Biology subjects

Nair, S.

Publications and source records attributed to Nair, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Genome-wide association studies (GWAS) of eye disorders have identified hundreds of genetic variants associated with ocular disease. However, the vast majority of these variants are noncoding, making it challenging to interpret their function. Here, we present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina with >50,000 cells, which we used to analyze noncoding single-nucleotide polymorphisms (SNPs) implicated by GWAS of age-related macular degeneration, glaucoma, diabetic retinopathy, myopia, and type 2 macular telangiectasia. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding SNPs with causal roles in eye disease, assess SNP impact on transcription factor binding, and define their known and novel target genes. Our efforts nominate pathogenic SNP-target gene interactions for multiple vision disorders and provide a potentially powerful resource for interpreting noncoding variation in the eye.

genomics↗

bioRxiv2022

Fitness costs of pfhrp2 and pfhrp3 deletions underlying diagnostic evasion in malaria parasites

BackgroundRapid diagnostic tests based on detection of histidine rich proteins (HRP) are widely used for malaria diagnosis, but parasites carrying pfhrp deletions can evade detection and are increasing in frequency in some countries. Models aim to predict conditions under which pfhrp2 and/or pfhrp3 deletions will increase, but a key parameter - the fitness cost of deletions - is unknown MethodsWe removed pfhrp2 and/or pfhrp3 from a Malawian parasite clone using CRISPR/Cas9 and measured fitness costs by conducting pairwise competition experiments. ResultsWe observed significant fitness costs of 0.087 {+/-} 0.008 (1 s.e.) per asexual cycle for pfhrp2 deletion and 0.113 {+/-} 0.008 (1 s.e.) for the pfhrp2/3 double deletion, relative to the unedited progenitor parasite. The results demonstrate [~]10% reduced survival of parasites bearing deletions of these loci. ConclusionsPrior modelling suggested that diagnostic selection may drive increased frequency of pfhrp2 and pfhrp3 deletions when fitness costs are [≤]10%. Our laboratory competition experiments are consistent with costs of pfhrp2/3 deletions lying at this critical tipping point. These results may inform future modelling efforts and help us to understand why pfhrp2/3 deletions are increasing in some locations (Ethiopia/Eritrea) but not in others (Mekong region).

microbiology↗

bioRxiv2021

Accelerating in-silico saturation mutagenesis using compressed sensing

In-silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the difference in model output. However, this method can be slow because systematically perturbing each position requires performing a number of forward passes proportional to the length of the sequence being examined. In this work, we propose a modification of ISM that leverages the principles of compressed sensing to require only a constant number of forward passes, regardless of sequence length, when applied to models that contain operations with a limited receptive field, such as convolutions. Our method, named Yuzu, can reduce the time that ISM spends in convolution operations by several orders of magnitude and, consequently, Yuzu can speed up ISM on several commonly used architectures in genomics by over an order of magnitude. Notably, we found that Yuzu provides speedups that increase with the complexity of the convolution operation and the length of the sequence being analyzed, suggesting that Yuzu provides large benefits in realistic settings. We have made this tool available at https://github.com/kundajelab/yuzu.

bioinformatics↗

bioRxiv2021

Dynamic brain activity during associative learning examined with MEG/fMRI co-processing

BackgroundDue to limitations of individual neuroimaging methods we examine spatial and temporal contributions to self-generation using multimodality imaging with functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) within the Bayesian framework Multiple Sparse Priors (MSP). New Method24 healthy participants performed an fMRI and MEG paired-associate learning task. FMRI data were processed within Group ICA fMRI Toolbox. Independent components (ICs) were temporally sorted by task time series (|r|>0.30 threshold identified task-related ICs). Task-positive ("generate") ICs were retained as spatial priors for MEG analyses. MEG data were processed by averaging trials to increase the signal-to-noise ratio within subjects and with an event-related theta power approach. MEG source reconstructions were constrained within the task-positive ICs for both analytical approaches. ResultsFor fMRI, five networks were identified as task-related. Four ICs underlying active generation spanned bilateral parietal, orbitofrontal, medial frontal and superior temporal regions, and occipital lobe. FMRI-constrained MEG source reconstructions yielded early visual cortex activity followed by left inferior frontal gyrus (IFG) and orbito-frontal cortex (OFC) recruitment to coalesce in the left inferior temporal lobe. For the event-related theta approach, reconstructions showed a progression of activity from bilateral temporal areas to left OFC and middle temporal gyrus, followed by right IFG. Comparison with Existing MethodsMSP analyses informed by fMRI produced more focused regional activity than reconstructions without priors suggesting increased attention and maintenance when selecting relevant semantic information during active generation. ConclusionsConstraining MEG source reconstruction to fMRI priors during active generation implicates interconnected fronto-temporal and fronto-parietal networks across time.

