Biology subjects

Waxman, D. J.

Publications and source records attributed to Waxman, D. J..

26 records · Page 2Linked to original sources

bioRxiv2020

MAnorm2 for quantitatively comparing groups of ChIP-seq samples

Eukaryotic gene transcription is regulated by a large cohort of chromatin associated proteins, and inferring their differential binding sites between cellular contexts requires a rigorous comparison of the corresponding ChIP-seq data. We present MAnorm2, a new computational tool for quantitatively comparing groups of ChIP-seq samples. MAnorm2 uses a hierarchical strategy to normalize ChIP-seq data and then performs differential analysis by assessing within-group variability of ChIP-seq signals under an empirical Bayes framework. In this framework, MAnorm2 considers the abundance of differential ChIP-seq signals between groups of samples and the possibility of different within-group variability between groups. When samples in each group are biological replicates, MAnorm2 can reliably identify differential binding events even between highly similar cellular contexts. Using a number of real ChIP-seq data sets, we observed that MAnorm2 clearly outperformed existing tools for differential ChIP-seq analysis, with the improvement in performance being most dramatic when the groups of samples being compared had distinct global within-group variability.

bioinformatics↗

bioRxiv2019

Delicate balances in cancer chemotherapy: modeling immune recruitment and emergence of systemic drug resistance

Metronomic chemotherapy can drastically enhance immunogenic tumor cell death. However, the responsible mechanisms are still incompletely understood. Here, we develop a mathematical model to elucidate the underlying complex interactions between tumor growth, immune system activation, and therapy-mediated immunogenic cell death. Our model is conceptually simple, yet it provides a surprisingly excellent fit to empirical data obtained from a GL261 mouse glioma model treated with cyclophosphamide on a metronomic schedule. The model includes terms representing immune recruitment as well as the emergence of drug resistance during prolonged metronomic treatments. Strikingly, a fixed set of parameters, not adjusted for individuals nor for drug schedule, excellently recapitulates experimental data across various drug regimens, including treatments administered at intervals ranging from 6 to 12 days. Additionally, the model predicts peak immune activation times, rediscovering experimental data that had not been used in parameter fitting or in model construction. The validated model was then used to make predictions about expected tumor-immune dynamics for novel drug administration schedules. Notably, the validated model suggests that immunostimulatory and immunosuppressive intermediates are responsible for the observed phenomena of resistance and immune cell recruitment, and thus for variation of responses with respect to different schedules of drug administration.

systems biology↗

bioRxiv2019

Widespread dysregulation of long non-coding genes associated with fatty acid metabolism, cell division, and immune response gene networks in xenobiotic-exposed rat liver

Xenobiotic exposure activates or inhibits transcription of hundreds of protein-coding genes in mammalian liver, impacting many physiological processes and inducing diverse toxicological responses. Little is known about the effects of xenobiotic exposure on long noncoding RNAs (lncRNAs), many of which play critical roles in regulating gene expression. Objective: to develop a computational framework to discover liver-expressed, xenobiotic-responsive lncRNAs (xeno-lncs) with strong functional, gene regulatory potential and elucidate the impact of xenobiotic exposure on their gene regulatory networks. We analyzed 115 liver RNA-seq data sets from male rats treated with 27 individual chemicals representing seven mechanisms of action (MOAs) to assemble the long non-coding transcriptome of xenobiotic-exposed rat liver. Ortholog analysis was combined with co-expression data and causal inference methods to infer lncRNA function and deduce gene regulatory networks, including causal effects of lncRNAs on protein-coding gene expression and biological pathways. We discovered >1,400 liver-expressed xeno-lncs, many with human and/or mouse orthologs. Xenobiotics representing different MOAs were often regulated common xeno-lnc targets: 123 xeno-lncs were dysregulated by at least 10 chemicals, and 5 xeno-lncs responded to at least 20 of the 27 chemicals investigated. 81 other xeno-lncs served as MOA-selective markers of xenobiotic exposure. Xeno-lnc-protein-coding gene co-expression regulatory network analysis identified xeno-lncs closely associated with exposure-induced perturbations of hepatic fatty acid metabolism, cell division, and immune response pathways. We also identified hub and bottleneck lncRNAs, which are expected to be key regulators of gene expression in cis or in trans. This work elucidates extensive networks of xeno-lnc-protein-coding gene interactions and provides a framework for understanding the extensive transcriptome-altering actions of diverse foreign chemicals in a key responsive mammalian tissue.

pharmacology and toxicology↗

bioRxiv2019

Long non-coding RNA Gm15441 attenuates hepatic inflammasome activation in response to metabolic stress

Fasting paradigms elicit a wide-range of health benefits including suppressing inflammation. Exploring the molecular mechanisms that prevent inflammation during caloric restriction may yield promising new therapeutic targets. During fasting, activation of the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARA) promotes the utilization of lipids as an energy source. Herein, we show that ligand activation of PPARA directly upregulates the long non-coding RNA gene Gm15441 through binding sites within its promoter. Gm15441 expression suppresses its antisense transcript, encoding thioredoxin interacting protein (TXNIP). This, in turn, decreases TXNIP-stimulated NLRP3 inflammasome activation, caspase-1 (CASP1) cleavage, and proinflammatory interleukin 1 beta (IL1B) maturation. Gm15441-null mice were developed and shown to be more susceptible to NLRP3 inflammasome activation and to exhibit elevated CASP1 and IL1B cleavage in response to metabolic and inflammatory stimuli. These findings provide evidence for a novel mechanism by which PPARA attenuates hepatic inflammasome activation in response to metabolic stress through lncRNA Gm15441 induction.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC=\"FIGDIR/small/675785v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@1db1d5dorg.highwire.dtl.DTLVardef@64c8b2org.highwire.dtl.DTLVardef@b4402borg.highwire.dtl.DTLVardef@1e0fbba_HPS_FORMAT_FIGEXP M_FIG Graphical abstract\n\nC_FIG

