Biology subjects

Srivastava, A.

Publications and source records attributed to Srivastava, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Two liverworts from same habitats developed many similar but few distinct seasonal adaptive strategies: Insights from a transcriptomic approach

Liverworts are among the first land plants to experience seasonal changes after terrestrialization Therefore, we conducted a seasonal transcriptome analysis of two representative liverwort species from India, Dumortiera hirsuta and Plagiochasma appendiculatum, during their distinct growing seasons: the pre-monsoon, monsoon, post-monsoon, and fruiting season to understand the seasonal adaptations. Phylogenetic trees and evolutionary timescale analyses showed that D. hirsuta is primitive compared to P. appendiculatum. The RNA-seq analysis showed that D. hirsuta primarily modifies its transcriptome in the post-monsoon season but mainly induces specific genes in the fruiting season, most likely to develop reproductive organs and to adapt strategically by conserving energy in the fruiting season to deal with the harsh environmental conditions of both seasons. Conversely, P. appendiculatum exhibited significant transcriptome variability during both the fruiting and post-monsoon seasons, albeit to a lesser degree than D. hirsuta. This suggests that, to survive in the harsh conditions of both seasons, it strategically modulated its necessary gene expression levels over an extended period of time while taking energy conservation into consideration. This study offers the first comprehensive view of seasonal adaptive strategies employed by two liverworts that coexist in the same habitat but diverged at different stages in their evolutionary history.

genomics↗

bioRxiv2024

Casein Kinases 2-dependent phosphorylation of the placental ligand VAR2CSA regulates Plasmodium falciparum-infected erythrocytes cytoadhesion

Placental malaria is characterized by the massive accumulation and sequestration of infected erythrocytes in the placental intervillous blood spaces, causing severe birth outcomes. The variant surface antigen VAR2CSA is associated with Plasmodium falciparum sequestration in the placenta via its capacity to adhere to chondroitin sulfate A. We have previously shown that the extracellular region of VAR2CSA is phosphorylated on several residues and that the phosphorylation enhances the adhesive properties of CSA-binding infected erythrocytes. Here, we aimed to identify the kinases mediating this phosphorylation. Here, we report that human and Plasmodium falciparum Casein Kinase 2 are involved in the phosphorylation of the extracellular region of VAR2CSA. We notably show that both CK2 can phosphorylate the extracellular region of recombinant and immunoprecipitated VAR2CSA. Mass spectrometry analysis of recombinant VAR2CSA phosphorylated by recombinant Human and P. falciparum CK2 combined with site-directed mutagenesis led to the identification of residue S1068 in VAR2CSA, which is phosphorylated by both enzymes and is associated with CSA binding. Furthermore, using CRISPR/Cas9 we generated a parasite line in which phosphoresidue, S1068, was changed to alanine. This mutation strongly impairs infected erythrocytes adhesion by abolishing VAR2CSA translocation to the surface of infected erythrocytes. We also report that two specific CK2 inhibitors reduce infected erythrocytes adhesion to CSA and decrease the phosphorylation of the recombinant extracellular region of VAR2CSA using either infected erythrocytes lysates as a source of kinases or recombinant Human and P. falciparum casein kinase 2. Taken together, these results undoubtedly demonstrate that host and P. falciparum CK2 phosphorylate the extracellular region of VAR2CSA and that this post-translational modification is important for VAR2CSA trafficking and for infected erythrocytes adhesion to CSA.

microbiology↗

bioRxiv2024

Structural insights into the recognition of RALF peptides by FERONIA receptor kinase during Brassicaceae Pollination

