Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions.

A few families of transposable elements (TEs) have been shown to evolve into cis-regulatory elements (CREs). Here, to extend these studies to all classes of TEs in the human genome, we identified widespread enhancer-like repeats (ELRs) and find that ELRs reliably mark cell identities, are enriched for lineage-specific master transcription factor binding sites, and are mostly primate-specific. In particular, elements of MIR and L2 TE families whose abundance co-evolved across chordate genomes, are found as ELRs in most human cell types examined. MIR and L2 elements frequently share long-range intra-chromosomal interactions and binding of physically interacting transcription factors. We validated that eight L2 and nine MIR elements function as enhancers in reporter assays, and among 20 MIR-L2 pairings, one MIR repressed and one boosted the enhancer activity of L2 elements. Our results reveal a previously unappreciated co-evolution and interaction between two TE families in shaping regulatory networks.

The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A.

How individual genes are regulated from a mitochondrial polycistronic transcript to have variable expression remains an enigma. Here, through bisulfite sequencing and strand-specific mapping, we show mitochondrial genomes in humans and other animals are strongly biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene-gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic local or global changes during development and aging. Knockout of DNMT3A alone perturbed mtDNA regional methylation patterns, but not global levels, and altered mitochondrial gene expression, copy number, and oxygen respiration. Overexpression of DNMT3A strongly increased mtDNA methylation and strand bias. Overall, methylation at gene bodies and boundaries was negatively associated with mitochondrial transcript abundance and also polycistronic transcript processing. Furthermore, HPLC-MS confirmed the methylation signals on mitochondria DNA. Together, these data provide high-resolution mtDNA methylation maps that revealed a strand-specific non-CpG methylation, its dynamic regulation, and its impact on the polycistronic mitochondrial transcript processing.

A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications.

BACKGROUND: Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the first line to define tumor types that are optimally responsive. Open data on the gene expression of the NCI-60 cell lines, provides a unique opportunity to add another dimension to the preclinical development of such drugs by interrogating correlations with gene expression patterns. Machine learning can be used to reduce the complexity of whole genome gene expression patterns to derive manageable signatures of response. Application of machine learning in early phases of preclinical development is likely to allow a better positioning and ultimate clinical success of molecules. LP-184 is a highly potent novel alkylating agent where the preclinical development is being guided by a dedicated machine learning-derived response signature. We show the feasibility and the accuracy of such a signature of response by accurately predicting the response to LP-184 validated using wet lab derived IC50s on a panel of cell lines. RESULTS: We applied our proprietary RADR® platform to an NCI-60 discovery dataset encompassing LP-184 IC50s and publicly available gene expression data. We used multiple feature selection layers followed by the XGBoost regression model and reduced the complexity of 20,000 gene expression values to generate a 16-gene signature leading to the identification of a set of predictive candidate biomarkers which form an LP-184 response gene signature. We further validated this signature and predicted response to an additional panel of cell lines. Considering fold change differences and correlation between actual and predicted LP-184 IC50 values as validation performance measures, we obtained 86% accuracy at four-fold cut-off, and a strong (r = 0.70) and significant (p value 1.36e-06) correlation between actual and predicted LP-184 sensitivity. In agreement with the perceived mechanism of action of LP-184, PTGR1 emerged as the top weighted gene. CONCLUSION: Integration of a machine learning-derived signature of response with in vitro assessment of LP-184 efficacy facilitated the derivation of manageable yet robust biomarkers which can be used to predict drug sensitivity with high accuracy and clinical value.

Accurate loop calling for 3D genomic data with cLoops.

