Circular RNA-ZNF532 regulates diabetes-induced retinal pericyte degeneration and vascular dysfunction

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Abstract

Diabetic retinopathy (DR) is the leading cause of blindness in working-age adults. Vascular pericyte degeneration is the predominant clinical manifestation of DR, yet the mechanism governing pericyte degeneration is poorly understood. Circular RNAs (circRNAs) play important roles in multiple biological processes and disease progression. Here, we investigated the role of circRNA in pericyte biology and diabetes-induced retinal vascular dysfunction. cZNF532 expression was upregulated in pericytes under diabetic stress, in the retinal vessels of a diabetic murine model, and in the vitreous humor of diabetic patients. cZNF532 silencing reduced the viability, proliferation, and differentiation of pericytes and suppressed the recruitment of pericytes toward endothelial cells in vitro. cZNF532 regulated pericyte biology by acting as a miR-29a-3p sponge and inducing increased expression of NG2, LOXL2, and CDK2. Knockdown of cZNF532 or overexpression of miR-29a-3p aggravated streptozotocin-induced retinal pericyte degeneration and vascular dysfunction. By contrast, overexpression of cZNF532 or inhibition of miR-29a-3p ameliorated human diabetic vitreous-induced retinal pericyte degeneration and vascular dysfunction. Collectively, these data identify a circRNA-mediated mechanism that coordinates pericyte biology and vascular homeostasis in DR. Induction of cZNF532 or antagonism of miR-29a-3p is an exploitable therapeutic approach for the treatment of DR.

Authors

Qin Jiang, Chang Liu, Chaopeng Li, Shanshan Xu, Mudi Yao, Huimin Ge, Yanan Sun, Xiumiao Li, Shujie Zhang, Kun Shan, Baihui Liu, Jin Yao, Chen Zhao, Biao Yan

The landscape of RNA polymerase II associated chromatin interactions in prostate cancer

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Abstract

Transcriptional dysregulation is a hallmark of prostate cancer (PCa). We mapped the RNA Polymerase II (RNA Pol II) associated chromatin interactions in normal prostate cells and PCa cells. We discovered thousands of enhancer-promoter, enhancer-enhancer, as well as promoter-promoter chromatin interactions. These transcriptional hubs operate within the framework set by structural proteins—CTCF and cohesins, and are regulated by the cooperative action of master transcription factors, such as the Androgen Receptor (AR) and FOXA1. By combining analyses from metastatic castration resistant PCa (mCRPC) specimens, we show that AR locus amplification contributes to the transcriptional up-regulation of AR gene by increasing the total number of chromatin interaction modules comprising of the AR gene and its distal enhancer. We deconvoluted the transcription control modules of several PCa genes, notably, the biomarker KLK3, lineage-restricted genes (KRT8, KRT18, HOXB13, FOXA1, ZBTB16), the drug target EZH2, and the oncogene MYC. By integrating clinical PCa data, we defined a novel germline-somatic interplay between the PCa risk allele rs684232 and the somatically acquired TMPRSS2-ERG gene fusion in the transcriptional regulation of multiple target genes—VPS53, FAM57A and GEMIN4. Our studies implicate changes in genome organization as a critical determinant of aberrant transcriptional regulation in PCa.

Authors

Susmita G. Ramanand, Yong Chen, Jiapei Yuan, Kelly Daescu, Maryou Lambros, Kathleen E. Houlahan, Suzanne Carreira, Wei Yuan, GuemHee Baek, Adam Sharp, Alec Paschalis, Mohammed Kanchwala, Yunpeng Gao, Adam Aslam, Nida Safdar, Xiaowei Zhan, Ganesh V. Raj, Chao Xing, Paul C. Boutros, Johann de Bono, Michael Q. Zhang, Ram S. Mani

Targeting glutamine metabolism enhances tumor specific immunity by modulating suppressive myeloid cells

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Abstract

Myeloid cells comprise a major component of the tumor-microenvironment (TME) promoting tumor growth and immune evasion. By employing a novel small molecule inhibitor of glutamine metabolism, not only were we able to inhibit tumor growth, but we markedly inhibited the generation and recruitment of myeloid-derived suppressor cells (MDSCs). Targeting tumor glutamine metabolism led to a decrease in CSF3 and hence recruitment of MDSCs as well immunogenic cell death leading to an increase in inflammatory tumor-associated macrophages (TAMs). Alternatively, inhibiting glutamine metabolism of the MDSCs themselves led to activation induced cell death and conversion of MDSCs to inflammatory macrophages. Surprisingly, blocking glutamine metabolism also inhibited IDO expression of both the tumor and myeloid derived cells leading to a marked decrease in kynurenine levels. This in turn inhibited the development of metastasis and further enhanced anti-tumor immunity. Indeed, targeting glutamine metabolism rendered checkpoint blockade-resistant tumors susceptible to immunotherapy. Overall, our studies define an intimate interplay between the unique metabolism of tumors and the metabolism of suppressive immune cells.