Ensuring species integrity and successful reproduction is pivotal for the survival of angiosperms. Members of Brassicaceae family employ a "lock and key" mechanism involving stigmatic (sRALFs) and pollen RALFs (pRALFs) binding to FERONIA, a Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) receptor, to establish a prezygotic hybridization barrier. In the absence of compatible pRALFs, sRALFs bind to FERONIA, inducing a lock state for pollen tube penetration. Conversely, compatible pRALFs act as a key, facilitating successful fertilization. Competing pRALFs reduce the sRALFs binding to FERONIA in a dose-dependent manner, enabling pollen tube penetration. Despite its crucial role in Brassicaceae hybridization, the structural basis of this binding remains elusive owing to the highly flexible nature of RALF peptides. Using advanced structural modeling techniques and flexible peptide molecular docking, this study reveals that pRALFs and sRALFs bind to negatively charged pockets in FERONIA with varying binding affinities. Our study unveils the structural basis of this binding, shedding light on the molecular mechanism underlying hybridization barriers in Brassicaceae.

plant biology↗

bioRxiv2024

Recovery after human bone marrow mesenchymal stem cells (hBM-MSCs)-derived extracellular vesicles (EVs) treatment in post-MCAO rats requires handling associated with repeated behavioral testing.

Rehabilitation is the only current intervention that improves sensorimotor function in ischemic stroke patients, similar to task-specific intensive training in animal models of stroke. Bone marrow mesenchymal stem cells (BM-MSCs)-derived extracellular vesicles (EVs) are promising in restoring brain damage and function in stroke models. Additionally, the non-invasive intranasal route allows EVs to reach the brain and target specific ischemic regions. Yet unclear is how handling might enhance recovery or influence other therapies such as EVs after stroke. We used the transient middle cerebral artery occlusion (MCAO) model of stroke in rats to assess how intensive handling alone, in the form of sensorimotor behavioral tests, or in combination with an intranasal multidose or single dose of EVs restored neurological function and ischemic damage. Handled rats were exposed to a battery of sensorimotor tests, including the modified Neurological Severity Score (mNSS), beam balance, corner, grid walking, forelimb placement, and cylinder tests, together with Magnetic Resonance Imaging (MRI) at 2, 7, 14, 21, and 28 days post-stroke (dps). Handled MCAO rats were also exposed to an intranasal multidose of EVs (8 doses in total across four weeks, each dose containing 0.8 x 109 EVs in 120 {micro}l) or a single dose of EVs (2.4 x 109 EVs in 200 {micro}l) at 2 dps. Non-handled rats were evaluated only by mNSS and MRI at 2, 28, and 56 dps and were treated with a single intranasal dose of EVs. Our results showed that handling animals after MCAO is necessary for EVs to work and that a single cumulative dose of EVs further improves the neurological function recovered during handling without affecting ischemic damage. These results show the importance of rehabilitation in combination with other treatments and highlight how intensive behavioral testing might influence functional recovery after stroke, especially when other treatments are also given.

neuroscience↗

bioRxiv2024

Direct β1/β2 AMPK activation reduces liver steatosis but not fibrosis in a mouse model of non-alcoholic steatohepatitis

5AMP-activated protein kinase (AMPK) activators show potential for treating Non-Alcoholic Fatty Liver Disease (NAFLD) and Non-Alcoholic Steatohepatitis (NASH) due to their inhibiting effects on fatty acid and cholesterol synthesis. The absence of treatments for NASH, and its propensity for progression to severe disease, lead us to identify and characterize BI9774, a small molecule AMPK activator, which we used to evaluate this potential, including its ability to reduce the NASH specific qualities of fibrosis and inflammation in a preclinical study. Male Lepob/Lepob mice on a control or NASH inducing (AMLN) diet, with liver fibrosis were given BI9774 or vehicle for 6 weeks while metabolic and NASH endpoints were evaluated. BI9774 treatment decreased plasma ALT, terminal liver weight, and liver lipids. RNA expression of collagen-related genes decreased, although collagen protein and inflammation remained unaltered. We also observed increased heart weight and glycogen levels, and increased expression of genes associated with cardiac hypertrophy. AMPK activation improved many metabolic endpoints, but lack of significant improvement in liver fibrosis and negative cardiac effects suggest systemic AMPK activation is not an ideal NASH therapy. Reductions in steatosis and fibrosis-related genes indicate that, with extended treatment, a liver specific AMPK activator has potential to resolve hepatic fibrosis. Summary StatementFatty liver disease affects up to 30 percent of adults worldwide with 30% of patients progressing to more sever liver disease. AMPK activation can help reduce liver fat.