molecular biology↗

bioRxiv2019

Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2

BackgroundSex differences in the incidence and progression of many liver diseases, including liver fibrosis and hepatocellular carcinoma, are associated with sex-biased expression of hundreds of genes in the liver. This sexual dimorphism is largely determined by the sex-specific pattern of pituitary growth hormone secretion, which controls a transcriptional regulatory network operative in the context of sex-biased chromatin states. Histone H3K27-trimethylation yields a major sex-biased repressive chromatin mark that is specifically deposited by polycomb repressive complex-2, via its homologous catalytic subunits Ezh1 and Ezh2, at many strongly female-biased genes in male mouse liver, but not at male-biased genes in female liver.\n\nResultsWe used Ezh1-knockout mice with a hepatocyte-specific knockout of Ezh2 to elucidate the sex bias of liver H3K27-trimethylation and its functional role in regulating sex-differences in the liver. Combined hepatic Ezh1/Ezh2 deficiency led to a significant loss of sex-biased gene expression, particularly in male liver, where many female-biased genes increased in expression while male-biased genes showed decreased expression. The associated loss of H3K27me3 marks, and increases in the active enhancer marks H3K27ac and H3K4me1, were also more pronounced in male liver. Many genes linked to liver fibrosis and hepatocellular carcinoma were induced in Ezh1/Ezh2-deficient livers, which may contribute to the increased sensitivity of these mice to hepatotoxin-induced liver pathology.\n\nConclusionsEzh1/Ezh2-catalyzed H3K27-trimethyation is thus essential for the sex-dependent epigenetic regulation of liver chromatin states controlling phenotypic sex differences in liver metabolism and liver fibrosis, and may be a critical determinant of the sex-bias in liver disease susceptibility.

genomics↗

bioRxiv2019

CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver

BackgroundSex differences in the transcriptome and epigenome are widespread in mouse liver and are associated with sex-bias in liver disease. Several thousand sex-differential distal enhancers have been identified; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization, DNA looping, and chromatin interactions are unknown. ResultsTo address these issues, we first characterized 1,847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were largely distal to sex-biased genes, but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors. A substantial subset of the sex-biased cohesin-non-CTCF binding sites, but not the sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. Furthermore, intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. ConclusionsThese findings elucidate how 3-dimensional genome organization contributes to sex differences in gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.

genomics↗

bioRxiv2018

Insulation of gene expression by CTCF and cohesin-based subTADs (ubiquitous intra-TAD loop structures) in mouse liver

CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present a computational method to identify cohesin-and-CTCF binding sites that form intra-TAD DNA loops (subTADs). We show that predicted subTAD anchors are structurally indistinguishable from those of TADs regarding their binding partners, sequence conservation, and resistance to cohesin knockdown; further, the subTAD loops retain key functional features of TADs, including insulation of chromatin contacts, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that subTADs form by the same loop extrusion mechanism as larger loops, and that their shorter length enables finer regulatory control over gene expression. 4C-seq analysis using an Alb promoter viewpoint illustrates the role of subTADs in restricting enhancer-promoter interactions. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization, and demonstrate that distal enhancer insulation by subTADs is widespread.

genomics↗

bioRxiv2018

Sex-biased long non-coding RNAs negatively correlated with sex-opposite protein coding gene co-expression networks in Diversity Outbred mouse liver

Sex differences in liver gene expression and disease susceptibility are regulated by pituitary growth hormone secretion patterns, which activate sex-dependent liver transcription factors and establish sex-specific chromatin states. Ablation of pituitary hormone by hypophysectomy (hypox) has identified two major classes of liver sex-biased genes, defined by their sex-dependent positive or negative responses to hypox, respectively; however, the mechanisms that determine the hypox responsiveness of each gene class are unknown. Here, we sought to discover candidate regulatory long noncoding RNAs (lncRNAs) that control hypox responsiveness. First, we used mouse liver RNA-seq data for 30 different biological conditions to discover gene structures and expression patterns for ~15,500 liver-expressed lncRNAs, including antisense and intragenic lncRNAs, as well as lncRNAs that overlap active enhancers, marked by enhancer RNAs. We identified >200 robust sex-specific liver lncRNAs, including 157 whose expression is regulated during postnatal liver development or is subject to circadian oscillations. Next, we utilized the high natural allelic variance of Diversity Outbred (DO) mice, a multi-parental outbred population, to discover tightly co-expressed clusters of sex-specific protein-coding genes (gene modules) in male liver, and separately, in female liver. Sex differences in the gene modules identified were extensive. Remarkably, many gene modules were strongly enriched for male-specific or female-specific genes belonging to a single hypox-response classes, indicating that the genetic heterogeneity of DO mice captures responsiveness to hypox. Hypox-responsiveness was shown to be facilitated by multiple, distinct gene regulatory mechanisms, indicating its complex nature. Further, we identified 16 sex-specific lncRNAs whose expression across DO mouse livers showed an unexpected significant negative correlation with protein-coding gene modules enriched for genes of the opposite-sex bias and inverse hypox response class, indicating strong negative regulatory potential for these lncRNAs. Thus, we used a genetically diverse outbred mouse population to discover tightly co-expressed sex-specific gene modules that reveal broad characteristics of gene regulation related to responsiveness to hypox, and generated testable hypotheses for regulatory roles of sex-biased liver lncRNAs that control the sex-bias in liver gene expression.

systems biology↗