Transcriptional Regulation Of Adipocyte Function

The increased white adipose tissue mass associated with obesity is the result of both hyperplasia and hypertrophy of adipocytes. While adipocyte development and transcriptional processes are well studied in vitro, regulation of in vivo genes (such as leptin), the identity of the adipocyte progenitor cells and the development of the adipose organ have not been defined invivo. In this thesis, firstly KLF4 was discovered to be an essential early regulator of adipogenesis. KLF4 together with Krox20 cooperatively transactivates C/EBPβ, suggesting that KLF4 and Krox20 are part of an immediate early transcriptional network. This network is upregulated in a lipodystrophic animal model, encoding a dominant negative transgene against C/EBP factors, suggesting that these animals carry hyper-adipogenic residual fat pads, which provide a niche for transplantation experiments for identifying possible adipocyte progenitors. When injected into the residual fat pads of lipodystrophic mouse, indeed, a cell population, sorted from stromavascular fraction reconstitutes a functional white adipose tissue. Next, through a leptin-luciferase animal model, where luciferase is expressed only in adipocytes (see below), the location and timing of embryonic adipose development were determined. Identification of the location and timing led the way to study gene regulation and morphology of the developing adipose tissue in embryos. Leptin is an in vivo regulated adipocyte hormone, which is the afferent signal in a negative feedback loop controlling body weight and energy expenditure. Leptin is secreted in proportion to adipose tissue mass. This suggests the possibility that cellular lipid content is sensed and that a fuller understanding of the mechanisms of leptin production could lead to the delineation of a lipid sensing mechanism in fat cells and possibly other cell types. To discover this mechanism, we searched for the region/s in the leptin gene promoter that control the transcription of the leptin gene using a deletion series of BAC transgenic mouse lines that express luciferase under the control of overlapping leptin regulatory sequences. Cis elements that confer qualitative and quantitative control of the leptin gene are located between – 762B and +8kb relative to the transcription start site. Since luciferase is driven by leptin regulatory sequences in leptin-luciferase animals and leptin levels are highly correlated with the amount of body fat, luciferase expression can be used as a surrogate for studying changes in the amount of adipose tissue. To study the responses of adipocytes to changes in weight, leptin-luciferase animals were used to show that weight loss induced by fasting or leptin treatment results in the retention of lipid-depleted adipocytes in adipose depots. This work led to the identification of a cellular program that controls the recovery of adipose fat mass after weight loss

A Diverse Array of Cancer-Associated MTOR Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity

Genes encoding components of the PI3K–AKT–mTOR signaling axis are frequently mutated in cancer, but few mutations have been characterized in MTOR, the gene encoding the mTOR kinase. Using publicly available tumor genome sequencing data, we generated a comprehensive catalog of mTOR pathway mutations in cancer, identifying 33 MTOR mutations that confer pathway hyperactivation. The mutations cluster in six distinct regions in the C-terminal half of mTOR and occur in multiple cancer types, with one cluster particularly prominent in kidney cancer. The activating mutations do not affect mTOR complex assembly, but a subset reduces binding to the mTOR inhibitor DEPTOR. mTOR complex 1 (mTORC1) signaling in cells expressing various activating mutations remains sensitive to pharmacologic mTOR inhibition, but is partially resistant to nutrient deprivation. Finally, cancer cell lines with hyperactivating MTOR mutations display heightened sensitivity to rapamycin both in culture and in vivo xenografts, suggesting that such mutations confer mTOR pathway dependency. Significance: We report that a diverse set of cancer-associated MTOR mutations confer increased mTORC1/2 pathway activity and that cells harboring these mutations are highly sensitive to rapamycin in culture and in vivo. These findings are clinically relevant as the MTOR mutations characterized herein may serve as biomarkers for predicting tumor responses to mTOR inhibitors.Starr Cancer ConsortiumDavid H. Koch Institute for Integrative Cancer Research at MITAlexander and Margaret Stewart TrustNational Institutes of Health (U.S.) (Grant CA103866)National Institutes of Health (U.S.) (Grant CA129105)National Institutes of Health (U.S.) (Grant AI07389