pharmacology and toxicology↗

bioRxiv2024

Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering

Accurately sampling the membrane-bound conformations of a peripheral membrane proteins (PMP) using classical all-atom molecular dynamics simulations (AAMD) is a formidable enterprise due to the rugged free energy landscape of the protein-membrane system. In general, AAMD-based extraction of binding geometry requires simulations of multiple systems with different initial user-defined binding poses that may not be exhaustive. As an alternative, advanced sampling methods are also applied to elucidate the membrane-binding mechanism of PMPs but these techniques are generally computationally expensive and often depend on choice of the collective variables (CV). In this work, we showcase the utility of CV-free replica exchange with hybrid tempering (REHT) method in capturing the membrane-bound conformations of PMPs by testing it on the Osh4 amphipathic lipid-packing sensor (ALPS) motif, a 27 amino-acid membrane binding peptide. We show that REHT samples all the membrane-bound conformations of the Osh4 ALPS peptide at their correct populations and does it in a highly efficient manner with minimum computational time. We clearly show that, out of the two significant conformations, the peptide prefers horizontal conformations over vertical ones. In both the conformations, REHT captures all the vital residue-wise membrane contacts. The transition between the two configuration is not uncommon as our calculations reveal a [~] 2 kT free energy difference between the two conformations. Interestingly, from our simulations we also find that the transition from vertical to horizontal conformation involves limited unfolding the main helixs last turn. From our findings, we conclude that REHT samples the membrane-bound conformations of Osh4 ALPS peptide very efficiently and also provides additional insights and information that are often not available with regular piece-wise AAMD simulations. The method can be used as an efficient tool to explore the membrane-binding mechanisms of PMPs.

biophysics↗

bioRxiv2024

SOP-MULTI: A self-organized polymer based coarse-grained model for multi-domain and intrinsically disordered proteins with conformation ensemble consistent with experimental scattering data

Multidomain proteins with long flexible linkers and full-length intrinsically disordered proteins (IDPs) are best defined as an ensemble of conformations rather than a single structure. Determining high-resolution ensemble structures of such proteins poses various challenges using tools from experimental structural biophysics. Integrative approaches combining available low-resolution ensemble-averaged experimental data and in silico biomolecular reconstructions are now often used for the purpose. However, an exhaustive Boltzmann weighted conformation sampling for large proteins, especially for ones where both the folded and disordered domains exist in the same polypeptide chain, remains a challenge. In this work, we present a 2-site per amino-acid resolution SOP-MULTI force field for simulating coarse-grained models of multidomain proteins. SOP-MULTI combines two well-established self-organized polymer (SOP) models --: (i) SOP-SC models for folded systems and (ii) SOP-IDP for IDPs. For the SOP-MULTI, we train the cross-interaction terms between the beads belonging to the folded and disordered regions to generate experimentally-consistent conformation ensembles for full-length multi-domain proteins such as hnRNPA1, TDP-43, G3BP1, hGHR-ECD, TIA1, HIV-1 Gag, Poly-Ubiquitin and FUS. When back-mapped to all-atom resolution, SOP-MULTI trajectories faithfully recapitulate the scattering data over the range of the reciprocal space. We also show that individual folded domains preserve native contacts with respect to solved folded structures, and root mean square fluctuations of residues in folded domains match those obtained from all-atom molecular dynamics simulations trajectories of the same folded systems. SOP-MULTI Force Field is made available as a LAMMPS-compatible user package along with setup codes for generating the required files for any full-length protein with folded and disordered regions.

