Biology subjects

Singh, M.

Publications and source records attributed to Singh, M..

At least 181 records · Page 10Linked to original sources

bioRxiv2019

Massive parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity

As a prototype of genomics-guided precision medicine, individualized thiopurine dosing based on pharmacogenetics is a highly effective way to mitigate hematopoietic toxicity of this class of drugs. Recently, NUDT15 deficiency was identified as a novel genetic cause of thiopurine toxicity, and NUDT15-informed preemptive dose reduction is quickly adopted in clinical settings. To exhaustively identify pharmacogenetic variants in this gene, we developed massively parallel NUDT15 function assays to determine variants effect on protein abundance and thiopurine cytotoxicity. Of the 3,097 possible missense variants, we characterized the abundance of 2,922 variants and found 54 hotspot residues at which variants resulted in complete loss of protein stability. Analyzing 2,935 variants in the thiopurine cytotoxicity-based assay, we identified 17 additional residues where variants altered NUDT15 activity without affecting protein stability. We identified structural elements key to NUDT15 stability and/or catalytical activity with single amino-acid resolution. Functional effects for NUDT15 variants accurately predicted toxicity risk alleles in 2,398 patients treated with thiopurines, with 100% sensitivity and specificity, in contrast with poor performance of bioinformatic prediction algorithms. In conclusion, our massively parallel variant function assays identified 1,103 deleterious NUDT15 variants, providing a comprehensive reference of variant function and vastly improving the ability to implement pharmacogenetics-guided thiopurine treatment individualization.

genomics↗

bioRxiv2019

An integrative approach uncovers genes with perturbed interactions in cancers

A major challenge in cancer genomics is to identify genes with functional roles in cancer and uncover their mechanisms of action. Here, we introduce a unified analytical framework that enables rapid integration of multiple sources of information in order to identify cancer-relevant genes by pinpointing those whose interaction or other functional sites are enriched in somatic mutations across tumors. Our accompanying method PertInInt combines knowledge about sites participating in interactions with DNA, RNA, peptides, ions or small molecules with domain, evolutionary conservation and gene-level mutation data. When applied to 10,037 tumor samples across 33 cancer types, PertInInt uncovers both known and newly predicted cancer genes, while simultaneously revealing whether interaction potential or other functionalities are disrupted. PertInInts analysis demonstrates that somatic mutations are frequently enriched in binding residues and domains in oncogenes and tumor suppressors, and implicates interaction perturbation as a pervasive cancer driving event.\n\n(Software at http://github.com/Singh-Lab/PertInInt.)

bioinformatics↗

bioRxiv2019

Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors

Although human endogenous retroviruses (HERVs) represent a substantial proportion of the human genome and some HERVs have been suggested to be involved in neurological disorders, little is known about their biological function and pathophysiological relevance. HERV-K(HML-2) comprises evolutionarily young proviruses transcribed in the brain. We report that RNA derived from an HERV-K(HML-2) env gene region binds to the human RNA-sensing Toll-like receptor (TLR) 8, activates human TLR8, as well as murine Tlr7, and causes neurodegeneration through TLR8 and Tlr7 in neurons and microglia. HERV-K(HML-2) RNA introduced extracellularly into the cerebrospinal fluid (CSF) of either C57BL/6 wild-type mice or APPPS1 mice, a mouse model for Alzheimers disease (AD), resulted in neurodegeneration. Tlr7-deficient mice were protected against neurodegenerative effects, but were re-sensitized towards HERV-K(HML-2) RNA when neurons ectopically expressed murine Tlr7 or human TLR8. Accordingly, transcriptome datasets of human brain samples from AD patients revealed a specific correlation of upregulated HERV-K(HML-2) and TLR8 RNA expression. HERV-K(HML-2) RNA was detectable more frequently in CSF from AD individuals compared to controls. Our data establish HERV-K(HML-2) RNA as an endogenous ligand for human TLR8 and murine Tlr7 and imply a functional contribution of specific human endogenous retroviral transcripts to neurodegenerative processes such as AD.