MOTIVATION: Sequencing-based 3D genome mapping technologies can identify loops formed by interactions between regulatory elements hundreds of kilobases apart. Existing loop-calling tools are mostly restricted to a single data type, with accuracy dependent on a predefined resolution contact matrix or called peaks, and can have prohibitive hardware costs. RESULTS: Here, we introduce cLoops ('see loops') to address these limitations. cLoops is based on the clustering algorithm cDBSCAN that directly analyzes the paired-end tags (PETs) to find candidate loops and uses a permuted local background to estimate statistical significance. These two data-type-independent processes enable loops to be reliably identified for both sharp and broad peak data, including but not limited to ChIA-PET, Hi-C, HiChIP and Trac-looping data. Loops identified by cLoops showed much less distance-dependent bias and higher enrichment relative to local regions than existing tools. Altogether, cLoops improves accuracy of detecting of 3D-genomic loops from sequencing data, is versatile, flexible, efficient, and has modest hardware requirements. AVAILABILITY AND IMPLEMENTATION: cLoops with documentation and example data are freely available at: https://github.com/YaqiangCao/cLoops. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Repression of human and mouse brain inflammaging transcriptome by broad gene-body histone hyperacetylation.

Brain "inflammaging," a low-grade and chronic inflammation, is a major hallmark for aging-related neurodegenerative diseases. Here, by profiling H3K27ac and gene expression patterns in human and mouse brains, we found that age-related up-regulated (Age-Up) and down-regulated (Age-Down) genes have distinct H3K27ac patterns. Although both groups show promoter H3K27ac, the Age-Up genes, enriched for inflammation-related functions, are additionally marked by broad H3K27ac distribution over their gene bodies, which is progressively reduced during aging. Age-related gene expression changes can be predicted by gene-body H3K27ac level. Contrary to the presumed transcription activation function of promoter H3K27ac, we found that broad gene-body hyper H3K27ac suppresses overexpression of inflammaging genes. Altogether, our findings revealed opposite regulations by H3K27ac of Age-Up and Age-Down genes and a mode of broad gene-body H3K27ac in repressing transcription.

Formation and activation of thermogenic fat.

Thermogenic fat cells that convert chemical energy into heat are present in both mice and humans. Recent years have witnessed great advances in our understanding of the regulation of these adipocytes and an increased appreciation of the potential these cells have to counteract obesity. We summarize recent efforts to understand the formation of these fat cells and critically review genetic models and other experimental tools currently available to further investigate the development and activation of both classical brown and inducible beige fat cells. We also discuss recent discoveries about the epigenetic regulation of these adipocytes, and finally present emerging evidence revealing the metabolic impacts of thermogenic fat in humans.

Role of AQP9 in transport of monomethyselenic acid and selenite.

AQP9 is an aquaglyceroporin with a very broad substrate spectrum. In addition to its orthodox nutrient substrates, AQP9 also transports multiple neutral and ionic arsenic species including arsenic trioxide, monomethylarsenous acid (MAsIII) and dimethylarsenic acid (DMAV). Here we discovered a new group of AQP9 substrates which includes two clinical relevant selenium species. We showed that AQP9 efficiently transports monomethylselenic acid (MSeA) with a preference for acidic pH, which has been demonstrated in Xenopus laevis oocyte following the overexpression of human AQP9. Specific inhibitors that dissipate transmembrane proton potential or change the transmembrane pH gradient, such as FCCP, valinomycin and nigericin did not significantly inhibit MSeA uptake, suggesting MSeA transport is not proton coupled. AQP9 was also found to transport ionic selenite and lactate, with much less efficiency compared with MSeA uptake. Selenite and lactate uptake via AQP9 is pH dependent and inhibited by FCCP and nigericin, but not valinomycin. The selenite and lactate uptake via AQP9 can be inhibited by different lactate analogs, indicating that their translocation share similar mechanisms. AQP9 transport of MSeA, selenite and lactate is all inhibited by a previously identified AQP9 inhibitor, phloretin, and the AQP9 substrate arsenite (AsIII). These newly identified AQP9 selenium substrates imply that AQP9 play a significant role in MSeA uptake and possibly selenite uptake involved in cancer therapy under specific microenvironments.

Conditional Dependency of LP-184 on Prostaglandin Reductase 1 is Synthetic Lethal in Pancreatic Cancers with DNA Damage Repair Deficiencies.