biophysics↗

bioRxiv2024

Investigating REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators

ABSTRACTREV-ERB{beta} is a nuclear receptor (NR) with heme as an endogenous ligand that regulates its transcriptional activity. With key role in cellular functions such as glucose metabolism, immune response, and dysregulation in pathologies such as Type-2 diabetes mellitus and obesity, small molecule agonists and antagonists targeting REV-ERBs have been discovered. However, due to lack of crystal structures in complex with these compounds, the structural and dynamical basis of these activities still remains elusive and hinders rational design of molecules targeting REV-ERB. Using molecular dynamics simulations and docking studies, we have characterized the dynamics of REV-ERB{beta} ligand-binding domain (LBD) in different conformational states. The presence of heme in the binding pocket within LBD was found to stabilize its dynamics as well as nuclear co-repressor (NCoR) peptide binding. We further show that the binding of antagonist destabilizes the NCoR peptide binding to LBD mediated by loss of interactions with residues at the NCoR-REV-ERB{beta} interface. These findings could be utilized to design molecular scaffolds with better activity and selectivity against REV-ERB{beta}.

bioinformatics↗

bioRxiv2024

Integrative Co-Registration of Elemental Imag-ing and Histopathology for Enhanced Spatial Multimodal Analysis of Tissue Sections through TRACE

SummaryElemental imaging provides detailed profiling of metal bioaccumulation, offering more precision than bulk analysis by targeting specific tissue areas. However, accurately identifying comparable tissue regions from elemental maps is challenging, requiring the integration of hematoxylin and eosin (H&E) slides for effective comparison. Facilitating the streamlined co-registration of Whole Slide Images (WSI) and elemental maps, TRACE enhances the analysis of tissue regions and elemental abundance in various pathological conditions. Through an interactive containerized web application, TRACE features real-time annotation editing, advanced statistical tools, and data export, supporting comprehensive spatial analysis. Notably, it allows for comparison of elemental abundances across annotated tissue structures and enables integration with other spatial data types through WSI co-registration. Availability and ImplementationAvailable on the following platforms- GitHub: jlevy44/trace_app, PyPI: trace_app, Docker: joshualevy44/trace_app, Singularity: joshualevy44/trace_app. Contactjoshua.levy@cshs.org Supplementary informationSupplementary data are available.

bioinformatics↗

bioRxiv2024

The atypical antipsychotic aripiprazole alters the outcome of disseminated Candida albicans infections.

Invasive fungal infections (IFIs) impose an enormous clinical, social, and economic burden on humankind. For many IFIs, [≥] 30% of patients fail therapy with existing antifungal drugs, including the widely used azole class. We previously identified a collection of 13 approved medications that antagonize azole activity. While gain-of-function mutants resulting in antifungal resistance are often associated with reduced fitness and virulence, it is currently unknown how exposure to azole antagonistic drugs impact C. albicans physiology, fitness, or virulence. In this study, we examined how exposure to azole antagonists affected C. albicans phenotype and capacity to cause disease. We discovered that most of the azole antagonists had little impact on fungal growth, morphology, stress tolerance, or gene transcription. However, aripiprazole had a modest impact on C. albicans hyphal growth and increased cell wall chitin content. It also worsened the outcome of disseminated infections in mice at human equivalent concentrations. This effect was abrogated in immunosuppressed mice, indicating an additional impact of aripiprazole on host immunity. Collectively, these data provide proof-of-principle that unanticipated drug-fungus interactions have the potential to influence the incidence and outcomes of invasive fungal disease. ImportanceAs natural inhabitants of the gastrointestinal and reproductive tracts, Candida sp. are routinely exposed to medications consumed by their human host. This study provides new insight into how drugs can modulate the physiology, fitness, and pathogenicity of Candida albicans - one of the most important human fungal pathogens. These results provide a proof of principle that co-administered medications consumed by at-risk patients may influence the initiation and/or outcome of life-threatening fungal disease.

microbiology↗

bioRxiv2024

LHX2 regulates dendritic morphogenesis in layer II/III of the neocortex via distinct pathways in progenitors and postmitotic neurons.