neuroscience↗

bioRxiv2019

Individualized Dynamic Brain Models: Estimation and Validation with Resting-State fMRI

A key challenge for neuroscience is to develop generative, causal models of the human nervous system in an individualized, data-driven manner. Previous initiatives have either constructed biologically-plausible models that are not constrained by individual-level human brain activity or used data-driven statistical characterizations of individuals that are not mechanistic. We aim to bridge this gap through the development of a new modeling approach termed Mesoscale Individualized Neurodynamic (MINDy) modeling, wherein we fit nonlinear dynamical systems models directly to human brain imaging data. The MINDy framework is able to produce these data-driven network models for hundreds to thousands of interacting brain regions in just 1-3 minutes per subject. We demonstrate that the models are valid, reliable, and robust. We show that MINDy models are predictive of individualized patterns of resting-state brain dynamical activity. Furthermore, MINDy is better able to uncover the mechanisms underlying individual differences in resting state activity than functional connectivity methods.

neuroscience↗

bioRxiv2019

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated By Cis Noncoding Mutations

Identifying cancer-relevant mutations in noncoding regions is extremely challenging due to the large numbers of such mutations, their low levels of recurrence, and the general difficulty in interpreting their impact. To uncover genes that are dysregulated due to somatic mutations in cis, we build upon the concept of differential allele-specific expression (ASE) and introduce methods to identify genes within an individuals cancer whose ASE differs from what is found in matched normal tissue. When applied to breast cancer tumor samples, our methods readily detect the known allele-specific effects of copy number variation and nonsense-mediated decay. Further, genes that are found to recurrently exhibit differential ASE across samples are cancer relevant. Genes with cis mutations are enriched for differential ASE, and we find 147 potentially functional noncoding mutations cis to genes that exhibit significant differential ASE. Overall, our results suggest that differential ASE is a promising means for discovering gene dysregulation within an individual due to cis noncoding mutations.

bioinformatics↗

bioRxiv2019

The Deubiquitinating Enzyme USP37 Stabilizes CHK1 to Promote the Cellular Response to Replication Stress

The deubiquitinating enzyme USP37 is known to contribute to timely S-phase onset. However, it is not clear if USP37 is essential beyond S-phase entry despite expression and activity of USP37 peaking within S-phase. Here, we determine that USP37-depleted cells exhibited altered S-phase kinetics and harbored increased levels of the replication stress and DNA damage markers {gamma}H2AX and 53BP1 in response to perturbed replication. Depletion of USP37 also reduced cellular proliferation and led to increased sensitivity to agents that induce replication stress. Underlying the increased sensitivity, we found that the checkpoint kinase CHK1 is destabilized in the absence of USP37, attenuating its function. We further demonstrated that USP37 deubquitinates and stabilizes CHK1. Our data contribute to an evolving understanding of UPS37 as a multifaceted regulator of genome regulation.

cell biology↗

bioRxiv2019

The Glycolytic Protein Phosphofructokinase Dynamically Relocalizes into Subcellular Compartments with Liquid-like Properties in vivo