Authors

Min-Hee Oh, Im-Hong Sun, Liang Zhao, Robert D. Leone, Im-Meng Sun, Wei Xu, Samuel L. Collins, Ada J. Tam, Richard L. Blosser, Chirag H. Patel, Judson M. Englert, Matthew L. Arwood, Jiayu Wen, Yee Chan-Li, Lukáš Tenora, Pavel Majer, Rana Rais, Barbara S. Slusher, Maureen R. Horton, Jonathan D. Powell

HDAC inhibitors elicit metabolic reprogramming by targeting super-enhancers in glioblastoma models

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Abstract

The Warburg effect is a tumor related phenomenon that may be targeted therapeutically. Here, we showed that glioblastoma cultures and patient tumors harbored super-enhancers in several genes related to the Warburg effect. By conducting a transcriptome analysis followed by chromatin immunoprecipitation (CHIP) sequencing coupled with a comprehensive metabolite analysis in GBM models, we unraveled that FDA-approved global (panobinostat, vorinostat) and selective (romidepsin) histone-deacetylase (HDAC) inhibitors elicited metabolic reprogramming in concert with disruption of several Warburg-effect related super-enhancers. Extracellular flux and carbon tracing analyses revealed that HDAC inhibitors blunted glycolysis in a c-Myc dependent manner accompanied by lower ATP levels. This resulted in engagement of oxidative phosphorylation (OXPHOS) driven by elevated fatty acid oxidation (FAO), rendering GBM cells dependent on these pathways. Mechanistically, interference with HDAC1/2 elicited a suppression of c-Myc protein levels and a concomitant increase of two transcriptional drivers of oxidative metabolism, PGC1A and PPARD, suggesting an inverse relationship. Rescue and CHIP experiments indicated that c-Myc bound to the promoter regions of PGC1A and PPARD to counteract their up-regulation driven by HDAC1/2 inhibition. Finally, we demonstrated that the combination treatment of HDAC and FAO inhibitors extended animal survival in patient-derived xenograft (PDX) model systems in vivo more potently than single treatments in the absence of toxicity.

Authors

Trang Nguyen, Yiru Zhang, Enyuan Shang, Chang Shu, Consuelo Torrini, Junfei Zhao, Elena Bianchetti, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Arif O. Harmanci, Zhengdeng Lei, Mark Maienschein-Cline, Catarina Maria Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N. Bruce, Peter Canoll, Markus D. Siegelin

HuR/ELAVL1 drives malignant peripheral nerve sheath tumour growth and metastasis

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Abstract

Cancer cells can develop a strong addiction to discrete molecular regulators, which control the aberrant gene expression programs that drive and maintain the cancer phenotype. Here, we report the identification of the RNA-binding protein HuR/ELAVL1 as a central oncogenic driver for malignant peripheral nerve sheath tumours (MPNSTs), which are highly aggressive sarcomas that originate from cells of the Schwann cell lineage. HuR was found to be highly elevated and bound to a multitude of cancer-associated transcripts in human MPNST samples. Accordingly, genetic and pharmacological inhibition of HuR had potent cytostatic and cytotoxic effects on tumour growth, and strongly supressed metastatic capacity in vivo. Importantly, we linked the profound tumorigenic function of HuR to its ability to simultaneously regulate multiple essential oncogenic pathways in MPNST cells, including the Wnt/beta-Catenin, YAP/TAZ, Rb-E2F and BET proteins, which converge on key transcriptional networks. Given the exceptional dependency of MPNST cells on HuR for survival, proliferation, and dissemination, we propose that HuR represents a promising therapeutic target for MPNST treatment.