In the mammalian neocortex, excitatory neurons that send projections via the corpus callosum are critical to integrating information across the two brain hemispheres. The molecular mechanisms governing the development of the dendritic arbours and spines of these callosal neurons are poorly understood, yet these features are critical to their physiological properties. LIM Homeodomain 2 (Lhx2), a regulator of fundamental processes in cortical development, is expressed in postmitotic callosal neurons occupying layer II/III of the neocortex and also in their progenitors residing in the embryonic day (E) 15.5 ventricular zone of the mouse neocortex. We tested whether this factor is essential for dendritic arbour configuration and spine morphogenesis of layer II/III neurons. Here, we report loss of Lhx2, either in postmitotic layer II/III neurons or their progenitors, resulted in shrunken dendritic arbours and perturbed spine morphology. The defects were more pronounced upon Lhx2 disruption in progenitors, and were recapitulated when this was driven exclusively in basal progenitors. In postmitotic neurons, LHX2 regulates dendritic and spine morphogenesis via the canonical Wnt /{beta} Catenin signalling pathway. Constitutive activation of this pathway in postmitotic neurons mimics the Lhx2 loss-of-function phenotype. In E15.5 progenitors, LHX2 acts in part via bHLH transcription factor NEUROG2 to regulate dendritic morphogenesis. We demonstrate that loss of Lhx2 causes a massive increase in Neurog2 expression, and that Neurog2 knockdown partially rescues the loss of Lhx2 phenotype. Our study uncovers novel LHX2 functions consistent with its temporally dynamic and diverse roles in development. TeaserThe mature architecture of a neuron is shaped by distinct genetic mechanisms that act in its mother cell and after it is born.

neuroscience↗

bioRxiv2023

Maximizing the potential of genomic and transcriptomic studies by nanopore sequencing

Nucleic acid sequencing is the process of identifying the sequence of DNA or RNA, with DNA used for genomes and RNA for transcriptomes. Deciphering this information has the potential to greatly advance our understanding of genomic features and cellular functions. In comparison to other available sequencing methods, nanopore sequencing stands out due to its unique advantages of processing long nucleic acid strands in real time, within a small portable device, enabling the rapid analysis of samples in diverse settings. Evolving over the past decade, nanopore sequencing remains in a state of ongoing development and refinement, resulting in persistent challenges in protocols and technology. This article employs an interdisciplinary approach, evaluating experimental and computational methods to address critical gaps in our understanding in order to maximize the information gain from this advancing technology. Here we present both overview and analysis of all aspects of nanopore sequencing by providing statistically supported insights. Thus, we aim to provide fresh perspectives on nanopore sequencing and give comprehensive guidelines for the diverse challenges that frequently impede optimal experimental outcomes.

bioinformatics↗

bioRxiv2023

Editing of highly homologous gamma-globin genes by nickase deficient Base Editor mitigates large intergenic deletions

Base editing in gamma-globin promoter is a promising approach for reactivation of fetal-hemoglobin. Recent studies have shown that base editing could result in genotoxic events at the gamma globin locus including 4.9 kb large deletion of intervening region due to nicking in the paralogous HBG1 and HBG2 genes. Although the deletion frequency is less than what is observed with Cas9, it could diminish the therapeutic potential. We sought to evaluate if large deletion could be overcome while maintaining the editing efficiency by replacing the nCas9 of ABE8e with a catalytically inactive deadCas9 (dCas9). Using 3 therapeutically relevant gRNAs targeting the gamma globin promoter, we performed a comprehensive evaluation of the editing outcome and frequency of large deletion using dCas9, nCas9, dCas9-ABE8e and nCas9-ABE8e. Our findings indicate that while nicking in itself induced large deletions, the frequency reduced upon efficient base editing. Notably, there was no appreciable deletion with the use of dCas9-ABE8e making it a safer approach, in terms of genome integrity, for therapeutic genome editing in the gamma-globin locus. Further, we also demonstrate that dCas9 ABE8e can edit efficiently in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) to achieve therapeutic benefits.

molecular biology↗

bioRxiv2023

Towards robust and generalizable representations of extracellular data using contrastive learning