While much is known about the biochemical regulation of glycolytic enzymes, less is understood about how they are organized inside cells. Here we built a hybrid microfluidic-hydrogel device for use in Caenorhabditis elegans to systematically examine and quantify the dynamic subcellular localization of the rate-limiting enzyme of glycolysis, phosphofructokinase-1/PFK-1.1. We determine that endogenous PFK-1.1 localizes to distinct, tissue-specific subcellular compartments in vivo. In neurons, PFK-1.1 is diffusely localized in the cytosol, but capable of dynamically forming phase-separated condensates near synapses in response to energy stress from transient hypoxia. Restoring animals to normoxic conditions results in the dispersion of PFK-1.1 in the cytosol, indicating that PFK-1.1 reversibly organizes into biomolecular condensates in response to cues within the cellular environment. PFK-1.1 condensates exhibit liquid-like properties, including spheroid shapes due to surface tension, fluidity due to deformations, and fast internal molecular rearrangements. Prolonged conditions of energy stress during sustained hypoxia alter the biophysical properties of PFK-1.1 in vivo, affecting its viscosity and mobility within phase-separated condensates. PFK-1.1s ability to form tetramers is critical for its capacity to form condensates in vivo, and heterologous self-association domain such as cryptochrome 2 (CRY2) is sufficient to constitutively induce the formation of PFK-1.1 condensates. PFK-1.1 condensates do not correspond to stress granules and might represent novel metabolic subcompartments. Our studies indicate that glycolytic protein PFK-1.1 can dynamically compartmentalize in vivo to specific subcellular compartments in response to acute energy stress via multivalency as phase-separated condensates.

cell biology↗

bioRxiv2019

Single cell multi-modal analysis with VDJPuzzle identifies clonality and gene expression profiles of T and B cells

BackgroundSingle cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information.\n\nResultsWe developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8+ T cells with available gene expression, TCR sequences, quantification of 15 surface proteins, and 44 antigen specificities (across viruses, cancer, and self-antigens). We performed quality control, filtering of tetramer non-specific cells, clustering, random sampling and hypothesis testing to discover antigen specific gene signatures which were associated with immune cell differentiation states and clonal expansion across the pathogen specific T cells. We also analysed 563 single cells (plate-based sorted) obtained from 11 subjects, revealing clonally expanded T and B cells across primary cancer tissues and metastatic lymph-node. These immune cells clustered with distinct gene signatures according to the breast cancer molecular subtype. VDJView has been tested in lab meetings and peer-to-peer discussions, showing effective data generation and discussion without the need to consult bioinformaticians.\n\nConclusionsVDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview.

bioinformatics↗

bioRxiv2019

A common tag nucleotide variant in MMP7 promoter increases risk for hypertension via enhanced interactions with CREB transcription factor

MMP7 (Matrilysin), a potent extracellular matrix degrading enzyme with wide substrate specificity, is emerging as a new regulator of cardiovascular diseases including coronary artery disease and atherosclerosis. However, potential contributions of MMP7 genetic variations to hypertension remain unknown. In this study, we first probed for the association of a tag single nucleotide polymorphism (SNP) in the MMP7 gene promoter (-181A/G; rs11568818) with hypertension in an urban south Indian population (n=1517). The heterozygous A/G genotype showed a strong association with hypertension as compared to the A/A wild-type genotype (OR=1.641, 95% CI=1.276-2.109; p=1x10-4); AG genotype carriers also displayed significantly higher diastolic blood pressure and mean arterial pressure than AA genotype subjects. The study was replicated in a north Indian population (n=977) as well (OR=1.520, 95% CI =1.106-2.090; p=0.01). Transient transfection experiments using MMP7 promoter-luciferase reporter constructs revealed that the variant -181G allele conferred greater promoter activity than the -181A allele. Computational prediction and structure-based conformational and molecular dynamics simulation studies suggested higher binding affinity for the transcription factor CREB to the -181G promoter. In corroboration, over-expression/down-regulation of CREB and chromatin immunoprecipitation experiments provided convincing evidence for stronger binding of CREB with the -181G promoter. Further, the -181G promoter also displayed an enhanced response to hypoxia and epinephrine-treatment. The higher promoter activity of -181G allele also translated to increased MMP7 protein levels. Indeed, MMP7-181A/G heterozygous individuals displayed elevated plasma MMP7 levels which positively correlated with blood pressure. In conclusion, the MMP7 A-181G promoter SNP increased expression of MMP7 under pathophysiological (such as hypoxic stress and catecholamine excess) conditions via increased interactions with the transcription factor CREB and enhanced the risk for hypertension in its carriers.

genetics↗

bioRxiv2019

Synthetic Dual-Acting Small-Molecule Inhibitors That Target Mycobacterial DNA Replication

Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium and a causative agent of tuberculosis (TB), a disease that kills more than 1.5 million people worldwide annually. One of the main reasons for this high mortality rate is the evolution of new Mtb strains that are resistant to available antibiotics. Therefore, new therapeutics for TB are in constant demand. Here we report the development of such inhibitors that target two DNA replication enzymes of Mtb, namely DnaG primase and DNA gyrase, which share a conserved TOPRIM fold near the inhibitors binding site. The molecules were developed on the basis of previously reported inhibitors for T7 DNA primase that bind near the TOPRIM fold. In order to improve the physicochemical properties of the molecules as well as their inhibitory effect on primase and gyrase, 49 novel compounds were synthesized as potential drug candidates in three stages of optimization. The last stage of chemical optimization yielded two novel inhibitors for the fast-growing nonpathogenic model Mycobacterium smegmatis (Msmg).

biochemistry↗

bioRxiv2019

Development and validation of microsatellite markers from de novo transcriptome assembly of eggplant (Solanum melongena L.) and its putative progenitor S. incanum L. cultivars

An elite cultivar of eggplant, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.) with contrasting horticultural traits were used as parental lines to develop a mapping population of RILs. To accelerate breeding programs and to develop large scale SSR markers to be used in QTL mapping, RNASeq libraries from different tissues of both the parental plants were deep sequenced and assembled into representation of a high quality de novo transcriptome using Illumina-based Next Generation Sequencing technology. 99.99% of high quality bases were obtained from all the tissues and deposited in TSA database at the NCBI link. Total 3, 156 and 3, 196 SNVs were detected in S. melongena and S. incanum, respectively. In S. melongena, 11, 262 SSR while in S. incanum 11, 829 SSR containing regions were identified. Based on functional annotation, 21, 914 unique genes could be identified for S. melongena, 21,706 unique genes for S. incanum and overall, 60 different transcription factors were identified in both the lines. Further, a total of 536 SSR markers were designed and screened for polymorphism of which, 157 markers produced polymorphism between the parental lines. The polymorphic SSRs shall be used for genotyping of RILs to map QTLs for various horticultural traits in eggplant and identification of candidate genes in response to biotic and abiotic stress.

genomics↗

bioRxiv2018

Semi-in vitro Reconstitution of Roseocin, a Two-Component Lantibiotic from an Actinomycete

Lantibiotics are lanthionine containing peptide natural products that belong to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs). Recent expansion in the availability of microbial genomic data and in silico analysis tools have accelerated the discovery of these promising alternatives to antibiotics. Following the genome-mining approach, a biosynthetic gene cluster for a putative two-component lantibiotic roseocin was identified in the genome of an Actinomycete, Streptomyces roseosporus NRRL 11379. Post-translationally modified lanthipeptides of this cluster were obtained by heterologous expression of the genes in E. coli, and were in vitro reconstituted to their bioactive form. The two lanthipeptides displayed antimicrobial activity against Gram-positive bacteria only synergistically, a property reminiscent of two-component lantibiotics. Structural analysis of the -component identified a disulfide bridge flanking two of its four thioether bridges and the {beta}-component having six thioether bridges with its C-terminus extended than the previously known two-component lantibiotics.

biochemistry↗

bioRxiv2018

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

High-throughput single-cell RNA-Sequencing is a powerful technique for gene expression profiling of complex and heterogeneous cellular populations such as the immune system. However, these methods only provide short-read sequence from one end of a cDNA template, making them poorly suited to the investigation of gene-regulatory events such as mRNA splicing, adaptive immune responses or somatic genome evolution. To address this challenge, we have developed a method that combines targeted long-read sequencing with short-read based transcriptome profiling of barcoded single cell libraries generated by droplet-based partitioning. We use Repertoire And Gene Expression sequencing (RAGE-seq) to accurately characterize full-length T cell (TCR) and B cell (BCR) receptor sequences and transcriptional profiles of more than 7,138 lymphocytes sampled from the primary tumour and draining lymph node of a breast cancer patient. With this method we show that somatic mutation, alternate splicing and clonal evolution of T and B lymphocytes can be tracked across these tissue compartments. Our results demonstrate that RAGE-Seq is an accessible and cost-effective method for high-throughput deep single cell profiling, applicable to a wide range of biological challenges.

