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Biology subjects

Brown, J. M.

Publications and source records attributed to Brown, J. M..

47 records · Page 3Linked to original sources

Membrane-Bound O-Acyltransferase 7 (MBOAT7) is a Key Regulator of Glycolysis in Clear Cell Renal Carcinoma.

ObjectiveThe most common and deadliest urological cancer is clear cell Renal Cell Carcinoma (ccRCC). ccRCC is characterized by striking reorganization of both carbohydrate and lipid metabolism. It was recently demonstrated that lipid remodeling enzyme Membrane-Bound O-Acyltransferase 7 (MBOAT7) that generates phosphatidylinositol (PI) is important for the ccRCC progression. However, whether MBOAT7-driven PI remodeling is associated with other metabolic alterations commonly found in ccRCC is poorly understood. MethodsMBOAT7 deficient ccRCC cell lines were generated by genome editing, and were characterized by a general reduction in glycolytic capactiy. Using targeted metabolomics approach in Caki-1 cells, we measured the glycolytic intermediates and the relative expression of key glycolytic enzymes. We also measured basal respiration and maximal respiration with MBOAT7 deficiency in the presence of glucose. Lastly, in vivo xenograft studies were performed with parental and MBOAT7 deficient cells. ResultsMBOAT7 deficiency was associated with a reduction in glycolytic gene expression and protein abundance. In parallel, we found that glycolytic intermediates similarly decreased which may contribute to a reduction in glycolysis. MBOAT7 deficiency reduces basal respiration and maximal respiration. Similarly, we see maximum glycolytic capacity also reduced with MBOAT7 loss of function. Finally, the in vivo xenograft demonstrated MBOAT7 knockout significantly increased overall survival and reduced glycolytic HK2 protein abundance in vivo. ConclusionsOur work highlights MBOAT7 as a key regulator of glycolysis in ccRCC. Our data provides additional evidence that suggests MBOAT7 as a novel target to regulate tumor growth in vivo.

cancer biology↗

Modelling erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I)

We employ and extensively characterise an ex vivo culture system to study terminal erythroid maturation of CD34+ progenitors from the peripheral blood of normal individuals and patients with Congenital Dyserythropoietic Anaemia type 1 (CDA-I). Using morphological analysis, FACS analysis and the proteomic approach CyTOF, we analysed patient-derived erythroblasts stage-matched with those from healthy donors during the expansion phase and into early differentiation. In patient cells, aspects of disordered erythropoiesis manifest midway through differentiation, including increased proliferation and changes in the DNA accessibility profile. We also show that cultured erythroblasts from CDA-I patients recapitulate the pathognomic feature of this erythroid disorder with up to 40% of the cells having abnormal spongy chromatin morphology by electron microscopy, as well as upregulation of GDF15, a marker of ineffective erythropoiesis. In the tertiary phase of culture, patient cells show significantly less enucleation and there is persistence of earlier erythroid precursors. Furthermore, the enucleation defect appears to be more severe in patients with mutations in C15orf41, as compared to the other known causative gene CDAN1, indicating a genotype/phenotype correlation in CDA-I. Such erythroblasts are a valuable resource for investigating the pathogenesis of this disease and provide the opportunity for streamlining diagnosis for CDA-I patients and ultimately other forms of unexplained anaemia.

genetics↗

MBOAT7-Driven Phosphatidylinositol Remodeling Promotes the Progression of Clear Cell Renal Cell Carcinoma.