Contrastive learning is quickly becoming an essential tool in neuroscience for extracting robust and meaningful representations of neural activity. Despite numerous applications to neuronal population data, there has been little exploration of how these methods can be adapted to key primary data analysis tasks such as spike sorting or cell-type classification. In this work, we propose a novel contrastive learning framework, CEED (Contrastive Embeddings for Extracellular Data), for high-density extracellular recordings. We demonstrate that through careful design of the network architecture and data augmentations, it is possible to generically extract representations that far outperform current specialized approaches. We validate our method across multiple high-density extracellular recordings. All code used to run CEED can be found at https://github.com/ankitvishnu23/CEED.

neuroscience↗

bioRxiv2023

Patient-derived tumor organoids from resected non-small cell lung cancers for high-throughput response testing with approved and repurposed drugs

BackgroundThe five-year survival for non-metastatic non-small cell lung cancer (NSCLC) patients undergoing curative surgery remains poor at [~]50% that is due to locoregional and/or distant metastatic recurrences. Patient-derived tumor organoids (PDTOs) have high potential as clinically relevant high-throughput drug testing platforms to personalize and improve treatment of NSCLC patients. We aimed to develop PDTOs from non-metastatic NSCLC patients to assess their suitability to study tumor heterogeneities and personalized drug responses. MethodsTen non-metastatic (stage I-IIIA) NSCLC patients undergoing curative surgical resection were prospectively enrolled. PDTOs were established from resected lung tumor tissues and were compared with matched primary tumors by histopathology, immunohistochemistry, whole exome and whole transcriptome sequencing analysis. PDTO responses to standard of care carboplatin/paclitaxel chemotherapy were determined by measuring organoid growth using bright-field 3D imaging. Transcriptomic differential gene expression analysis identified molecular targets for drug repurposing to overcome chemoresistance. ResultsNSCLC PDTOs were successfully generated from all 10 (100%) primary tumors with a median time of 12 days (range 4-16 days). All 10 PDTOs could be grown from cryopreserved tumor tissues or reconstituted from frozen PDTOs (living biobank). PDTOs retained histopathological, immunohistochemical protein expression and mutational landscape of the matched primary tumors. Microenvironment cell population analysis revealed epithelial cell signatures of the PDTOs that matched the patients lung tumor tissues. Treatment responses of PDTOs to carboplatin/paclitaxel were determined by growth differences versus vehicle control group. 5/10 (50%) PDTOs were chemo-sensitive, whereas 5/10 (50%) were chemo-resistant. Upregulation of aldo-keto reductases (AKR1B10/15) was observed in chemoresistant PDTOs by differential gene expression analysis and confirmed by real-time PCR and immunohistochemistry in PDTOs and tumor tissues. Epalrestat, an anti-diabetic AKR1B10 inhibitory drug, was repurposed to effectively sensitize PDTOs to carboplatin/paclitaxel. ConclusionsPDTOs can be established from resected NSCLC primary tumor tissues with high success rates and conserve cellular, molecular and genomic characteristics of the matched NSCLC tumors. PDTOs can serve as clinically applicable and relevant personalized drug screening platforms to evaluate the therapeutic efficacy of drugs, including repurposed drugs, to overcome chemoresistance.

cancer biology↗

bioRxiv2023

Critical Behavioral Traits Foster Peer Engagement in Online Mental Health Communities

Online Mental Health Communities (OMHCs), such as Reddit, have witnessed a surge in popularity as go-to platforms for seeking information and support in managing mental health needs. Platforms like Reddit offer immediate interactions with peers, granting users a vital space for seeking mental health assistance. However, the largely unregulated nature of these platforms introduces intricate challenges for both users and society at large. This study explores the factors that drive peer engagement within counseling threads, aiming to enhance our understanding of this critical phenomenon. We introduce BeCOPE, a novel behavior encoded Peer counseling dataset comprising over 10,118 posts and 58,279 comments sourced from 21 mental health-specific subreddits. The dataset is annotated using three major fine-grained behavior labels: (a) intent, (b) criticism, and (c) readability, along with the emotion labels. Our analysis indicates the prominence of "self-criticism" as the most prevalent form of criticism expressed by help-seekers, accounting for a significant 43% of interactions. Intriguingly, we observe that individuals who explicitly express their need for help are 18.01% more likely to receive assistance compared to those who present "surveys" or engage in "rants." Furthermore, we highlight the pivotal role of well-articulated problem descriptions, showing that superior readability effectively doubles the likelihood of receiving the sought-after support. Our study emphasizes the essential role of OMHCs in offering personalized guidance and unveils behavior-driven engagement patterns.