neuroscience↗

bioRxiv2021

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans

Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open- angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, is the major cause of elevated IOP. Here, we demonstrate that mice deficient in the Kruppel- like zinc finger transcriptional factor GLI-similar-1 (GLIS1) develop chronically elevated IOP. Magnetic resonance imaging and histopathological analysis reveal that deficiency in GLIS1 expression induces progressive degeneration of the TM, leading to inefficient AqH drainage from the anterior chamber and elevated IOP. Transcriptome and cistrome analyses identified several glaucoma- and extracellular matrix-associated genes as direct transcriptional targets of GLIS1. We also identified a significant association between GLIS1 variant rs941125 and glaucoma in humans (P=4.73x10-6), further supporting a role for GLIS1 into glaucoma etiology. Our study identifies GLIS1 as a critical regulator of TM function and maintenance, AqH dynamics, and IOP.

molecular biology↗

bioRxiv2021

Epigenetic therapy suppresses endocrine-resistant breast tumour growth by re-wiring ER-mediated 3D chromatin interactions

Three-dimensional (3D) epigenome remodelling is an important mechanism of gene deregulation in cancer. However, its potential as a target to overcome therapy resistance remains largely unaddressed. Here we show that FDA-approved epigenetic therapy Decitabine (5-Aza-mC) suppresses tumour growth in preclinical metastatic ER+ breast tumour xenograft models. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher order chromatin structure and loss of topologically associated domain boundary insulation. Significant DNA hypomethylation at ER-enhancer elements was associated with gain in ER binding, creation of ectopic 3D enhancer-promoter interactions and concordant activation of ER-mediated transcription pathways. Importantly long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates how epigenetic therapy has potential to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions associated with suppression of tumour growth.

molecular biology↗

bioRxiv2021

A midbody component homolog, too much information/prc1-like, is required for microtubule reorganization during both cytokinesis and axis induction in the early zebrafish embryo

We show that the zebrafish maternal-effect mutation too much information (tmi) corresponds to zebrafish prc1-like (prc1l), which encodes a member of the MAP65/Ase1/PRC1family of microtubule-associated proteins. Embryos from tmi/prc1l homozygous mutant mothers display cytokinesis defects in meiotic and mitotic divisions in the early embryo, indicating that tmi/prc1l has a role in midbody formation during cell division at the egg-to-embryo transition. Unexpectedly, maternal tmi/prc1l function is also essential for the reorganization of vegetal pole microtubules required for embryonic axis induction. While Prc1 is widely regarded to crosslink microtubules in an antiparallel conformation, our studies provide evidence for an additional function of Prc1 in the bundling of parallel microtubules in the vegetal cortex of the early embryo during cortical rotation and prior to mitotic cycling. These findings highlight common yet distinct aspects of microtubule reorganization that occur during the egg-to-embryo transition, driven by maternal product for the midbody component Prc1l and required for embryonic cell division and pattern formation.

developmental biology↗

bioRxiv2021

Understanding the complexity of Epimorphic Regeneration in zebrafish: A Transcriptomic and Proteomic approach.

