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Srivastava, A.

Publications and source records attributed to Srivastava, A..

At least 109 records · Page 6Linked to original sources
bioRxiv2022

Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins

LexA, a well-characterized transcriptional repressor of the SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, in light of the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd stress tolerance, with regulation over a variety of Cd stress-responsive genes in addition to the regulation on genes related with photosynthetic redox poising. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, carbon metabolism, antioxidative defence, protein turnover, chaperones, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, as well as six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of LexA on several genes and proteins of various functional categories in Anabaena that are responsive to Cd stress, hence expanding the regulatory role of LexA under Cd stress. HighlightsO_LILexA overexpression was earlier shown to decrease Cd stress tolerance in Anabaena. C_LIO_LIWe examined the combined effect of LexA overexpression and Cd on Anabaena proteome. C_LIO_LIUpon LexA overexpression or Cd stress or both, 36 differential proteins were found. C_LIO_LIIn silico, transcript and EMSA proved LexA regulation on them and few transporters. C_LIO_LIThe findings of this study extended the regulatory role of LexA in Cd tolerance. C_LI

molecular biology↗
bioRxiv2022

Using Packing Defects in Heterogeneous Biological Membrane as a Lens to Explore Protein Localization Propensity and Small Molecule Permeability

Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment is not well understood due to the inherent complexities associated with the relevant length and time scales that limit both direct experimental measurements and their interpretation. In this context, computer simulation holds immense potential to investigate molecular-level interactions that lead to PM heterogeneity and the related functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the topological changes in lipid local environment using the non-affine parameter (NAP) frame-work. Furthermore, we probe the packing defects in membrane with coexisting fluid phases, which can be considered as the conjugate of membrane order assessed in terms of the NAP. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind preferential localization of proteins in mixed phase membranes and membrane permeability of small molecules. Our observations suggest that heterogeneity in mixed phase membranes follow some generic features, where functions may arise based on packing-related basic design principles. SignificanceFunctionally important complex lateral and transverse structures in biological membrane result from the differential molecular interactions among a rich variety of lipids and other building blocks. The nature of molecular packing in membrane is a manifestation of these interactions. In this work, using some of the ideas from the Physics of amorphous materials and glasses, we quantify the correlation between heterogeneous membrane organization and the three dimensional packing defects. Subsequently, we investigate the packing-based molecular design-level features that drive preferential localization of peptides in heterogeneous membrane and membrane permeation of small molecules.

biophysics↗
bioRxiv2022

Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome

THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 facilitates the formation of the Transcription Export complex (TREX) tetramer, composed of four THO monomers. The TREX tetramer supports mammalian mRNA processing that is distinct from yeast TREX dimer functions. Human and mouse TIDS model systems allow novel THOC6-dependent TREX tetramer functions to be investigated. Biallelic loss-of-function (LOF) THOC6 variants do not influence the expression and localization of TREX members in human cells, but our data suggests reduced binding affinity of ALYREF. Impairment of TREX nuclear export functions were not detected in cells with biallelic THOC6 LOF. Instead, mRNA mis-splicing was observed in human and mouse neural tissue, revealing novel insights into THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions that may inform TIDS neuropathology.

molecular biology↗
bioRxiv2022

PROTEIN CODING VARIATION IN OUTBRED LABORATORY MOUSE STOCKS PROVIDES A MOLECULAR BASIS FOR DISTINCT RESEARCH APPLICATIONS

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice for biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that ensures research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined the novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for on-going genetic quality control. We also compared these data to protein coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. That individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.

genetics↗
bioRxiv2022

Protein as evolvable functionally-constrained amorphous matter

We explore current ideas around the representation of a protein as an amorphous material, in turn represented by an abstract graph [G] with edges weighted by elastic stiffnesses. By embedding this graph in physical space, we can map every graph to a spectrum of conformational fluctuations and responses (as a result of say, ligand-binding). This sets up a "genotype-phenotype" map, which we use to evolve the amorphous material to select for fitness. Using this, we study the emergence of allosteric interaction, hinge joint, crack formation and a slide bolt in functional proteins such as Adenylate kinase, HSP90, Calmodulin and GPCR proteins. We find that these emergent features are associated with specific geometries and mode spectra of floppy or liquid-like regions. Our analysis provides insight into understanding the architectural demands on a protein that enable a prescribed function and its stability to mutations.

biophysics↗
bioRxiv2022

Aberrant extracellular matrix and cardiac development in models lacking the PR-DUB component ASXL3