The greater efficacy of DNA-damaging drugs for pancreatic adenocarcinoma (PDAC) relies on targeting cancer-specific vulnerabilities while sparing normal organs and tissues due to their inherent toxicities. We tested LP-184, a novel acylfulvene analog, for its activity in preclinical models of PDAC carrying mutations in the DNA damage repair (DDR) pathways. Cytotoxicity of LP-184 is solely dependent on prostaglandin reductase 1 (PTGR1), so that PTGR1 expression robustly correlates with LP-184 cytotoxicity in vitro and in vivo. Low-passage patient-derived PDAC xenografts with DDR deficiencies treated ex vivo are more sensitive to LP-184 compared with DDR-proficient tumors. Additional in vivo testing of PDAC xenografts for their sensitivity to LP-184 demonstrates marked tumor growth inhibition in models harboring pathogenic mutations in ATR, BRCA1, and BRCA2. Depletion of PTGR1, however, completely abrogates the antitumor effect of LP-184. Testing combinatorial strategies for LP-184 aimed at deregulation of nucleotide excision repair proteins ERCC3 and ERCC4 established synergy. Our results provide valuable biomarkers for clinical testing of LP-184 in a large subset of genetically defined characterized refractory carcinomas. High PTGR1 expression and deleterious DDR mutations are present in approximately one third of PDAC making these patients ideal candidates for clinical trials of LP-184.

Preclinical Efficacy of LP-184, a Tumor Site Activated Synthetic Lethal Therapeutic, in Glioblastoma.

PURPOSE: Glioblastoma (GBM) is the most common brain malignancy with median survival <2 years. Standard-of-care temozolomide has marginal efficacy in approximately 70% of patients due to MGMT expression. LP-184 is an acylfulvene-derived prodrug activated by the oxidoreductase PTGR1 that alkylates at N3-adenine, not reported to be repaired by MGMT. This article examines LP-184 efficacy against preclinical GBM models and identifies molecular predictors of LP-184 efficacy in clinical GBM. EXPERIMENTAL DESIGN: LP-184 effects on GBM cell viability and DNA damage were determined using cell lines, primary PDX-derived cells and patient-derived neurospheres. GBM cell sensitivities to LP-184 relative to temozolomide and MGMT expression were examined. Pharmacokinetics and CNS bioavailability were evaluated in mice with GBM xenografts. LP-184 effects on GBM xenograft growth and animal survival were determined. Machine learning, bioinformatic tools, and clinical databases identified molecular predictors of GBM cells and tumors to LP-184 responsiveness. RESULTS: LP-184 inhibited viability of multiple GBM cell isolates including temozolomide-resistant and MGMT-expressing cells at IC50 = approximately 22-310 nmol/L. Pharmacokinetics showed favorable AUCbrain/plasma and AUCtumor/plasma ratios of 0.11 (brain Cmax = 839 nmol/L) and 0.2 (tumor Cmax = 2,530 nmol/L), respectively. LP-184 induced regression of GBM xenografts and prolonged survival of mice bearing orthotopic xenografts. Bioinformatic analyses identified PTGR1 elevation in clinical GBM subtypes and associated LP-184 sensitivity with EGFR signaling, low nucleotide excision repair (NER), and low ERCC3 expression. Spironolactone, which induces ERCC3 degradation, decreased LP-184 IC50 3 to 6 fold and enhanced GBM xenograft antitumor responses. CONCLUSIONS: These results establish LP-184 as a promising chemotherapeutic for GBM with enhanced efficacy in intrinsic or spironolactone-induced TC-NER-deficient tumors.

Sediments of soft spheres arranged by effective density.

Colloidal sedimentation has been studied for decades from both thermodynamic and dynamic perspectives. In the present work, binary mixtures of colloidal spheres are observed to separate spontaneously into two distinct layers on sedimentation. Both layers have a high volume fraction and contain distinct compositions of particles. Although predicting these compositions using settling dynamics is challenging, here we show that the compositions are readily predicted thermodynamically by minimizing the gravitational energy of the system. As the random packing fraction of a mixture of spheres exceeds that of monodisperse spheres of either type, the mixture produces a denser suspension that forms the bottom phase. Experimentally, the use of charged particles and low-ionic-strength solutions provides interparticle repulsions that keep the packed particles mobile, avoiding a glassy state that would prevent particles from reaching their equilibrium configuration. We extend this work beyond binary systems, showing similar separated layers for a five-component mixture of particles.