Authors

Marta Palomo-Irigoyen, Encarnación Pérez-Andrés, Marta Iruarrizaga-Lejarreta, Adrián Barreira Manrique, Miguel Tamayo-Caro, Laura Vila-Vecilla, Leire Moreno-Cugnon, Nagore Beitia Telletxea, Daniela Medrano, David Fernández-Ramos, Juan-Jose Lozano, Satoshi Okawa, José Luis Lavín, Natalia Martin-Martin, James D. Sutherland, Virginia Gutiérrez-de Juan, Monika Gonzalez-Lopez, Nuria Macias-Camara, David Mosén-Ansorena, Liyam Laraba, C. Oliver Hanemann, Emanuela Ercolano, David B. Parkinson, Christopher W. Schultz, Marcos J. Araúzo-Bravo, Alex M. Ascensión, Daniela Gerovska, Haizea Iribar, Ander Izeta, Peter Pytel, Philipp Krastel, Alessandro Provenzani, Pierfausto Seneci, Ruben D. Carrasco, Antonio del Sol, Maria L. Martinez Chantar, Rosa Barrio, Eduard Serra, Conxi Lázaro, Adrienne M. Flanagan, Myriam Gorospe, Nancy Ratner, Arkaitz Carracedo, Ana María Aransay, Marta Varela-Rey, Ashwin Woodhoo

Macrophages utilize a bet-hedging strategy for antimicrobial activity in phagolysosomal acidification

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Abstract

Microbial ingestion by a macrophage results in the formation of an acidic phagolysosome but the host cell has no information on the pH susceptibility of the ingested organism. This poses a problem for the macrophage and raises the fundamental question of how the phagocytic cell optimizes the acidification process to prevail. We analyzed the dynamical distribution of phagolysosomal pH in murine and human macrophages that had ingested live or dead Cryptococcus neoformans cells, or inert beads. Phagolysosomal acidification produced a range of pH values that approximated normal distributions, but these differed from normality depending on ingested particle type. Analysis of the increments of pH reduction revealed no forbidden ordinal patterns, implying that phagosomal acidification process was a stochastic dynamical system. Using simulation modeling, we determined that by stochastically acidifying a phagolysosome to a pH within the observed distribution, macrophages sacrificed a small amount of overall fitness to reduce their overall variation in fitness. Hence, chance in the final phagosomal pH introduces unpredictability to the outcome of the macrophage-microbe, which implies a bet-hedging strategy that benefits the macrophage. While bet hedging is common in biological systems at the organism level, our results show its use at the organelle and cellular level.

Authors

Quigly Dragotakes, Kaitlin M. Stouffer, Man Shun Fu, Yehonatan Sella, Christine Youn, Olivia Insun Yoon, Carlos M. De Leon-Rodriguez, Joudeh Freij, Aviv Bergman, Arturo Casadevall

IL-1β Suppression of VE-cadherin transcription underlies sepsis-induced inflammatory lung injury

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Abstract

Unchecked inflammation is a hallmark of inflammatory tissue injury in diseases such as acute respiratory distress syndrome (ARDS). Yet the mechanisms of inflammatory lung injury remain largely unknown. Here we showed that bacterial endotoxin lipopolysaccharide (LPS) and cecal ligation and puncture (CLP)-induced polymicrobial sepsis decreased the expression of transcription factor cAMP Response Element Binding (CREB) in lung endothelial cells. We demonstrated that endothelial CREB was crucial for VE-cadherin transcription and the formation of the normal restrictive endothelial adherens junctions. The inflammatory cytokine IL-1β reduced cAMP generation and CREB-mediated transcription of VE-cadherin. Furthermore, endothelial cell-specific deletion of CREB induced lung vascular injury whereas ectopic expression of CREB in the endothelium prevented the injury. We also observed that rolipram, which inhibits PDE4-mediated hydrolysis of cAMP, prevented endotoxemia-induced lung vascular injury since it preserved CREB-mediated VE-cadherin expression. These data demonstrate the fundamental role of endothelial cAMP-CREB axis in promoting lung vascular integrity and suppressing inflammatory injury. Therefore, strategies aimed at enhancing endothelial CREB-mediated VE-cadherin transcription are potentially useful in preventing sepsis-induced lung vascular injury in ARDS.

Authors

Shiqin Xiong, Zhigang Hong, Long Shuang Huang, Yoshikazu Tsukasaki, Saroj Nepal, Anke Di, Ming Zhong, Wei Wu, Zhiming Ye, XiaoPei Gao, Gadiparthi Rao, Dolly Mehta, Jalees Rehman, Asrar B. Malik

Pro-inflammatory P2Y14 receptor inhibition protects against ischemic acute kidney injury in mice

