulation of cell survival in response to environmental cues.

cell biology↗
bioRxiv2019

The demyelinating agent cuprizone induces a male-specific reduction in binge eating in the binge-prone C57BL/6NJ strain

Binge eating (BE) is a heritable symptom of eating disorders with an unknown genetic etiology. Rodent models for BE of palatable food permit the study of genetic and biological mechanisms. We previously used genetic mapping and transcriptome analysis to map a coding mutation in Cyfip2 associated with increased BE in the BE-prone C57BL/6NJ substrain compared to the BE-resistant C57BL/6J substrain. The increase in BE in C57BL/6NJ mice was associated with a decrease in transcription of genes enriched for myelination in the striatum. Here, we tested the hypothesis that decreasing myelin levels with the demyelinating agent cuprizone would enhance BE. Mice were treated with a 0.3% cuprizone home cage diet for two weeks. Following a three-week recovery period, mice were trained for BE in an intermittent, limited access procedure. Cuprizone induced similar weight loss in both substrains and sexes that recovered within 48 h after removal of the cuprizone diet. Surprisingly, cuprizone reduced BE in male but not female C57BL/6NJ mice while having no effect in C57BL/6J mice. Cuprizone also reduced myelin basic protein (MBP) at seven weeks post-cuprizone removal while having no effect on myelin-associated glycoprotein (MAG) at this time point. C57BL/6N mice also showed less MBP than C57BL/6J mice. There were no statistical interactions of Treatment with Sex on MBP levels, indicating that differences in MBP are unlikely to account for sex differences in BE. To summarize, cuprizone induced an unexpected, male-specific reduction in BE which could indicate sex-specific biological mechanisms that depend on genetic background.

neuroscience↗
bioRxiv2019

BET proteins are required for transcriptional activation of the senescent beta cell secretome in Type 1 Diabetes

OBJECTIVEType 1 Diabetes (T1D) results from progressive loss of pancreatic beta cells due to autoimmune destruction. We recently reported that during the natural history of T1D in humans and the female nonobese diabetic (NOD) mouse model, beta cells acquire a senescence-associated secretory phenotype (SASP) that is a major driver of disease onset and progression, but the mechanisms that activate SASP in beta cells were not explored. The objective of this study was to identify transcriptional mechanisms of SASP activation in beta cells.\n\nMETHODSWe used the female NOD mouse model of spontaneous autoimmune T1D and ex vivo experiments on NOD mouse and human islets to test the hypothesis that Bromodomain Extra-Terminal domain (BET) proteins activate the beta cell SASP transcriptional program.\n\nRESULTSHere we show that beta cell SASP is transcriptionally controlled by BET proteins, including BRD4. Chromatin analysis of key beta cell SASP genes in NOD islets revealed binding of BRD4 at active regulatory regions. BET protein inhibition in NOD islets diminished not only the transcriptional activation and secretion of SASP factors but also the non-cell autonomous activity. BET protein inhibition also decreased the extent of SASP induction in human islets exposed to DNA damage. The BET protein inhibitor iBET-762 prevented diabetes in NOD mice and also attenuated SASP in beta cells in vivo.\n\nCONCLUSIONSTaken together, our findings support a crucial role for BET proteins in the activation of the beta cell SASP transcriptional program. These studies suggest avenues for preventing T1D by transcriptional inhibition of SASP.

physiology↗
bioRxiv2019

Optogenetic Modulation of Cortical Neurons Using Organic Light Emitting Diodes (OLEDs)