BackgroundClinical and research based genetic testing has uncovered genes that encode chromatin modifying complex components required for organogenesis. Covalent histone modifications play a key role in establishing transcriptional plasticity during development, required for cell fate specification, and have been implicated as a developmental mechanism that accounts for autism spectrum disorder (ASD) and CHD co-occurrence. ASXL3 has been identified as a high confidence ASD gene. ASXL3 is a component of the Polycomb Repressive Deubiquitination (PR-DUB) complex, which deubiquitinates histone H2A. However, the role of ASXL3 in cardiac development remains unknown. MethodsWe used CRISPR/Cas9 gene editing to generate clinically relevant Asxl3 frameshift alleles in a mouse model and human embryonic stem cells (hESCs). To evaluate ASXL3 function in developing hearts, we performed structural, molecular, immunostaining and histological analyses. Transcriptomic and cellular compositional changes were assessed with bulk RNA sequencing of mouse hearts and single-cell RNA sequencing (scRNA-seq) of human cardiac tissue differentiated from isogenic hESC lines. ResultsBiallelic genetic inactivation of Asxl3 leads to perinatal lethality and increased levels of histone H2A mono-ubiquitination, which are regulated by PR-DUB. Asxl3+/fs and Asxl3fs/fs mice display cardiac abnormalities including ventricular hypoplasia, septal defects, and bifid cardiac apex with variable penetrance. The presence of underdeveloped ventricles is preceded by increased progenitor proliferation in the ventricles, as determined by EdU incorporation. Differential gene expression, assessed by bulk RNA sequencing implicates extracellular matrix dysfunction as a pathogenic mechanism. This correlates with a reduction in vimentin-positive cardiac fibroblasts. scRNA-seq of cardiac cultures differentiated from human ASXL3fs/fs ESC lines exhibit altered ratios of cardiac fibroblasts and cardiomyocytes. Similar to the mouse data, genes essential for extracellular matrix composition and signaling are differentially expressed between ASXL3+/+ and ASXL3fs/fs human in vitro differentiated cardiac tissue. The observed transcriptomic changes predict diminished cell-cell signaling interactions between cardiac fibroblasts and cardiomyocyte progenitors in ASXL3 cultures. ConclusionsCollectively, our data implicates species-specific roles for ASXL3 in both human and mouse cardiac development. These results highlight the role of extracellular matrix gene programs by cardiac fibroblast during cardiomyocyte development and provide insight into mechanisms of altered cardiogenesis by autism risk genes.

developmental biology↗
bioRxiv2022

Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies

Reactivation of fetal hemoglobin (HbF) is the commonly adapted strategy to ameliorate {beta}-hemoglobinopathies. However, the continued production of defective adult hemoglobin (HbA) limits the HbF tetramer production affecting the therapeutic benefits. Here, we tested various deletional hereditary persistence of fetal hemoglobin (HPFH) mutations and identified a 11 kb sequence, encompassing Putative Repressor Region (PRR) to {beta}-globin Exon-1 ({beta}E1), as the core deletion that ablates HbA and exhibit superior production of HbF compared to HPFH or other well-established targets. The PRR-{beta}E1 edited hematopoietic stem and progenitor cells (HSPCs) retained engraftment potential to repopulate for long-term hematopoiesis in immunocompromised mice generating HbF+ cells in vivo. Importantly, the editing induces therapeutically relevant levels of HbF to reverse the phenotypes of both sickle cell disease and {beta}-thalassemia major. These results indicate that the PRR-{beta}E1 gene editing in patient HSPCs can potentially lead to superior therapeutic outcomes for {beta}-hemoglobinopathies gene therapy.

biochemistry↗
bioRxiv2022

Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes

High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma ({gamma})-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon {gamma}-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by {gamma}-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating {gamma}-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of {gamma}-radiation-responsive genes in cyanobacteria at large. HighlightsO_LI{gamma}-radiation alters PSII photophysiology and thylakoid proteome profile in Anabaena. C_LIO_LILexA modulates the cytosolic and thylakoid proteome of Anabaena under {gamma}-radiation. C_LIO_LILexA functions as one of the regulators of radiation-responsive genes in Anabaena. C_LI

molecular biology↗
bioRxiv2022

Precise modelling and correction of a spectrum of β-thalassemic mutations in human erythroid cells by base editors