Identification of an S-adenosylmethionine (SAM) dependent arsenic methyltransferase in Danio rerio.

Arsenic methylation is an important cellular metabolic process that modulates arsenic toxicity and carcinogenicity. Biomethylation of arsenic produces a series of mono-, di- and tri-methylated arsenic metabolites that can be detected in tissues and excretions. Here we report that zebrafish exposed to arsenite (As(III)) produces organic arsenicals, including MMA(III), MMA(V) and DMA(V) with characteristic tissue ratios, demonstrating that an arsenic methylation pathway exists in zebrafish. In mammals, cellular inorganic arsenic is methylated by a SAM-dependent arsenic methyltransferase, AS3MT. A zebrafish arsenic methyltransferase homolog, As3mt, was identified by sequence alignment. Western blotting analysis showed that As3mt was universally expressed in zebrafish tissues. Prominent expression in liver and intestine correlated with methylated arsenic metabolites detected in those tissues. As3mt was expressed in and purified from Escherichia coli for in vitro functional studies. Our results demonstrated that As3mt methylated As(III) to DMA(V) as an end product and produced MMA(III) and MMA(V) as intermediates. The activity of As3mt was inhibited by elevated concentrations of the substrate As(III) as well as the metalloid selenite, which is a well-known antagonistic micronutrient of arsenic toxicity. The activity As3mt was abolished by substitution of either Cys160 or Cys210, which corresponds to conserved cysteine residues in AS3MT homologs, suggesting that they are involved in catalysis. Expression in zebrafish of an enzyme that has a similar function to human and rodent orthologs in catalyzing intracellular arsenic biomethylation validates the applicability of zebrafish as a valuable vertebrate model for understanding arsenic-associated diseases in humans.

Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants.

Rice accumulates high level of arsenic (As) in its edible parts and thus plays an important role in the transfer of As into the food chain. However, the mechanisms of As uptake and its detoxification in rice are not well understood. Recently, members of the Nodulin 26-like intrinsic protein (NIP) subfamily of plant aquaporins were shown to transport arsenite in rice and Arabidopsis. Here we report that members of the rice plasma membrane intrinsic protein (PIP) subfamily are also involved in As tolerance and transport. Based on the homology search with the mammalian AQP9 and yeast Fps1 arsenite transporters, we identified and cloned five rice PIP gene subfamily members. qRT-PCR analysis of PIPs in rice root and shoot tissues revealed a significant down regulation of transcripts encoding OsPIP1;2, OsPIP1;3, OsPIP2;4, OsPIP2;6, and OsPIP2;7 in response to arsenite treatment. Heterologous expression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Xenopus laevis oocytes significantly increased the uptake of arsenite. Overexpression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Arabidopsis yielded enhanced arsenite tolerance and higher biomass accumulation. Further, these transgenic plants showed no significant accumulation of As in shoot and root tissues in long term uptake assays. Whereas, short duration exposure to arsenite caused both active influx and efflux of As in the roots. The data suggests a bidirectional arsenite permeability of rice PIPs in plants. These rice PIPs genes will be highly useful for engineering important food and biofuel crops for enhanced crop productivity on contaminated soils without increasing the accumulation of toxic As in the biomass or edible tissues.

Self-generated diffusioosmotic flows from calcium carbonate micropumps.