Genomic and Proteomic changes play a crucial role in perpetuating regeneration of complex tissues through differentiation and growth. The complex Epimorphic regeneration of zebrafish caudal fin tissue is hasty and absolute. This study was executed to understand the role of various genes/proteins involved in the regeneration of zebrafish caudal fin tissue through differential expression analysis. High throughput transcriptomics analysis involving Next Generation Sequencing approach and iTRAQ based quantitative proteomics analyses were performed on the regenerating tissue samples for various regenerating time points. Based on our study 1408 genes and 661 proteins were found differentially regulated in the regenerating caudal fin tissue for having at least 1-log fold change in their expression at 12hpa, 1, 2, 3 and 7dpa stages against control non-regenerating tissue. Interleukin, SLC, PRMT, HOX, neurotransmitter and several novel genes were found to be associated with regeneration for its differential regulation during the mechanism. Based on the network and pathway analysis the differentially regulated genes and proteins were found allied with activation of cell proliferation, cell viability, cell survival & cell movement and inactivation of organismal death, morbidity, necrosis, death of embryo & cell death. Network pathways such as Cancer & development disorder, Cell signaling molecular transport, organismal injury & abnormalities and Cellular development, growth & proliferation were found most significantly associated with the zebrafish caudal fin regeneration mechanism. This study has mapped a detailed insight of the genes/proteins expression associated with the epimorphic regeneration more profoundly.

developmental biology↗

bioRxiv2021

Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels

Neuronal ankyrins cluster and link membrane proteins to the actin and spectrin-based cytoskeleton. Among the three vertebrate ankyrins, little is known about neuronal Ankyrin-R (AnkR). We report AnkR is highly enriched in Pv+ fast-spiking interneurons in mouse and human. We identify AnkR-associated protein complexes including cytoskeletal proteins, cell adhesion molecules (CAMs), and perineuronal nets (PNNs). We show that loss of AnkR from forebrain interneurons reduces and disrupts PNNs, decreases anxiety-like behaviors, and changes the intrinsic excitability and firing properties of Pv+ fast-spiking interneurons. These changes are accompanied by a dramatic reduction in Kv3.1b K+ channels. We identify a novel AnkR-binding motif in Kv3.1b, and show that AnkR is both necessary and sufficient for Kv3.1b membrane localization in interneurons and at nodes of Ranvier. Thus, AnkR regulates Pv+ fast-spiking interneuron function by organizing ion channels, CAMs, and PNNs, and linking these to the underlying {beta}1 spectrin-based cytoskeleton.

neuroscience↗

bioRxiv2020

Prioritization prostate cancer to immune checkpoint therapy by ranking tumors along IFN-γ axis and identification of immune resistance mechanisms

We propose priotirization of prostate cancer patients to PD-L1 checkpoint therapy by assessing activity of IFN-{gamma}/PD-L1 signaling in tumor from transcriptional profile. To this end, we introduced a new approach for inferring pathway activity and suppression (IPAS) by assessing significance of positioning pathways genes expression levels at top (activation) or bottom (suppression) in gene expression profile of a given tumor. By ordering tumors along IFN-{gamma}/PD-L1 axis, we determined distinct "IFN-{gamma}-depleted" and "IFN-{gamma}-enriched" immune subtypes, genes involved in immune evasion and potential targets for combination therapy. Using IPAS scoring method, we proposed biomarker panels for accurate ranking tumors along IFN-{gamma}/PD-L1 axis.

bioinformatics↗

bioRxiv2020

fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks

Deep learning models such as convolutional neural networks are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In-silico saturation mutagenesis (ISM) is a popular feature attribution technique for inferring contributions of all characters in an input sequence to the models predicted output. The main drawback of ISM is its runtime, as it involves multiple forward propagations of all possible mutations of each character in the input sequence through the trained model to predict the effects on the output. We present fastISM, an algorithm that speeds up ISM by a factor of over 10x for commonly used convolutional neural network architectures. fastISM is based on the observations that the majority of computation in ISM is spent in convolutional layers, and a single mutation only disrupts a limited region of intermediate layers, rendering most computation redundant. fastISM reduces the gap between backpropagation-based feature attribution methods and ISM. It far surpasses the runtime of backpropagation-based methods on multi-output architectures, making it feasible to run ISM on a large number of sequences. An easy-to-use Keras/TensorFlow 2 implementation of fastISM is available at https://github.com/kundajelab/fastISM, and a hands-on tutorial at https://colab.research.google.com/github/kundajelab/fastISM/blob/master/notebooks/colab/DeepSEA.ipynb.

bioinformatics↗

bioRxiv2020

Genetic background modifies vulnerability to glaucoma related phenotypes in Lmx1b mutant mice