neuroscience↗

bioRxiv2023

A Deep Learning method for classification of HNSCC and HPV patients using single-cell transcriptomics

Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most highly prevalent cancer type worldwide. Early detection of HNSCC is one of the important challenges in managing the treatment of the cancer patients. Existing techniques for detecting HNSCC are costly, expensive, and invasive in nature. In this study, we aimed to address this issue by developing classification models using machine learning and deep learning techniques, focusing on single-cell transcriptomics to distinguish between HNSCC and normal samples. Additionally, we built models to classify HNSCC samples into HPV-positive (HPV+) and HPV-negative (HPV-) categories. The models developed in this study have been trained on 80% of the GSE181919 dataset and validated on the remaining 20%. To develop an efficient model, we performed feature selection using mRMR method to shortlist a small number of genes from a plethora of genes. Artificial Neural Network based model trained on 100 genes outperformed the other classifiers with an AUROC of 0.91 for HNSCC classification for the validation set. The same algorithm achieved an AUROC of 0.83 for the classification of HPV+ and HPV-patients on the validation set. We also performed Gene Ontology (GO) enrichment analysis on the 100 shortlisted genes and found that most genes were involved in binding and catalytic activities. To facilitate the scientific community, a software package has been developed in Python which allows users to identify HNSCC in patients along with their HPV status. It is available at https://webs.iiitd.edu.in/raghava/hnscpred/. Key PointsO_LIApplication of single cell transcriptomics in cancer diagnosis C_LIO_LIDevelopment of models for predicting HNSCC patients C_LIO_LIClassification of HPV+ and HPV-HNSCC patients C_LIO_LIIdentification of gene biomarkers from single cell sequencing C_LIO_LIA standalone software package HNSCpred for predicting HNSCC patients C_LI Authors BiographyO_LIAkanksha Jarwal is currently pursuing an M. Tech. in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIAnjali Dhall is currently pursuing a Ph.D. in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIAkanksha Arora is currently pursuing a Ph.D. in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LISumeet Patiyal is currently pursuing a Ph.D. in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIAman Srivastava is currently pursuing an M. Tech. in Computational Biology at the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LIO_LIGajendra P. S. Raghava is currently working as a Professor and Head of the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LI

bioinformatics↗

bioRxiv2023

Atomic-scale structural insights into the functional roles of the full low complexity domain of the hnRNPA1 protein

hnRNPA1, a protein from the heterogeneous-nuclear ribonucleoprotein fam-ily, mediates cellular processes such as RNA metabolism and DNA telomere maintenance. Besides the folded RNA recognition motifs, hnRNPA1 has a [~] 135 amino-acids long low-complexity domain (LCD) consisting of an RGG-rich region and a prion-like domain (PrLD). Biochemical data suggest that RGG-rich region modulates recognition of G-quadruplexes (GQs) in the telomeric repeats. Here, we utilize an in-house developed replica exchange technique (REHT) to generate the heterogeneous conformation ensemble of hnRNPA1-RGG and explore its functional significance in telomere maintenance. Single chain statistics and abundance of structural motifs, as well as consistency with experimentally reported struc-tural data, suggest faithful recapitulation of local interactions. We also introduce a protocol to generate functionally significant IDP-nucleic acid complex structures that corroborate well with the experimental knowledge of their binding. We find that RGG-box preferentially binds to the grooves and loops of GQs providing specificity towards certain GQ structures with its Phe, Tyr, and Asn residues forming essential hydrogen bonds and electrostatic interactions. Several of these residues were also identified as important by the reported HSQC chemical shift data. Our binding and simulations studies also revealed that a minor population of the RGG-box can destabilize telomeric GQs, thereby expediting the unfolding activities of hnRNPA1-UP1 at the telomeric end.

biophysics↗