ObjectiveThere is a need for low power, scalable photoelectronic devices and systems for emerging optogenetic needs in neuromodulation. Conventional light emitting diodes (LEDs) are constrained by power and lead-counts necessary for scalability. Organic LEDs (OLEDs) offer an exciting approach to decrease power and lead-counts while achieving high channel counts on thin, flexible substrates that conform to brain surfaces or peripheral neuronal fibers. In this study, we investigate the potential for using OLEDs to modulate neuronal networks cultured in vitro on a transparent microelectrode array (MEA) and subsequently validate neurostimulation in vivo in a transgenic mouse model.\n\nApproachCultured mouse cortical neurons were transfected with light-sensitive opsins such as blue-light sensitive channel-rhodopsin (ChR2) and green-light sensitive chimeric channel-rhodopsin (C1V1tt) and stimulated using blue and green OLEDs (with 455 and 520 nm peak emission spectra respectively) at a power of 1 mW/mm2 under pulsed conditions.\n\nMain resultsWe demonstrate neuromodulation and optostimulus-locked, single unit-neuronal activity in neurons expressing stimulating and inhibiting opsins (n=4 MEAs, each with 16 recordable channels). We also validated the optostimulus-locked response in a channel-rhodopsin expressing transgenic mouse model, where at least three isolatable single neuronal cortical units respond to OLED stimulation.\n\nSignificanceThe above results indicate the feasibility of generating sufficient luminance from OLEDs to perform neuromodulation both in vitro and in vivo. This opens up the possibility of developing thin, flexible OLED films with multiple stimulation sites that can conform to the shape of the neuronal targets in the brain or the peripheral nervous system. However, stability of these OLEDs under chronic conditions still needs to be carefully assessed with appropriate packaging approaches.

bioengineering↗
bioRxiv2019

Loss of adipocyte identity through synergistic repression of PPARγ by TGF-β and mechanical stress

Adipocytes convert into myofibroblasts in a TGF-{beta}-dependent mouse model of fibrosis. The molecular steps and timing underlying this conversion are poorly understood, hindering development of antifibrotic therapies. Here we used two single-cell approaches, lineage tracing and live-cell imaging of an adipocyte marker PPAR{gamma}, to track the fate of adipocytes induced to convert by TGF-{beta}. We found that TGF-{beta} alone was not sufficient to activate the TGF-{beta} pathway and to induce myofibroblast conversion in cells with high PPAR{gamma} expression. However, robust conversion was observed when an additional PPAR{gamma}-inhibiting stimulus, mechanical stress applied by increasing adhesion area on a stiff matrix, was applied simultaneously with TGF-{beta}. We show that the PPAR{gamma} downregulation in response to increased adhesion area required both fibronectin and a sufficiently stiff extracellular matrix (ECM) and was partially mediated by Rho. Our results show for the first time the order of the molecular processes driving fat tissue fibrosis and the requirement for signal convergence for the loss of adipocyte identity.

cell biology↗
bioRxiv2019

HIV infection and incidence of cardiovascular diseases: an analysis of a large healthcare database

BackgroundPersons living with HIV (PLWH) experience higher risk of cardiovascular diseases (CVD) such as myocardial infarction (MI) and heart failure (HF) compared to uninfected individuals. Risk of other CVDs in PLWH has received less attention. MethodsWe studied 19,798 PLWH and 59,302 age and sex-matched uninfected individuals identified from the MarketScan Commercial and Medicare databases in the period 2009-2015. Incidence of CVDs, including MI, HF, atrial fibrillation (AF), peripheral artery disease (PAD), stroke and any CVD-related hospitalization, were identified using validated algorithms. We used adjusted Cox models to estimate hazard ratios (HR) and 95% confidence interval (95%CI) of CVD endpoints and performed probabilistic bias analysis to control for unmeasured confounding by race. ResultsAfter a mean (median) follow-up of 20 (17) months, study patients experienced 154 MIs, 223 HF, 93 stroke, 397 AF, 98 PAD and 935 CVD hospitalizations. HR (95%CI) comparing PLWH to uninfected controls were 1.3 (0.9, 1.9) for MI, 3.2 (2.4, 4.2) for HF, 2.7 (1.7, 4.0) for stroke, 1.2 (1.0, 1.5) for AF, 1.1 (0.7, 1.7) for PAD, and 1.7 (1.5, 2.0) for any CVD-related hospitalization. Adjustment for unmeasured confounding led to similar associations [1.2 (0.8, 1.8) for MI, 2.8 (2.0, 3.8) for HF, 2.3 (1.5, 3.6) for stroke, 1.3 (1.0, 1.7) for AF, 0.9 (0.5, 1.4) for PAD, and 1.6 (1.3, 1.9) for CVD hospitalization]. ConclusionUsing a large health insurance database, we showed that PLWH have an elevated risk of CVD, particularly HF and stroke. With the aging of the HIV population, developing interventions for cardiovascular health promotion and CVD prevention is imperative.