genomics↗

bioRxiv2018

Mutant Screen Reveals the Piccolo’s Control over Depression and Brain-Gonad Crosstalk

Successful sexual reproduction involves complex, genetically encoded interplay between animal physiology and behavior. The rat provides a highly fecund mammalian model for studying how the brain impacts reproduction. Here, we report a forward genetics screen in rats to identify genes that affect reproduction. A panel of 18 distinct rat strains harboring Sleeping Beauty gene trap mutations were analyzed for the ability to reproduce. As expected, our mutant screen identified genes where reproductive failure was connected to gametogenesis (Btrc, Pan3, Spaca6, Ube2k) and embryogenesis (Alk3, Exoc6b, Slc1a3, Tmx4, Zmynd8). In addition, we identified Ata13 (longevity) and Pclo (neuronal disorders), previously not associated with an inability to conceive. Neurologically, Pclo is known to regulate the size of presynaptic vesicle pools. Here, dominant traits in Pclo mutant rats caused epileptiform activity and affected genes supporting GABAergic synaptic transmission (Gabra6, Gabrg3). Recessive traits in Pclo mutant rats transmitted altered reproductive behavior, as homozygous Pclo mutant rats produced gametes but neither sex would mate with wildtype rats. Pclo mutant rat behavior was linked to endophenotypes signifying compromised brain-gonad crosstalk via disturbed GnRH signaling and allelic markers for major depressive disorder in humans (Grm5, Htr2a, Sorcs3, Negr1, Drd2). Thus, by rat genetics, we identified Pclo as a candidate presynaptic factor required for reproduction. Author SummaryPiccolo gene mutations have previously been identified in human cohorts diagnosed with behavioral syndromes that impact ones emotions, including depression and bipolar disorder. Although studies in human populations implicate changes to Piccolos DNA sequence to enhanced susceptibility for behavioral disorders, studies in mouse models have yet to link Piccolo mutations to altered behavior. Here, by a novel genetics approach, we report Piccolo mutation-dependent effects on reproductive behavior in rats, a finding that may turn out to be relevant to the behavioral effects that are associated with human Piccolo gene mutations. Thus, research aimed at understanding how Piccolo functions to regulate reproduction in rats could prove pivotal in our ability to understand neurological mechanisms that influence human emotions.

genetics↗

bioRxiv2018

Systematic domain-based aggregation of protein structures highlights DNA-, RNA-, and other ligand-binding positions

Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein-DNA, protein-RNA and other protein-ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here we introduce an approach to identify per-domain-position interaction \"propensities\" by aggregating protein co-complex structures by domain and ascertaining how frequently residues mapping to each domain position interact with ligands. We perform this domain-based analysis on [~]82,000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions, or small molecules across 4,120 domains, which we refer to collectively as the InteracDome. Cross-validation testing reveals that ligand-binding positions for 1,327 domains can be confidently modeled and used to identify residues facilitating interactions in [~]60-69% of human genes. Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. The InteracDome is available at http://interacdome.princeton.edu.