{beta}-thalassemia and HbE result from mutations in the {beta}-globin locus that impedes the production of functional {beta}-hemoglobin and represents one of the most common genetic disorders worldwide. Recent advances in genome engineering have opened up new therapeutic opportunities to directly correct these pathogenic mutations using base editors that install transition mutations (A>G and C>T) in the target region with minimal generation of indels. Herein, for the first time, we demonstrate the usage of base editor in the correction of point mutations spanning multiple regions of the HBB gene, including promoter, intron and exon. To this end, we have engineered human erythroid cells harbouring the diverse HBB mutations, thus eliminating the requirement of patient CD34+ HSPCs with desired mutations for the primary screening by base editors. We further performed precise creation and correction of individual HBB point mutations in human erythroid cells using base editors, which were effectively corrected in the HBB-engineered erythroid model. Intriguingly, most bystander effects produced by the base editor at the target site were reported to exhibit normal hemoglobin variants. Overall, our study provides the proof-of-concept for the precise, efficient and scarless creation and correction of various pathogenic mutations at the coding and non-coding regions of HBB gene in human erythroid cells using base editors and establishes a novel therapeutic platform for the treatment of {beta}-thalassemia/HbE patients. This study can be further explored in correcting the other monogenic disorders caused due to single base substitutions.

genomics↗
bioRxiv2022

Identification of m6A and m5C RNA modifications at single-molecule resolution from Nanopore sequencing

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUIs capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

bioinformatics↗
bioRxiv2022

A Genomically and Clinically Annotated Patient Derived Xenograft (PDX) Resource for Preclinical Research in Non-Small Cell Lung Cancer

Patient-derived xenograft models (PDXs) are an effective preclinical in vivo platform for testing the efficacy of novel drug and drug combinations for cancer therapeutics. Here we describe a repository of 79 genomically and clinically annotated lung cancer PDXs available from The Jackson Laboratory that have been extensively characterized for histopathological features, mutational profiles, gene expression, and copy number aberrations. Most of the PDXs are models of non-small cell lung cancer (NSCLC), including 37 lung adenocarcinoma (LUAD) and 33 lung squamous cell carcinoma (LUSC) models. Other lung cancer models in the repository include four small cell carcinomas, two large cell neuroendocrine carcinomas, two adenosquamous carcinomas, and one pleomorphic carcinoma. Models with both de novo and acquired resistance to targeted therapies with tyrosine kinase inhibitors are available in the collection. The genomic profiles of the LUAD and LUSC PDX models are consistent with those observed in patient tumors of the same tumor type from The Cancer Genome Atlas (TCGA) and to previously characterized gene expression-based molecular subtypes. Clinically relevant mutations identified in the original patient tumors were confirmed in engrafted tumors. Treatment studies performed for a subset of the models recapitulated the responses expected based on the observed genomic profiles. SignificanceThe collection of lung cancer Patient Derived Xenograft (PDX) models maintained at The Jackson Laboratory retain both the histologic features and treatment-relevant genomic alterations observed in the originating patient tumors and show expected responses to treatment with standard-of-care agents. The models serve as a valuable preclinical platform for translational cancer research. Information and data for the models are freely available from the Mouse Models of Human Cancer database (MMHCdb, http://tumor.informatics.jax.org/mtbwi/pdxSearch.do).

cancer biology↗
bioRxiv2022

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative to unsupervised analysis. Reference datasets, however, are predominantly constructed from single-cell RNA-seq data, and cannot be used to annotate datasets that do not measure gene expression. Here we introduce bridge integration, a method to harmonize singlecell datasets across modalities by leveraging a multi-omic dataset as a molecular bridge. Each cell in the multi-omic dataset comprises an element in a dictionary, which can be used to reconstruct unimodal datasets and transform them into a shared space. We demonstrate that our procedure can accurately harmonize transcriptomic data with independent single cell measurements of chromatin accessibility, histone modifications, DNA methylation, and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to substantially improve computational scalability, and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach aims to broaden the utility of single-cell reference datasets and facilitate comparisons across diverse molecular modalities. AvailabilityInstallation instructions, documentations, and vignettes are available at http://www.satijalab.org/seurat

genomics↗
bioRxiv2022

Identification of a novel interaction between Theileria Prohibitin (TaPHB-1) and bovine RUVBL-1