epidemiology↗
bioRxiv2018

Enhancer Reprogramming Confers Dependence on Glycolysis and IGF signaling in KMT2D Mutant Melanoma

Epigenetic modifiers have emerged as important regulators of tumor progression. We identified histone methyltransferase KMT2D as a potent tumor-suppressor through an in vivo epigenome-focused pooled RNAi screen in melanoma. KMT2D harbors frequent somatic point mutations in multiple tumor types. How these events contribute to tumorigenesis and whether they impart therapeutic vulnerability are poorly understood. To address these questions, we generated a genetically engineered mouse model of melanoma based on conditional and melanocyte-specific deletion of KMT2D. We demonstrate KMT2D as a bona fide tumor suppressor which cooperates with activated BRAF. KMT2D-deficient tumors showed substantial reprogramming of key metabolic pathways including glycolysis. Glycolysis enzymes, intermediate metabolites and glucose consumption rate were aberrantly upregulated in KMT2D mutant cells. The pharmacological inhibition of glycolysis reduced proliferation and tumorigenesis preferentially in KMT2D mutant cells. Mechanistically, KMT2D loss caused drastic reduction of H3K4me1-marked active enhancer states. Loss of distal enhancer and subsequent reduction in expression of IGFBP5 activated IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating increased usage of glycolysis pathway for enhanced biomass needs via enhancer reprogramming. Our data imply that inhibition of glycolysis or IGFR pathway could be a potential therapeutic strategy in KMT2D mutant tumors.

cancer biology↗
bioRxiv2018

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence elements in their target transcripts. Despite the expanding list of RBPs with in vivo binding sites mapped genomewide using crosslinking and immunoprecipitation (CLIP), defining precise RBP binding specificity remains challenging. We previously demonstrated that the exact protein-RNA crosslink sites can be mapped using CLIP data at single-nucleotide resolution and observed that crosslinking frequently occurs at specific positions in RBP motifs. Here we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the resulting motifs by genome-wide analysis of allelic binding sites also detected by CLIP. We found that the prototypical SR protein SRSF1 recognizes GGA clusters to regulate splicing in a much larger repertoire of transcripts than previously appreciated.

molecular biology↗
bioRxiv2018

Metabolically activated macrophages in mammary adipose tissue link obesity to triple-negative breast cancer

Obesity is associated with increased incidence and severity of triple-negative breast cancer (TNBC); however, mechanisms underlying this relationship are incompletely understood. Macrophages, which accumulate in adipose tissue and are activated during obesity, are an attractive mechanistic link. Here, we show that, during obesity, murine and human mammary adipose tissue macrophages adopt a pro-inflammatory, metabolically- activated (MMe) macrophage phenotype that promotes TNBC stem-like markers and functions, including increased tumorsphere growth in vitro and tumor-initiating potential in vivo. We demonstrate that MMe macrophages release cytokines in an NADPH oxidase 2 (NOX2)-dependent manner that signal through glycoprotein 130 (GP130) on TNBC cells to promote their stem-like properties. Accordingly, deleting Nox2 in myeloid cells or depleting GP130 in TNBC cells attenuates the ability of obesity to drive TNBC tumor formation. Our studies implicate MMe macrophage accumulation in mammary adipose tissue during obesity as a mechanism for promoting TNBC stemness and tumorigenesis.\n\nHIGHLIGHTS Obesity promotes TNBC tumor formation and stemness.\nMammary adipose tissue macrophages are metabolically activated (MMe) in obese mice and humans.\nMMe macrophages in mammary adipose tissue contribute to obesity-induced stemness.\nMMe macrophages promote TNBC stemness through GP130 signaling.

cancer biology↗