Calcium carbonate particles, ubiquitous in nature and found extensively in geological formations, behave as micropumps in an unsaturated aqueous solution. The mechanism causing this pumping is diffusioosmosis, which drives flows along charged surfaces. Our calcium carbonate microparticles, roughly ∼10 µm in size, self-generate ionic gradients as they dissolve in water to produce Ca(2+), HCO(3)(-), and OH(-) ions that migrate into the bulk. Because of the different diffusion coefficients of these ions, spontaneous electric fields of roughly 1-10 V/cm arise in order to maintain electroneutrality in the solution. This electric field drives the diffusiophoresis of charged tracers (both positive and negative) as well as diffusioosmotic flows along charged substrates. Here we show experimentally how the directionality and speed of the tracers can be engineered by manipulating the tracer zeta potential, the salt gradients, and the substrate zeta potential. Furthermore, because the salt gradients are self-generated, here by the dissolution of solid calcium carbonate microparticles another manipulated variable is the placement of these particles. Importantly, we find that the zeta potentials on surfaces vary with both time and location because of the adsorption or desorption of Ca(2+) ions; this change affects the flows significantly.

Leucocytoclastic vasculitis in severe ulcerative colitis.

Ulcerative colitis may be associated with a number of extraintestinal skin manifestations including erythema nodosum and pyoderma gangrenosum. We describe an unusual case of a 26-year-old military pilot with ulcerative colitis and skin lesions diagnosed as leucocytoclastic vasculitis. The skin lesions occurred twice during the severe flare. The first occurrence was treated successfully with corticosteroids. When the lesions recurred several weeks later, concomitant with the ongoing flare, treatment with mesalamine and infliximab resolved the lesions. Ultimately, the patient required total colectomy for flare unresponsive to maximum medical therapy. The leucocytoclastic vasculitis did not recur after colectomy. We propose a potential immunopathophysiologic mechanism linking the 2 conditions based on recent biochemical and clinical research.

Diagnostic Evaluation of Hypoglycemia Due To an Insulinoma in a Deployed Infantryman: Significance of Neuroglycopenia and the Role of the Military Health System.

Insulinoma, the prototype of endogenous hyperinsulinemic hypoglycemia, is a very rare condition, with an incidence of four cases per million person-years. Its rate of occurrence in the U.S. military population is unknown. Two cases of insulinomas involving active duty service members have been published. However, there has been no reported case of an insulinoma in a deployed service member. We report the case of a 21-year-old infantryman with clinical hypoglycemia of insidious onset, manifesting with overt neuroglycopenic symptoms during his deployment as a combatant soldier, and the ultimate diagnosis of an insulinoma as the underlying cause. The series of multiple clinical evaluations and the unique circumstances leading to the formal evaluation of the patient's hypoglycemia and treatment are chronicled. The significance of neuroglycopenia and the diagnostic approach to any suspected case of hypoglycemia, the potential challenges and opportunities, and educational aspects of evaluation and management of the insulinoma are elaborated. The potential role of the Military Health System in facilitating the detection and treatment of this rare condition in the service member is discussed as well.

The acylfulvene alkylating agent, LP-184, retains nanomolar potency in non-small cell lung cancer carrying otherwise therapy-refractory mutations.

More than 40% of non-small cell lung cancer (NSCLC) patients lack actionable targets and require non-targeted chemotherapeutics. Many become refractory to drugs due to underlying resistance-associated mutations. KEAP1 mutant NSCLCs further activate NRF2 and upregulate its client PTGR1. LP-184, a novel alkylating agent belonging to the acylfulvene class is a prodrug dependent upon PTGR1. We hypothesized that NSCLC with KEAP1 mutations would continue to remain sensitive to LP-184. LP-184 demonstrated highly potent anticancer activity both in primary NSCLC cell lines and in those originating from brain metastases of primary lung cancers. LP-184 activity correlated with PTGR1 transcript levels but was independent of mutations in key oncogenes (KRAS and KEAP1) and tumor suppressors (TP53 and STK11). LP-184 was orders of magnitude more potent in vitro than cisplatin and pemetrexed. Correlative analyses of sensitivity with cell line gene expression patterns indicated that alterations in NRF2, MET, EGFR and BRAF consistently modulated LP-184 sensitivity. These correlations were then extended to TCGA analysis of 517 lung adenocarcinoma patients, out of which 35% showed elevated PTGR1, and 40% of those further displayed statistically significant co-occurrence of KEAP1 mutations. The gene correlates of LP-184 sensitivity allow additional personalization of therapeutic options for future treatment of NSCLC.