Bovine tropical theileriosis causes huge economic loss worldwide. It is a tick borne disease of bovine caused by the parasite Theileria annulata. T. annulata is an intracellular parasite that belongs to the phylum Apicomplexa. The sporozoites of T. annulata are released by the tick into the bloodstream of the host during the blood meal that invades bovine B cells, macrophages, or monocytes. This infection leads to the transformation of the host cells and brings cancer-like phenotype in the host cells. The parasite proteins play a vital role in the transformation of the host cell. However, the parasite factors involved in the host cell transformation are not well explored. Previously, TaPIN1, a peptidyl-prolyl isomerase of T. annulata, was shown to be secreted to the host cytosol and play a role in the host cell transformation. The present study was carried out to explore the parasite-host interactions that may play an important role in the host cell transformation. We identified the parasite proteins that are expressed in the schizont stage with a signal peptide. We narrow down our search to a parasite prohibitin. The in silico analysis of T. annulata prohibitin (TA04375, TaPHB-1) showed that TaPHB-1 shares homology with the mammalian prohibitin 1. With the localization experiments, we confirmed that TaPHB-1 is exported to the parasite surface and also to the host cell cytosol. Further, we observed that the localization of host prohibitin differs in the parasite-infected cells and could not be reverted back by the elimination of the parasite in the infected cells. We found through the yeast-two-hybrid studies that bovine RUVBL1 (BoRUVBL-1) interacts with TaPHB-1. The interaction between BoRUVBL1 and TaPHB-1 was predominantly observed on the parasite surface in the infected bovine cells. The interaction was further confirmed with immunoprecipitation and LC-MS/MS analysis. Further, the LC-MS/MS based TaPHB-1 interactome study reveals that it interacts with proteins that regulate actin cytoskeleton organization, protein folding, mRNA processing, and metabolic processes. Our finding suggests that the parasite releases prohibitin protein into the cytoplasm of the host cell where it interacts with the host RUVBL-1. This finding has implications not only in the understanding of Theileria parasite biology in greater depth but also in the cancer biology where previously differential localization of prohibitin proteins was observed but its interaction partner was not known. Author summaryTheileria annulata, an apicomplexan, is a unique parasite which can transform host leucocytes. This parasite uses this strategy for its own multiplication. The cells infected with this parasite, when treated with buparvaquone, an anti-theilerial drug, cannot survive without the parasite. This observation suggests that the parasite derived factors are required to maintain the cancerous phenotype of the host cell. We mined the parasite proteome to find out the proteins with signal sequence that may be secreted to the host cell cytosol and being expressed in the schizont stage. The parasite prohibitin (TaPHB-1) chosen for this study was found to be secreted to the host cytoplasm and on the parasite surface. Interestingly, we observed a noticeable change in the localization of the host prohibitin in the parasite infected cells. The host prohibitin that is normally localized to the mitochondria in the uninfected cells was observed in the host cell nucleus similar to the cancerous cells. Since the parasite protein is exported to the host cytoplasm we looked for its interacting partner. We performed yeast-two-hybrid screening with TaPHB-1 with in-house prepared the cDNA library of the infected bovine leucocytes. We identified bovine RUVBL1 as the interacting partner of TaPHB-1. Interestingly, the interaction between parasite prohibitin and bovine RUVBL1 was observed on the parasite surface. Further, analysis of the parasite prohibitin interactome in the infected cells shows that it might be involved with those proteins which regulate actin cytoskeleton organization, protein folding, mRNA processing and metabolic process. Since parasite infected cells have cancer like phenotype, the identification of this novel interaction will open up new avenues not only in the arena of parasite biology but also in the domain of cancer biology.

microbiology↗
bioRxiv2022

RET activation controlled by MAB21L4-CacyBP interaction drives squamous cell carcinoma

Epithelial squamous cell carcinomas (SCC) most commonly originate in the skin, where they display disruptions in the normally tightly regulated homeostatic balance between keratinocyte proliferation and terminal differentiation. We performed a transcriptome-wide screen for genes of unknown function that possess inverse expression patterns in differentiating keratinocytes compared to cutaneous SCC (cSCC) and identified MAB21L4 (C2ORF54) as an enforcer of terminal differentiation that suppresses carcinogenesis. Loss of MAB21L4 in human cSCC organoids enabled malignant transformation through increased expression of the receptor tyrosine kinase rearranged during transfection (RET). In addition to transcriptional upregulation of RET, MAB21L4 deletion preempted recruitment of the CacyBP-Siah1 E3 ligase complex to RET and reduced its ubiquitylation. Both genetic disruption of RET or selective RET inhibition with BLU-667 (pralsetinib) suppressed tumorigenesis in SCC organoids and in vivo tumors while inducing concomitant differentiation. Our results suggest that targeting RET activation is a potential therapeutic strategy for treating SCC. Statement of SignificanceFew targeted therapies are available to individuals with cSCC who seek or require non-surgical management. Our study demonstrates that downregulation of RET is required for epithelial differentiation and opposes carcinogenesis in cSCC as well as SCC arising from other epithelial tissues.