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Abstract

Ischemic acute kidney injury (AKI), a complication that frequently occurs in hospital settings, is often associated with hemodynamic compromise, sepsis, cardiac surgery or exposure to nephrotoxicants. Here, using a murine renal ischemia-reperfusion injury (IRI) model we show that intercalated cells (ICs) rapidly adopted a pro-inflammatory phenotype post-IRI. During the early phase of AKI, we demonstrate that either blocking the pro-inflammatory P2Y14 receptor located on the apical membrane of ICs, or ablation of the gene encoding the P2Y14 receptor in ICs: 1) inhibited IRI-induced chemokine expression increase in ICs; 2) reduced neutrophil and monocyte renal infiltration; 3) reduced the extent of kidney dysfunction; and 4) attenuated proximal tubule (PT) damage. These observations indicate that the P2Y14 receptor participates in the very first inflammatory steps associated with ischemic AKI. In addition, we show that the concentration of the P2Y14 receptor ligand, uridine diphosphate-glucose (UDP-Glc), was higher in urine samples from intensive care unit patients who developed AKI compared to patients without AKI. In particular, we observed a strong correlation between UDP-Glc concentration and the development of AKI in cardiac surgery patients. Our study identifies the UDP-Glc/P2Y14 receptor axis as a potential target for the prevention and/or attenuation of ischemic-AKI.

Authors

Maria Agustina Battistone, Alexandra C. Mendelsohn, Raul German Spallanzani, Andrew S. Allegretti, Rachel N. Liberman, Juliana Sesma, Sahir Kalim, Susan M. Wall, Joseph V. Bonventre, Eduardo R. Lazarowski, Dennis Brown, Sylvie Breton

T follicular regulatory cells and IL-10 promote food antigen-specific IgE

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Abstract

Food allergies are a major clinical problem and are driven by IgE antibodies specific for food antigens. T follicular regulatory (TFR) cells are a specialized subset of Foxp3+ T cells that modulate antibody responses. Here we analyzed the role of TFR cells in regulating antigen-specific IgE using a peanut-based food allergy model in mice. Peanut-specific IgE titers and anaphylaxis responses were significantly blunted in TFR cell-deficient Foxp3-cre Bcl6-fl/fl mice. Loss of TFR cells led to greatly increased non-specific IgE levels, showing that TFR cells have both helper and suppressor functions on IgE production in the GC that work together to facilitate the production of antigen-specific IgE. Foxp3-cre Pten-fl/fl mice with augmented TFR cell responses had markedly higher levels of peanut-specific IgE, revealing an active helper function by TFR cells on antigen-specific IgE. The helper function of TFR cells for IgE production involves IL-10, and the loss of IL-10 signaling by B cells led to a severely curtailed peanut-specific IgE response, decreased GC B cell survival and loss of GC dark zone B cells after peanut sensitization. We thus reveal that TFR cells have an unexpected helper role in promoting food allergy and are a novel target for drug development.

Authors

Markus M. Xie, Qiang Chen, Hong Liu, Kai Yang, Byunghee Koh, Hao Wu, Soheila J. Maleki, Barry K. Hurlburt, Joan Cook-Mills, Mark H. Kaplan, Alexander L. Dent

Notch signaling licenses allergic airway inflammation by promoting Th2 cell lymph node egress

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Abstract

Allergic asthma is mediated by T helper 2 (Th2) responses to inhaled allergens. Although previous experiments indicated that Notch signaling activates expression of the key Th2 transcription factor Gata3, it remains controversial how Notch promotes allergic airway inflammation. Here we show that T cell-specific Notch deficiency in mice prevented house dust mite-driven eosinophilic airway inflammation and significantly reduced Th2 cytokine production, serum IgE levels and airway hyperreactivity. However, transgenic Gata3 overexpression in Notch-deficient T cells only partially rescued this phenotype. We found that Notch signaling was not required for T cell proliferation or Th2 polarization. Instead, Notch-deficient in vitro polarized Th2 cells showed reduced accumulation in the lungs upon in vivo transfer and allergen challenge, as Notch-deficient Th2 cells were retained in the lung draining lymph nodes. Transcriptome analyses and sequential adoptive transfer experiments revealed that while Notch-deficient lymph node Th2 cells established competence for lung migration, they failed to upregulate the sphingosine 1-phosphate receptor (S1PR1) and its critical upstream transcriptional activator Krüppel-like factor 2 (KLF2). As this KLF2-S1PR1 axis represents the essential cell-intrinsic regulator of T cell lymph node egress, we conclude that the druggable Notch signaling pathway licenses the Th2 response in allergic airway inflammation via promoting lymph node egress.

Authors

Irma Tindemans, Anne van Schoonhoven, Alex KleinJan, Marjolein J.W. de Bruijn, Melanie Lukkes, Menno van Nimwegen, Anouk van den Branden, Ingrid M. Bergen, Odilia B. J. Corneth, Wilfred F.J. van IJcken, Ralph Stadhouders, Rudi W. Hendriks