Functional colloidal trimers by quenched electrostatic assembly.

It is shown how to assemble three particles into a single "colloidal trimer". The particles may consist of different materials and be different sizes, and they can be assembled in a particular sequence (i.e. 1-2-3 or 2-1-3 or 2-3-1). Several trimer assemblies are demonstrated, including polystyrene-silica-polystyrene, gold-polystyrene-silver, and gold-silicon-silver. The gold-silicon-silver assembly operates as a catalytic motor, moving rapidly by autoelectrophoresis when placed in a hydrogen peroxide solution. The assemblies are made by allowing oppositely-charged particles to aggregate in a diffusion-limited manner for a time, and then quenching the aggregation by the addition of a nanoparticle coating on one of the particles. We call this method "Quenched Electrostatic Assembly", and it serves as a general, scalable method for synthesizing multi-component colloidal trimers, including those requiring a certain sequential order, but not requiring particular orientations. In addition, when polymer nanoparticles are used to quench the aggregation, they can be fused above their glass transition temperature to produce assemblies that are mechanically stable.

Pentavalent methylated arsenicals are substrates of human AQP9.

Liver aquaglyceroporin AQP9 facilitates movement of trivalent inorganic arsenite (As(III)) and organic monomethylarsonous acid (MAs(III)). However, the transport pathway for the two major pentavalent arsenic cellular metabolites, MAs(V) and DMAs(V), remains unknown in mammals. These products of arsenic metabolism, in particular DMAs(V), are the major arsenicals excreted in the urine of mammals. In this study, we examined the uptake of the two pentavalent organic arsenicals by human AQP9 in Xenopus laevis oocytes. Xenopus laevis oocytes microinjected with AQP9 cRNA exhibited uptake of both MAs(V) and DMAs(V) in a pH-dependent manner. The rate of transport was much higher at acidic pH (pH5.5) than at neutral pH. Hg(II), an aquaporin inhibitor, inhibited transport of As(III), MAs(III), MAs(V) and DMAs(V) via AQP9. However, phloretin, which inhibits water and glycerol permeation via AQP9, can only inhibit transport of pentavalent MAs(V) and DMAs(V) but not trivalent As(III) and MAs(III), indicating the translocation mechanisms of these arsenic species are not exactly the same. Reagents such as FCCP, valinomycin and nigericin that dissipate transmembrane proton potential or change the transmemebrane pH gradient did not significantly inhibit all arsenic transport via AQP9, suggesting the transport of pentavalent arsenic is not proton coupled. The results suggest that in addition to the initial uptake of trivalent inorganic As(III) inside cells, AQP9 plays a dual role in the detoxification of arsenic metabolites by facilitating efflux from cells.

The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16.

Aging is characterized by the loss of homeostasis and the general decline of physiological functions, accompanied by various degenerative diseases and increased rates of mortality. Aging targeting small molecule screens have been performed many times, however, few have focused on endogenous metabolic intermediates-metabolites. Here, using C. elegans lifespan assays, we conducted a worm metabolite screen and identified an eukaryotes conserved metabolite, myo-inositol (MI), to extend lifespan, increase mobility and reduce fat content. Genetic analysis of enzymes in MI metabolic pathway suggest that MI alleviates aging through its derivative PI(4,5)P2. MI and PI(4,5)P2 are precursors of PI(3,4,5)P3, which is negatively related to longevity. The longevity effect of MI is dependent on the tumor suppressor gene, daf-18 (homologous to mouse Pten), independent of its classical pathway downstream genes, akt or daf-16. Furthermore, we found MI effects on aging and lifespan act through mitophagy regulator PTEN induced kinase-1 (pink-1) and mitophagy. MI's anti-aging effect is also conserved in mouse, indicating a conserved mechanism in mammals.