Molecular Profiling of Activated Neurons by Phosphorylated Ribosome Capture

The mammalian brain is composed of thousands of interacting neural cell types. Systematic approaches to establish the molecular identity of functional populations of neurons would advance our understanding of neural mechanisms controlling behavior. Here, we show that ribosomal protein S6, a structural component of the ribosome, becomes phosphorylated in neurons activated by a wide range of stimuli. We show that these phosphorylated ribosomes can be captured from mouse brain homogenates, thereby enriching directly for the mRNAs expressed in discrete subpopulations of activated cells. We use this approach to identify neurons in the hypothalamus regulated by changes in salt balance or food availability. We show that galanin neurons are activated by fasting and that prodynorphin neurons restrain food intake during scheduled feeding. These studies identify elements of the neural circuit that controls food intake and illustrate how the activity-dependent capture of cell-type-specific transcripts can elucidate the functional organization of a complex tissue

Ferroptosis in health and disease

Ferroptosis is a pervasive non-apoptotic form of cell death highly relevant in various degenerative diseases and malignancies. The hallmark of ferroptosis is uncontrolled and overwhelming peroxidation of polyunsaturated fatty acids contained in membrane phospholipids, which eventually leads to rupture of the plasma membrane. Ferroptosis is unique in that it is essentially a spontaneous, uncatalyzed chemical process based on perturbed iron and redox homeostasis contributing to the cell death process, but that it is nonetheless modulated by many metabolic nodes that impinge on the cells’ susceptibility to ferroptosis. Among the various nodes affecting ferroptosis sensitivity, several have emerged as promising candidates for pharmacological intervention, rendering ferroptosis-related proteins attractive targets for the treatment of numerous currently incurable diseases. Herein, the current members of a Germany-wide research consortium focusing on ferroptosis research, as well as key external experts in ferroptosis who have made seminal contributions to this rapidly growing and exciting field of research, have gathered to provide a comprehensive, state-of-the-art review on ferroptosis. Specific topics include: basic mechanisms, in vivo relevance, specialized methodologies, chemical and pharmacological tools, and the potential contribution of ferroptosis to disease etiopathology and progression. We hope that this article will not only provide established scientists and newcomers to the field with an overview of the multiple facets of ferroptosis, but also encourage additional efforts to characterize further molecular pathways modulating ferroptosis, with the ultimate goal to develop novel pharmacotherapies to tackle the various diseases associated with – or caused by – ferroptosis.Fil: Berndt, Carsten. Heinrich-Heine University; AlemaniaFil: Alborzinia, Hamed. Heidelberg Institute for Stem Cell Technology and Experimental Medicine; AlemaniaFil: Amen, Vera Skafar. University of Würzburg; AlemaniaFil: Ayton, Scott. University of Melbourne; AustraliaFil: Barayeu, Uladzimir. Heidelberg University; Alemania. German Cancer Research Center; Alemania. Tohoku University Graduate School of Medicine; JapónFil: Bartelt, Alexander. Ludwig Maximilians Universitat; AlemaniaFil: Bayir, Hülya. Columbia University; Estados UnidosFil: Bebber, Christina M.. University of Cologne; AlemaniaFil: Birsoy, Kivanc. The Rockefeller University; Estados UnidosFil: Böttcher, Jan P.. Universitat Technical Zu Munich; AlemaniaFil: Brabletz, Simone. Friedrich-Alexander University of Erlangen-Nürnberg; AlemaniaFil: Brabletz, Thomas. Friedrich-Alexander University of Erlangen-Nürnberg; AlemaniaFil: Brown, Ashley R.. Columbia University; Estados UnidosFil: Brunner Bernhardt, Mauricio Andrés. Goethe Universitat Frankfurt; AlemaniaFil: Bulli, Giorgia. Ludwig Maximilians Universitat; AlemaniaFil: Bruneau, Alix. Goethe Universitat Frankfurt; AlemaniaFil: Chen, Quan. Nankai University; ChinaFil: DeNicola, Gina M.. Moffitt Cancer Center; Estados UnidosFil: Dick, Tobias P.. Ruprecht Karls Universitat Heidelberg; AlemaniaFil: Distefano, Ayelen Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Dixon, Scott J.. University of Stanford; Estados UnidosFil: Engler, Jan B.. University Medical Center Hamburg-Eppendorf; AlemaniaFil: Pagnussat, Gabriela Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Wilhelm, Christoph. Universitat Bonn; AlemaniaFil: Wölk, Michele. University Hospital Carl Gustav Carus; AlemaniaFil: Wu, Katherine. University of New York; Estados UnidosFil: Yang, Xin. Columbia University; Estados UnidosFil: Yu, Fan. Nankai University; ChinaFil: Zou, Yilong. Westlake University; ChinaFil: Conrad, Marcus. Helmholtz Center Munich; Alemani