The most common kidney cancer, clear cell Renal Cell Carcinoma (ccRCC) is closely associated with obesity. In fact, the \"clear cell\" variant of RCC is given this name due to large lipid droplets within the tumor cells. Although it is well appreciated that renal lipid metabolism is altered in ccRCC, the mechanisms driving this are not well understood. Leveraging a shotgun lipidomics approach we have identified a lipid signature for ccRCC that includes an increase in arachidonic acid-enriched phosphatidylinositols (AA-PI). In parallel, we found that ccRCC tumors have increased expression of the acyltransferase enzyme membrane bound O-acyltransferase domain containing 7 (MBOAT7) that contributes to AA-PI synthesis. In ccRCC patients, MBOAT7 expression increases with tumor grade, and increased MBOAT7 expression correlates with poor survival. Genetic deletion of MBOAT7 in ccRCC cells decreases proliferation and induces cell cycle arrest, and MBOAT7-/- cells fail to form tumors in vivo. RNAseq of MBOAT7-/- cells identified alterations in cell migration and extracellular matrix organization, which were functionally validated in migration assays. Our work highlights the accumulation of AA-PI in ccRCC and demonstrate a novel way to decrease the AA-PI pool in ccRCC by limiting MBOAT7. Our data reveal that metastatic ccRCC is associated with altered AA-PI metabolism, and identify MBOAT7 as a novel target in advanced ccRCC.

cancer biology↗

Differences in proteome response to cold acclimation in Zoysia japonica cultivars with different levels of freeze tolerance

Zoysiagrasses (Zoysia spp.) are warm season turfgrasses primarily grown in the southern and transition zones of the United States. An understanding of the physiological changes that zoysiagrasses undergo during cold acclimation may shed light on physiological phenotypic traits useful in selection of freeze tolerant genotypes. We investigated the relationship between cold acclimation, protein expression, and freeze tolerance in cold-acclimated (CA) and non-acclimated (NCA) plants of Zoysia japonica Steud. cultivars Meyer (freeze-tolerant) and Victoria (freeze-susceptible). Freeze tolerance was assessed using chambers reaching -6, -8, -10, and -12{degrees}C. Additionally, meristematic tissues from the grass crowns of Meyer and Victoria were harvested for proteomic analysis after a four week cold acclimation period. Freeze testing indicated that cold acclimation accounted for a 1.9-fold increase in plant survival compared to the non-acclimation treatment. Overall, proteomic analysis identified 62 protein spots having at least a twofold change in abundance under cold acclimation. Nine and 22 unique protein spots were identified for Meyer and Victoria, respectively, with increased abundance (up-regulated) or decreased abundance (down-regulated). In addition, 23 shared protein spots were found among the two cultivars having differential expression in response to cold acclimation. In Meyer, protein response to cold acclimation was primarily upregulated, while in Victoria, protein response was primarily downregulated. These cold acclimation responsive proteins were found to be involved primarily in transcription, metabolism, protein destination and storage, and energy production. As identified through MALDI-TOF/TOF mass spectrometry followed matching of protein homologues against the NCBI Arabidopsis database, major proteins of interest for their association with cold acclimation were LEA 3, MAPK, SOD, GAST1, Phytochrome A, ATP synthase, AGP, PLD, and PSII. Further investigation of these proteins and their functional categories may contribute to increase our understanding of the differences in freezing tolerance among zoysiagrass germplasm.

physiology↗

Chromatin arranges in filaments of blobs with nanoscale functional zonation

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular [~]200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in post-replicative chromatin, but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

genomics↗

Malignant liver cancers have distinct myeloid-derived suppressor cell signatures

Myeloid-derived suppressor cells (MDSCs) are immunosuppressive cells that are increased in patients with numerous malignancies including viral-derived hepatocellular carcinoma (HCC). Here, we report an elevation of MDSC in other hepatobiliary malignancies including non-viral HCC, neuroendocrine tumors (NET), colorectal carcinoma with liver metastases (CRLM), but not cholangiocarcinoma (CCA). Investigation of myeloid cell infiltration in HCC, NET and intrahepatic CCA tumors further established that the frequency of antigen-presenting cells was limited compared to benign lesions suggesting that primary and metastatic hepatobiliary cancers have distinct peripheral and tumoral myeloid signatures. Bioinformatics analysis of the Cancer Genome Atlas demonstrated that a high MDSC score in HCC patients predicted poor disease outcome. Mechanistic studies indicated that the oncometabolite D-2-hydroxyglutarate resulting from isocitrate dehydrogenase 1 mutation could be a limiting factor of MDSC accumulation in CCA patients. Given our observation that MDSCs are increased in non-CCA malignant liver cancers, they may comprise suitable targets for effective immunotherapy approaches.

pathology↗

Object Detection Networks and Augmented Reality for Cellular Detection in Fluorescence Microscopy Acquisition and Analysis.