bioinformatics↗

bioRxiv2018

The phylogenetically distinct early human embryo

Is the human early embryo unique in lacking an inner cell-mass (ICM) and having parallel development? We reanalyse single-cell transcriptomic data and stain human embryos in situ to reveal both classical step-wise development and a transcriptomically homologous ICM. This apparent classicism obscures phylogenetic singularity: unlike mice, human epiblast has self-renewal hallmarks and we have abundant blastocyst non-committed cells (NCCs), part of an apoptosis-mediated purging process. The transcriptomes of the pluripotent cells are fast evolving, in large part owing to endogenous retrovirus H (ERVH) activity, rendering all primate embryos unique. Each species is characterised by the ERVHs that are active and the neighbour genes whose expression are modulated. ERVH is associated with recent major gene expression gain and loss events of pluripotency{-}associated genes. Not least through lack of HERVH expression, the current portfolio of naive cultures, putative in vitro mimics of pluripotent cells, are both developmentally and phylogenetically "confused". O_LIAnalysis of single cell transcriptomics and in situ stainings uncover, and enable characterization of, human inner cell mass (ICM) C_LIO_LICell purging via apoptosis defines a phylogenetically restricted class of blastocyst non-committed cells (NCCs), whereas HERVs in conjunction with host defence mark the committed cells of ICM C_LIO_LIFast transcriptome evolution is particular to the pluripotent epiblast and is mostly due to the primate-specific transposable element, HERVH C_LIO_LICurrent naive cultures dont reflect human uniqueness being phylogenetically and developmentally "confused". C_LI

developmental biology↗

bioRxiv2018

22-hydroxycholesterol leads to efficient dopaminergic specification of human Mesenchymal Stem Cells

In the current study, we aim to investigate the neurogenic effect of 22 (R)- hydroxycholesterol (22-HC), on hMSCs obtained from bone marrow, adipose tissue and dental pulp. The effect was evaluated on the basis of detailed morphological and morphometric analysis, expression of genes and proteins associated with maturation of neurons (NF, MAP2, TUJ1, TH), channel ion proteins (Kv4.2 & SCN5A), chemical functionality (DAT), synapse forming tendency of neurons (Synaptophysin) and transcription factors (ngn2 & Pitx3), efficiency of generation of dopaminergic neurons and functional assessment. The percentage of non- DA cells generation (Ach, TPH2, S100 and GFAP positive cells) was also evaluated to confirm selective neurogenic potential of 22-HC. Post analysis, it was observed that 22-HC yields higher percentage of functional DA neurons and has differential effect on various tissue- specific primary human MSCs. This study, which is one of its kinds, may help in improvising the approach of cell based treatment regimes and drug testing in pharmaceutical industry for Parkinsons disease.

neuroscience↗

bioRxiv2017

Targeting temporal dynamics of microenvironmental factors halts tumor migration and alleviates effects of dynamic tumor heterogeneity

Targeting microenvironmental factors that foster migratory cell phenotypes is a promising strategy for halting tumor migration. However, lack of mechanistic understanding of the process impedes pharmaceutical drug development. Using a novel 3D microtumor model with tight control over tumor size, we recapitulated tumor size-induced hypoxic microenvironment and emergence of migratory phenotypes in epithelial T47D breast microtumors as well as those of patient-derived primary metastatic breast cancer cells, mesothelioma cells and lung cancer xenograft cells (PDX). The microtumor models from various patient-derived tumor cells and PDX cells revealed upregulation of tumor secretome, matrix metalloproteinase-9 (MMP9), fibronectin (FN), and soluble E-cadherin (sE-CAD) consistent with the clinically reported elevated levels of FN and MMP9 in the patient breast tumors compared to healthy mammary gland. We further showed that the tumor secretome induces migratory phenotype in non-hypoxic, non-migratory small microtumors. Subsequent mathematical model analysis identified a two-stage microtumor progression and migration mechanism, i.e., hypoxia induces migratory phenotype in the early initialization stage, which then becomes self-sustained through positive feedback loop established among the secretome. Both computational and experimental studies showed that inhibition of tumor secretome effectively halts microtumor migration despite tumor heterogeneity, while inhibition of the hypoxia is effective only within a time window and is compromised by tumor-to-tumor variation of the growth dynamics, supporting our notion that hypoxia initiates migratory phenotypes but does not sustain it. In summary, we show that targeting temporal dynamics of evolving microenvironments during tumor progression can halt and bypass major hurdle of tumor heterogeneity.

cancer biology↗