cancer biology↗
bioRxiv2021

PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery

We created the PDX Network (PDXNet) Portal (https://portal.pdxnetwork.org/) to centralize access to the National Cancer Institute-funded PDXNet consortium resources (i.e., PDX models, sequencing data, treatment response data, and bioinformatics workflows), to facilitate collaboration among researchers, and to make resources easily available for research. The portal includes sections for resources, analysis results, metrics for PDXNet activities, data processing protocols, and training materials for processing PDX data. The initial portal release highlights PDXNet model and data resources, including 334 new models across 33 cancer types. Tissue samples of these models were deposited in the NCIs Patient-Derived Model Repository (PDMR) for public access. These models have 2,822 associated sequencing files from 873 samples across 307 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal also includes results from standardized analysis workflows on PDXNet sequencing files and PDMR data (2,594 samples from 463 patients across 78 disease types). These 15 analysis workflows for whole-exome and RNA-Seq data are freely available, robust, validated, and standardized. The model and data lists will grow substantially over the next two years and will be continuously updated as new data are available. PDXNet models support multi-agent treatment studies, determination of sensitivity and resistance mechanisms, and preclinical trials. The PDXNet portal is a centralized location for these data and resources, which we expect to be of significant utility for the cancer research community.

cancer biology↗
bioRxiv2021

Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

MotivationAllelic expression analysis aids in detection of cis-regulatory mechanisms of genetic variation which produce allelic imbalance (AI) in heterozygotes. Measuring AI in bulk data lacking time or spatial resolution has the limitation that cell-type-specific (CTS), spatial-, or time-dependent AI signals may be dampened or not detected. ResultsWe introduce a statistical method airpart for identifying differential CTS AI from single-cell RNA-sequencing (scRNA-seq) data, or other spatially- or time-resolved datasets. airpart outputs discrete partitions of data, pointing to groups of genes and cells under common mechanisms of cis-genetic regulation. In order to account for low counts in single-cell data, our method uses a Generalized Fused Lasso with Binomial likelihood for partitioning groups of cells by AI signal, and a hierarchical Bayesian model for AI statistical inference. In simulation, airpart accurately detected partitions of cell types by their AI and had lower RMSE of allelic ratio estimates than existing methods. In real data, airpart identified differential AI patterns across cell states and could be used to define trends of AI signal over spatial or time axes. AvailabilityThe airpart package is available as an R/Bioconductor package at https://bioconductor.org/packages/airpart.

bioinformatics↗
bioRxiv2021

Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 Case Fatality Rate among Indian populations

SARS-CoV2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the difference in population disease susceptibility. The haplotype-based genetic sharing and structure of TMPRSS2 among global populations have not been studied so far. Therefore, in the present work, we used this approach with a focus on South Asia to study the haplotypes and their sharing among various populations worldwide. We have used next-generation sequencing data of 393 individuals and analysed the TMPRSS2 gene. Our analysis of genetic relatedness for this gene showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. We have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate. Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the case fatality rate in India. It has been shown that the GG genotype of rs2070788 allele tends to have a higher expression of TMPRSS2 in the lung compared to the AG and AA genotypes, thus it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in underscoring the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.

genetics↗
bioRxiv2021

Membrane remodeling due to mixture of multiple curvature proteins: Insights from mesoscopic continuum modeling

We present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family. We also study the effect membrane anisotropy, which manifest as membrane localization and differential binding affinity of a given curvature protein, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphology of deformed vesicles that depend on the curvatures and number of the participating proteins as well as on the protein-protein and membrane-proteins interactions. SignificanceMembrane remodeling requires highly orchestrated interactions between several types of lipids and curvature proteins. Experimentally probing the membrane deformation intermediates is non-trivial. For example, it is not known exactly how two or more different kinds of BAR domain proteins work in concert to induce and stabilize certain membrane curvatures. In this work, we use mesoscopic continuum modeling and explore the factors that induce and stabilize a range of membrane deformation due to a mixture of positive and negative curvature proteins.

biophysics↗