In this paper we demonstrate the application of object detection networks for the classification and localization of cells in fluorescence microscopy. We benchmark two leading object detection algorithms across multiple challenging 2-D microscopy datasets as well as develop and demonstrate an algorithm which can localize and image cells in 3-D, in real-time. Furthermore, we exploit the fast processing of these algorithms and develop a simple and effective Augmented Reality (AR) system for fluorescence microscopy systems. Object detection networks are well-known high performance networks famously applied to the task of identifying and localizing objects in photography images. Here we show their application and efficiency for localizing cells in fluorescence microscopy images. Object detection algorithms are typically trained on many thousands of images, which can be prohibitive within the biological sciences due to the cost of imaging and annotating large amounts of data. Through taking different cell types and assays as an example, we show that with some careful considerations it is possible to achieve very high performance with datasets with as few as 26 images present. Using our approach, it is possible for relatively non-skilled users to automate detection of cell classes with a variety of appearances and enable new avenues for automation of conventionally manual fluorescence microscopy acquisition pipelines.

bioinformatics↗

Single-cell chromatin interactions reveal regulatory hubs in dynamic compartmentalized domains

The promoters of mammalian genes are commonly regulated by multiple distal enhancers, which physically interact within discrete chromatin domains. How such domains form and how the regulatory elements within them interact within single cells is not understood. To address this we developed Tri-C, a new Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions at individual alleles within single cells. The heterogeneity of interactions observed between such cells shows that CTCF-mediated formation of chromatin domains and interactions within them are dynamic processes. Importantly, our analyses reveal higher-order structures involving simultaneous interactions between multiple enhancers and promoters within individual cells. This provides a structural basis for understanding how multiple cis-elements act together to establish robust regulation of gene expression.

genetics↗

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

ecology↗

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

A variety of self-interacting domains, defined at different levels of resolution, have been described in mammalian genomes. These include Chromatin Compartments (A and B)1, Topologically Associated Domains (TADs)2,3, contact domains4,5, sub-TADs6, insulated neighbourhoods7 and frequently interacting regions (FIREs)8. Whereas many studies have found the organisation of self-interacting domains to be conserved across cell types389, some do form in a lineage-specific manner6710. However, it is not clear to what degree such tissue-specific structures result from processes related to gene activity such as enhancer-promoter interactions or whether they form earlier during lineage commitment and are therefore likely to be prerequisite for promoting gene expression. To examine these models of genome organisation in detail, we used a combination of high-resolution chromosome conformation capture, a newly-developed form of quantitative fluorescence in-situ hybridisation and super-resolution imaging to study a 70 kb self-interacting domain containing the mouse -globin locus. To understand how this self-interacting domain is established, we studied the region when the genes are inactive and during erythroid differentiation when the genes are progressively switched on. In contrast to many current models of long-range gene regulation, we show that an erythroid-specific, decompacted self-interacting domain, delimited by convergent CTCF/cohesin binding sites, forms prior to the onset of robust gene expression. Using previously established mouse models we show that formation of the self-interacting domain does not rely on interactions between the -globin genes and their enhancers. As there are also no tissue-specific changes in CTCF binding, then formation of the domain may simply depend on the presence of activated lineage-specific cis-elements driving a transcription-independent mechanism for opening chromatin throughout the 70 kb region to create a permissive environment for gene expression. These findings are consistent with a model of loop-extrusion in which all segments of chromatin, within a region delimited by CTCF boundary elements, can contact each other. Our findings suggest that activation of tissue-specific element(s)within such a self-interacting region is sufficient to influence all chromatin within the domain.

cell biology↗

Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological?

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of these biological versus methodological factors in explaining gene tree variation is a major unresolved question in phylogenetics. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and that critical evaluation of the fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

evolutionary biology↗