Variants in the LIM homeobox transcription factor 1-beta gene (LMX1B) predispose individuals to elevated intraocular pressure (IOP), a key risk factor for glaucoma. However, the effect of LMX1B mutations varies widely between individuals. To better understand mechanisms underlying LMX1B-related phenotypes and individual differences, we backcrossed the Lmx1bV265D (also known as Lmx1bIcst) allele onto the C57BL/6J (B6), 129/Sj (129), C3A/BLiA-Pde6b+/J (C3H), and DBA/2J-Gpnmb+ (D2-G) strain backgrounds. Strain background had a significant effect on the onset and severity of ocular phenotypes in Lmx1bV265D/+ mutant mice. Mice of the B6 background were the most susceptible to developing elevated IOP, severe anterior segment developmental anomalies (including malformed eccentric pupils, iridocorneal strands, and corneal abnormalities) and glaucomatous nerve damage. In contrast, Lmx1bV265D mice of the 129 background were the most resistant to developing anterior segment abnormalities, had less severe IOP elevation than B6 mutants at young ages, and showed no detectable nerve damage. To identify genetic modifiers of susceptibility to Lmx1bV265D-induced glaucoma-associated phenotypes, we performed a mapping cross between mice of the B6 (susceptible) and 129 (resistant) backgrounds. We identified a modifier locus on Chromosome 18, with the 129 allele(s) substantially lessening severity of ocular phenotypes, as confirmed by congenic analysis. By demonstrating a clear effect of genetic background in modulating Lmx1b-induced phenotypes, by providing a panel of strains with different phenotypic severities and by identifying a modifier locus, this study lays a foundation for better understanding the roles of LMX1B in glaucoma with the goal of developing new treatments.

genetics↗

bioRxiv2020

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch

BackgroundMicrobial whole-genome sequencing (WGS) is now increasingly used to inform public health investigations of infectious disease. This approach has transformed our understanding of the global population structure of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever. WGS has been particularly informative for understanding the global spread of multi-drug resistant (MDR) typhoid. As WGS capacity becomes more decentralised, there is a growing opportunity for collaboration and sharing of surveillance data within and between countries to inform disease control policies. This requires freely available, community driven tools that reduce the barriers to access genomic data for public health surveillance and that deliver genomic data on a global scale. MethodsHere we present the Pathogenwatch (https://pathogen.watch/styphi) scheme for S. Typhi, a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data to identify high-risk clones at a population level. Data are delivered in single genome reports or in collections of genomes combined with geographic and other data using trees, maps and tables. ResultsWe show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are largely concordant with phenotypic drug susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from over 4,300 public genomes available in the application. ConclusionsPathogenwatch democratises genomic epidemiology of S. Typhi by providing an intuitive entry point for the analysis of WGS and linked epidemiological data, enabling international public health monitoring of the emergence and spread of high risk clones.

genomics↗

bioRxiv2020

Identification of ADAMTS19 as a novel retinal factor involved in ocular growth regulation

Refractive errors are the most common ocular disorders and are a leading cause of visual impairment worldwide. Although ocular axial length is well established to be a major determinant of refractive errors, the molecular and cellular processes regulating ocular axial growth are poorly understood. Mutations in genes encoding the PRSS56 and MFRP are a major cause of nanophthalmos. Accordingly, mouse models with mutations in the genes encoding the retinal factor PRSS56 or MFRP, a gene predominantly localized in the retinal pigment epithelial (RPE) exhibit ocular axial length reduction and extreme hyperopia. However, the precise mechanisms underlying PRSS56- and MFRP-mediated ocular axial growth remain elusive. Here, we show that Adamts19 expression is significantly upregulated in retina of mice lacking either Prss56 or Mfrp. Using a combination of genetic approaches and mouse models, we show that while ADAMTS19 is not required for ocular growth during normal development, its inactivation exacerbates ocular axial length reduction in both Prss56 or Mfrp mutant mice. These results suggest that the upregulation of retinal Adamts19 expression is part of an adaptive molecular response to counteract impaired ocular growth. Using a complementary genetic approach. We further demonstrate that loss of PRSS56 or MFRP function prevents excessive ocular axial growth in a mouse model of developmental myopia caused by a null mutation in Irpb, demonstrating that ocular axial elongation in Irbp-/- mice is fully dependent on PRSS56 and MFRP functions. Collectively, our findings provide insight into the molecular network involved in ocular axial growth regulation and refractive development and support the notion that relay of the signal between the retina and RPE could be critical for promoting ocular axial elongation.

genetics↗

bioRxiv2020

A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer's disease

We conducted a large multi-ethnic meta-analysis of genome-wide association studies for primary open-angle glaucoma (POAG) on a total of 34,179 cases vs 349,321 controls, and identified 127 independent risk loci, almost doubling the number of known loci for POAG. The majority of loci have broadly consistent effect across European, Asian and African ancestries. We identify a link, both genome-wide and at specific loci, between POAG and Alzheimers disease. Gene expression data and bioinformatic functional analyses provide further support for the functional relevance of the POAG risk genes. Several drug compounds target these risk genes and may be potential candidates for developing novel POAG treatments.

genetics↗

bioRxiv2019

Donor monocyte-derived macrophages promote human acute graft versus host disease

Myelopoiesis is invariably present, and contributes to pathology, in animal models of graft versus host disease (GVHD). In humans, a rich inflammatory infiltrate bearing macrophage markers has also been described in histological studies. In order to determine the origin, functional properties and role in pathogenesis of these cells, we isolated single cell suspensions from acute cutaneous GVHD and subjected them to genotype, transcriptome and in vitro functional analysis. A donor-derived population of CD11c+CD14+ cells was the dominant population of all leukocytes in GVHD. Surface phenotype and nanostring gene expression profiling indicated the closest steady-state counterpart of these cells to be monocyte-derived macrophages. In GVHD, however, there was upregulation of monocyte antigens SIRP and S100A8/9, and transcripts associated with leukocyte trafficking, pattern recognition, antigen presentation, and co-stimulation. Isolated GVHD macrophages stimulated greater proliferation and activation of allogeneic T cells, and secreted higher levels of inflammatory cytokines than their steady-state counterparts. In HLA-matched mixed leukocyte reactions, we also observed differentiation of activated macrophages with a similar phenotype. These exhibited cytopathicity to a cell line and mediated pathological damage to skin explants, independently of T cells. Together, these results define the origin, functional properties and potential pathogenic roles of human GVHD macrophages.

immunology↗

bioRxiv2019

Predicting and Designing therapeutics against the Nipah virus

Though every outbreak of the Nipah Virus has resulted in high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified putative peptides (against G, F, and M proteins) and small molecules inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modelling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To this end, we have designed 4 peptide inhibitors and predicted 70 small molecules (13 with high confidence) against 3 and 5 Nipah proteins respectively. To counter the threat of drug resistance, we have analyzed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.\n\nAuthor SummaryNipah virus infections have killed 72-86% of the infected individuals in Bangladesh and India. The infections are spread via bodily secretions of bats, pigs and other infected individuals. Even though, the disease was first detected in the human population in 1998, there are no approved drugs/vaccines against it. In this study, we have tried to model the 3D structures of the Nipah virus proteins. We have then used these models to design/predict small inhibitory molecules that would bind them and prevent their function. We have also analyzed the different strains of the virus to identify conservation patterns of amino acids in the proteins, which in turn informs us of the efficacy of the drugs. The designed/docked compounds as well as the protein models are freely accessible for experimental validation and hypothesis testing.

bioinformatics↗

bioRxiv2019

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

MotivationGenome-wide profiles of chromatin accessibility and gene expression in diverse cellular contexts are critical to decipher the dynamics of transcriptional regulation. Recently, convolutional neural networks (CNNs) have been used to learn predictive cis-regulatory DNA sequence models of context-specific chromatin accessibility landscapes. However, these context-specific regulatory sequence models cannot generalize predictions across cell types.\n\nResultsWe introduce multi-modal, residual neural network architectures that integrate cis-regulatory sequence and context-specific expression of trans-regulators to predict genome-wide chromatin accessibility profiles across cellular contexts. We show that the average accessibility of a genomic region across training contexts can be a surprisingly powerful predictor. We leverage this feature and employ novel strategies for training models to enhance genome-wide prediction of shared and context-specific chromatin accessible sites across cell types. We interpret the models to reveal insights into cis and trans regulation of chromatin dynamics across 123 diverse cellular contexts.\n\nAvailabilityThe code is available at https://github.com/kundajelab/ChromDragoNN\n\nContactakundaje@stanford.edu

genomics↗