SHMT2 drives glioma cell survival in the tumor microenvironment but imposes a dependence on glycine clearance

SUMMARY Cancer cells adapt their metabolic processes to support rapid proliferation, but less is known about how cancer cells alter metabolism to promote cell survival in a poorly vascularized tumor microenvironment1–3. Here, we identify a key role for serine and glycine metabolism in the survival of brain cancer cells within the ischemic zones of gliomas. In human glioblastoma multiforme (GBM), mitochondrial serine hydroxymethyltransferase (SHMT2) and glycine decarboxylase (GLDC) are highly expressed in the pseudopalisading cells that surround necrotic foci. We find that SHMT2 activity limits that of pyruvate kinase (PKM2) and reduces oxygen consumption, eliciting a metabolic state that confers a profound survival advantage to cells in poorly vascularized tumor regions. GLDC inhibition impairs cells with high SHMT2 levels as the excess glycine not metabolized by GLDC can be converted to the toxic molecules aminoacetone and methylglyoxal. Thus, SHMT2 is required for cancer cells to adapt to the tumor environment, but also renders these cells sensitive to glycine cleavage system inhibition

mTORC1 in the Paneth cell niche couples intestinal stem cell function to calorie intake

How adult tissue stem and niche cells respond to the nutritional state of an organism is not well understood. Here we find that Paneth cells, a key constituent of the mammalian intestinal stem-cell (ISC) niche, augment stem-cell function in response to calorie restriction. Calorie restriction acts by reducing mechanistic target of rapamycin complex 1 (mTORC1) signalling in Paneth cells, and the ISC-enhancing effects of calorie restriction can be mimicked by rapamycin. Calorie intake regulates mTORC1 in Paneth cells, but not ISCs, and forced activation of mTORC1 in Paneth cells during calorie restriction abolishes the ISC-augmenting effects of the niche. Finally, increased expression of bone stromal antigen 1 (Bst1) in Paneth cells—an ectoenzyme that produces the paracrine factor cyclic ADP ribose—mediates the effects of calorie restriction and rapamycin on ISC function. Our findings establish that mTORC1 non-cell-autonomously regulates stem-cell self-renewal, and highlight a significant role of the mammalian intestinal niche in coupling stem-cell function to organismal physiology.National Institutes of Health (U.S.) (CA103866)National Institutes of Health (U.S.) (CA129105)David H. Koch Institute for Integrative Cancer Research at MIT (Initiator Award)Ellison Medical FoundationNational Cancer Institute (U.S.) (NCI (T32CA09216) fellowship support)Academy of FinlandFoundations’ Postdoc PoolNational Institutes of Health (U.S.) (NIH (1F32AG032833-01A1))Jane Coffin Childs Memorial Fund for Medical Researc

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment