Biology subjects

Srinivasan, S.

Publications and source records attributed to Srinivasan, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Investigating the impact of carbamazepine on tomato plant metabolism using genome-scale metabolic modelling

A comprehensive mechanistic analysis of emerging pharmaceutical pollutants stress response in plants is needed to understand its chronic impact on food-chain contamination and agricultural productivity. To unravel this at systems-level, the current study employs insights from green-liver concept and establishes the utility of constraint-based modelling approach for elucidating perturbations in a plants metabolism due to pharmaceutical stress. In this study, the stress response of an emerging recalcitrant anticonvulsant pollutant, carbamazepine (CBZ), was simulated in tomato crop under phototrophic conditions. For this, an updated genome-scale metabolic model of tomato leaf (CBZ_iSL3433) was developed and augmented with CBZ transformation reactions based on the green-liver concept. The model was able to capture energy and co-factor competition-induced biomass reduction in presence of CBZ stress. Further, the study provides an in silico mechanistic proof for abiotic stress response induced by CBZ in tomato with altered flux states in nutrient assimilation, synthesis of key precursors of leaf biomass and secondary metabolites. Additionally, to extend the applicability of model, potential ameliorative effects of biostimulants such as proline, spermine, glycerol, and ethanol were investigated through model predictions. Through systematic computational analysis, 154 significantly altered reactions were identified in the presence of CBZ stress, of which 92 % of reactions were ameliorated with biostimulants. Amino acid biosynthesis was found to be the most significantly altered pathway under CBZ stress in the presence of biostimulants. Overall, the proposed framework can aid in screening and developing rational strategies to maintain agricultural yields amid rising plant stress due to such anthropogenic pollutants.

plant biology↗

bioRxiv2025

The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

The NIH Common Fund Data Ecosystem (CFDE) program was established to facilitate data accessibility and interoperability across multiple Common Fund (CF) programs and promote collaborations and new discoveries by combining data from different CF programs. The CFDE Data Resource Center (DRC) was tasked with developing two web-based portals: an Information Portal to serve information about the CFDE, and a Data Portal to host harmonized metadata and processed data contributed by participating CF Data Coordination Centers (DCCs) and other sources. To achieve these goals, the CFDE DRC developed the CFDE Workbench, a web-based platform that hosts highly processed data, metadata, tools, use cases, and analyses developed by the CFDE. The Crosscut Metadata Model (C2M2) and several other processed data formats are hosted by the CFDE Workbench, including set libraries (XMTs), Knowledge Graph (KG) assertions, and attribute tables. These processed data formats make information derived from CF programs more findable, accessible, interoperable, and reusable (FAIR) and artificial intelligence (AI)-ready for cross-DCC knowledge discovery. In addition to these processed data formats, several other assets are served by the Workbench, including Extract Transform Load (ETL) pipelines, OpenAPI-documented and SmartAPI-registered Representational State Transfer (REST) Application Programming Interfaces (APIs), entity pages such as gene, drug, disease, or tissue landing pages, Playbook Workflow Builder (PWB) metanodes which are codified workflow steps involving DCC APIs, and chatbot specifications which are prompts helping chatbots to use DCC APIs to answer a wide range of user queries. Besides serving data, metadata, and code assets, the CFDE Workbench also has several tools that use these data, metadata, and code assets to enable cross-CF-program knowledge discovery use cases. Overall, the CFDE Workbench is a platform that consolidates efforts toward making CF programs funded resources harmonized, FAIR, and AI-ready. The CFDE Workbench website is available from: https://cfde.info/.

bioinformatics↗

bioRxiv2025

Autoantibody hotspots reveal origin and impact of immunogenic XIST ribonucleoprotein complex

Four out of five patients with autoimmune diseases are women. The XIST ribonucleoprotein (RNP) complex, comprising the female-specific long noncoding RNA XIST and over 100 associated proteins, may drive several autoimmune diseases that disproportionately affect women, who have elevated levels of autoantibodies against the XIST RNP. However, the structural distribution, potential origin, and clinical significance of XIST RNP autoantibodies remained unexplored. Here, we find that XIST RNP is associated with autoantigens associated with six female-biased autoimmune conditions. Mapping autoantibody targets to their occupancy sites on XIST shows that these autoantigens are concentrated at discrete "hotspots" along the XIST lncRNA, notably the A-repeat. Cell type-specific protein expression data nominated neutrophils as a predominant source of hotspot antigens, and we confirmed the presence of both XIST and hotspot antigens in neutrophil extracellular traps during NETosis, an immunogenic programmed cell death pathway triggered by neutrophil activation upon which neutrophils extrude their nuclear content. Furthermore, we found that levels of autoantibodies against a top hotspot antigen, SPEN, that binds the A-repeat, correlate with severe digital ischemia in systemic sclerosis in two independent cohorts. Together, these data show a plausible mechanism for the origin of AXA, guided by RNA structure and RNA-protein interactions, and show that antibodies to XIST RNP holds promise for disease endotyping and prognostication in female-biased autoimmune conditions. One Sentence SummaryNovel autoantibodies target hotspots on XIST ribonucleoprotein complex in female-biased autoimmune diseases.

immunology↗

bioRxiv2025

Hsa-MiR-483 -3p Regulates the Extracellular Matrix Proteins via TGFbeta2/SMAD4 Signaling in the Glucocorticoid-responsive Human Trabecular Meshwork Cells

PurposeTo investigate the role of hsa-miR-483-3p on the regulation of extracellular matrix (ECM) in cultured human trabecular meshwork (HTM) cells with known steroid response. MethodsPrimary cultures of HTM cells with known steroid responsiveness [GC-responder (GC-R) and GC-Non-responder (GC-NR) cells] were grown on coverslip in 12-well plate until 80% confluence and treated with 100 nM dexamethasone (DEX) for 24 h and transfected with different concentrations of synthetic miRNA 483-3p mimic or inhibitor. After 24 h or 72 h post transfection, the cells were harvest for the following experiments: (i) percentage transfection efficiency (ii) RNA isolation for qPCR analysis and (iii) immunofluorescence staining, (iv) protein isolation for Western blotting respectively. All experiments were performed in triplicate with three biological samples (n{square}={square}3). ResultsGC-R HTM cells showed significantly higher expression of SMAD4 as compared to GC-NR HTM cells. Similarly, DEX treatment up-regulated the SMAD4-dependent ECM proteins. The presence of a miR-483-3p mimic down-regulated SMAD4 expression and SMAD4-dependent ECM production in a dose-dependent manner by negatively down- regulating SMAD4/TGF-{beta}2 signalling. The inhibition of SMAD4-dependent ECM production by miR-483-3p was more pronounced in GC-R HTM cells as compared to GC- NR cells. ConclusionThe down-regulation in ECM production by miR-483-3p is SMAD4 dependent and may play a protective role in mitigating steroid response in GC-R HTM cells. Using miR-483-3p mimics demonstrates therapeutic potential for the management of steroid induced ocular hypertension and glaucoma.

cell biology↗

bioRxiv2024

A complete collagen IV fluorophore knock-in toolkit reveals -chain diversity in basement membrane

The type IV collagen triple helix, composed of three -chains, is a core basement membrane (BM) component that assembles into a network within BMs. Endogenous tagging of all -chains with genetically encoded fluorophores has remained elusive, limiting our understanding of this crucial BM component. Through genome editing, we show that the C-termini of the C. elegans type IV collagen -chains EMB-9 and LET-2 can be fused to a variety of fluorophores to create a strain toolkit with wild-type health. Using quantitative imaging, our results suggest a preference for LET-2-LET-2-EMB-9 trimer construction, but also tissue-specific flexibility in trimers assembled driven by differences in -chain expression levels. By tagging emb-9 and let-2 mutants that model human Gould Syndrome, a complex multi-tissue disorder, we further discover defects in extracellular accumulation and turnover that might help explain disease pathology. Together, our findings identify a permissive tagging site that will allow diverse studies on type IV collagen regulation and function in animals. SummarySrinivasan et al., construct a collagen IV fluorophore knock-in toolkit in C. elegans using a newly identified permissive genome editing site and reveal tissue-specific -chain diversity and basement membrane turnover defects in collagen IV mutants modeling human COL4A1/A2 (Gould) syndrome.

developmental biology↗

bioRxiv2024

The benefits of estradiol on cognitive aging in rats are independent from its effects on cardiometabolic health

Research in preclinical models of menopause indicates that exogenously administered estrogens positively impact cognitive aging. However, clinical evidence indicates that the effects of estrogen therapy on cognition are inconsistent and may be modulated by pre-existing cardiometabolic conditions. The extent to which cardiometabolic health affects the cognitive outcomes of estrogen therapy remains unclear. This study aimed to determine whether variations in cardiometabolic health, both prior to and resulting from different estradiol treatment regimens, are related to the ability of estradiol to improve the cognitive aging trajectory in ovariectomized Long-Evans rats. Cognitive function and health status were assessed at 10 months of age after which rats were ovariectomized and administered vehicle or various estradiol treatments. Rats were assessed again at 18 (middle age) and 22 (old age) months. Cognition was evaluated using a spatial memory radial-maze task. Health status was determined through body composition (dual-energy X-ray absorptiometry), glucose tolerance testing, and blood pressure (tail-cuff plethysmography). Results demonstrated that both continuous ongoing estradiol treatment and a previous 40-day estradiol exposure (terminated long before testing) significantly improved the cognitive aging trajectory from middle to old age. However, only continuous estradiol treatment had positive impacts on health measures; previous estradiol treatment provided no benefits to aging cardiometabolic systems. In contrast, a delayed estradiol treatment (initiated months after ovariectomy) provided no benefits for cognition but provided health benefits. Results indicated that estradiol impacts on cognition in healthy aging rats are separate from and not secondary to its effects on cardiometabolic health.

animal behavior and cognition↗

bioRxiv2024

Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

Identifying noncoding single nucleotide variants (SNVs) in regulatory DNA linked to polygenic disease risk, the transcription factors (TFs) they bind, and the target genes they dysregulate is a goal in polygenic disease research. Massively parallel reporter gene analysis (MPRA) of 3,451 SNVs linked to risk for polygenic skin diseases characterized by disrupted epidermal homeostasis identified 355 differentially active SNVs (daSNVs). daSNV target gene analysis, combined with daSNV editing, underscored dysregulated epidermal differentiation as a pathomechanism shared across common polygenic skin diseases. CRISPR knockout screens of 1772 human TFs revealed 108 TFs essential for epidermal progenitor differentiation, uncovering novel roles for ZNF217, CXXC1, FOXJ2, IRX2 and NRF1. Population sampling CUT&RUN of 27 homeostatic TFs identified allele-specific DNA binding (ASB) differences at daSNVs enriched near epidermal homeostasis and monogenic skin disease genes, with notable representation of SP/KLF and AP-1/2 TFs. This resource implicates dysregulated differentiation in risk for diverse polygenic skin diseases.

genetics↗

bioRxiv2024

WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer

It is unclear how cells counteract the potentially harmful effects of uncoordinated DNA replication in the context of oncogenic stress. Here, we identify the WRAD (WDR5/RBBP5/ASH2L/DPY30) core as a modulator of DNA replication in pancreatic ductal adenocarcinoma (PDAC) models. Molecular analyses demonstrated that the WRAD core interacts with the replisome complex, with disruption of DPY30 resulting in DNA re-replication, DNA damage, and chromosomal instability (CIN) without affecting cancer cell proliferation. Consequently, in immunocompetent models, DPY30 loss induced T cell infiltration and immune-mediated clearance of highly proliferating cancer cells with complex karyotypes, thus improving anti-tumor efficacy upon anti-PD-1 treatment. In PDAC patients, DPY30 expression was associated with high tumor grade, worse prognosis, and limited response to immune checkpoint blockade. Together, our findings indicate that the WRAD core sustains genome stability and suggest that low intratumor DPY30 levels may identify PDAC patients who will benefit from immune checkpoint inhibitors.

cancer biology↗

bioRxiv2024

The molecular chronology of mammary epithelial cell fate switching

The adult mammary gland is maintained by lineage-restricted progenitor cells through pregnancy, lactation, involution, and menopause. Injury resolution, transplantation-associated mammary gland reconstitution, and tumorigenesis are unique exceptions, wherein mammary basal cells gain the ability to reprogram to a luminal state. Here, we leverage newly developed cell-identity reporter mouse strains, and time-resolved single-cell epigenetic and transcriptomic analyses to decipher the molecular programs underlying basal-to-luminal fate switching in vivo. We demonstrate that basal cells rapidly reprogram toward plastic cycling intermediates that appear to hijack molecular programs we find in bipotent fetal mammary stem cells and puberty-associatiated cap cells. Loss of basal-cell specifiers early in dedifferentiation coincides with activation of Notch and BMP, among others. Pharmacologic blockade of each pathway disrupts basal-to-luminal transdifferentiation. Our studies provide a comprehensive map and resource for understanding the coordinated molecular changes enabling terminally differentiated epithelial cells to transition between cell lineages and highlights the stunning rapidity by which epigenetic reprogramming can occur in response to disruption of tissue structure.

cell biology↗

bioRxiv2024

Real-Time Spatiotemporal Tracking of Infectious Outbreaks in Confined Environments with a Host-Pathogen Agent-Based System

Deadly infection outbreaks in confined spaces, whether it is a COVID-19 outbreak on a cruise ship or at a veteran home, or measles and stomach flu outbreaks in schools, can be characterized by their rapid spread due to the abundance of common spaces, shared airways, and high population density. Preventing future infectious outbreaks and developing efficient mitigation protocols can benefit from advanced computational modeling approaches. Here, we developed an agent-based modeling approach to study the spatiotemporal dynamics of an infection outbreak in a confined environment caused by a specific pathogen and to determine effective infection containment protocols. The approach integrates the 3D geographic information system of a confined environment, the behavior of the hosts, key biological parameters about the pathogen obtained from the experimental data, and the general mechanics of host-pathogen and pathogen-fomite interactions. To assess our approach, we applied it to the historical data of infectious outbreak caused by norovirus, H1N1 influenza A, and SARS-CoV-2 viruses. As a result our model was able to accurately predict the number of infections per day, correctly identify the day when the CDC vessel sanitation protocol would be triggered, single out key biological parameters affecting the infection spread, and propose important changes to existing containment protocols, specific for different pathogens. This research not only contributes to our understanding of infection spread and containment in cruise ships but also offers insights applicable to other similar confined settings, such as nursing homes, schools, and hospitals. By providing a robust framework for real-time outbreak modeling, this study proposes new, more effective containment protocols and enhances our preparedness for managing infectious diseases and emerging pathogens in confined environments.

bioinformatics↗

bioRxiv2024

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein associations on RNA

RNA binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport, and translation1-3. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease1,4,5, however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodeling in response to epidermal growth factor (EGF), uncovering EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships seen in irCLIP-RNP and detected simultaneous HNRNPC and UPF1 co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

molecular biology↗

bioRxiv2024

The first assembled chromosome-level genome of an individual from Karnataka, India

We present the first chromosome-level assembled genome of an individual from Karnataka, India (KIn1), using de novo assembly of 12x coverage of PacBio HiFi reads generated in-house and 30x Hi-C data from the most ethnically related individual to KIn1 from Andhra Pradesh (HG04712), publicly available under International Genome Sample Resource (IGSR). We achieved an N50 of 137 Mb and an L50 of 9--very close to the maximum achievable N50 of 147 Mb and minimum achievable L50 of 8 respectively for human genomes. A comparison of the KIn1 assembly with assemblies of four other individual genomes from a Puerto Rican (PR1), Ashkenazi (Ash1), Hans Chinese (Hans1), and Northern European (T2T) reported to date from resources like IGSR and/or Genome-in-a-Bottle (GIBR) collections shows that the longest scaffolds from KIn1 cover 80-90% of the reference chromosomes and exhibit near collinearity. We find a unique inversion in the chromosome 7 euchromatic region and other major translocations in chromosomes 17 and 20 in KIn1. We also produced a chromosome-level assembly for another individual from Punjab, Lahore (HG03492), for use in our comparison. The analysis of variants among select IGSR individuals using the KIn1 assembly as a reference reveals that the Indian Telugu from the UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Sri Lankan Tamil from the UK (STU) as representatives of South Asian ancestry.

genomics↗

bioRxiv2024

Peripubertal antagonism of corticotropin-releasing factor receptor 1 results in sustained, sex-specific changes in behavioral plasticity and the transcriptomic profile of the amygdala

Peripuberty is a significant period of neurodevelopment with long-lasting effects on the brain and behavior. Blocking type 1 corticotropin-releasing factor receptors (CRFR1) in neonatal and peripubertal rats attenuates detrimental effects of early-life stress on neural plasticity, behavior, and stress hormone action, long after exposure to the drug has ended. CRFR1 antagonism can also impact neural and behavioral development in the absence of stressful stimuli, suggesting sustained alterations under baseline conditions. To investigate this further, we administered the CRFR1 antagonist (CRFR1a) R121919 to young adolescent male and female rats across 4 days. Following each treatment, rats were tested for locomotion, social behavior, mechanical allodynia, or prepulse inhibition (PPI). Acute CRFR1 blockade immediately reduced PPI in peripubertal males, but not females. In adulthood, each assay was repeated without CRFR1a exposure to test for persistent effects of the adolescent treatment. Males continued to experience deficits in PPI while females displayed altered locomotion, PPI, and social behavior. The amygdala was collected to measure long-term effects on gene expression. In the adult amygdala, peripubertal CRFR1a induced alterations in pathways related to neural plasticity and stress in males. In females, pathways related to central nervous system myelination, cell junction organization, and glutamatergic regulation of synaptic transmission were affected. Understanding how acute exposure to neuropharmacological agents can have sustained impacts on brain and behavior, in the absence of further exposures, has important clinical implications for developing adolescents.

neuroscience↗

bioRxiv2024

Caught in the act of triplication: TNF superfamily

In humans, the signaling mechanisms of the 19 paralogs of the tumor necrosis factor superfamily (TNFSF) and the 29 receptor paralogs of the tumor necrosis factor receptor superfamily (TNFRSF) are extensively characterized because of their therapeutic relevance. The functional expansion of TNFSF in vertebrates from a single ancestral gene through successive duplication events is also well established. However, apart from the first identification of a TNFSF homolog, Eiger (dmEiger), in Drosophila melanogaster in 2002, together with its receptor homologs Wengen (dmWgn) and Grindelwald (dmGrnd), this signaling system has remained largely unexplored in invertebrates. More recently, the implication of an Eiger homolog in Plasmodium resistance in malaria vectors has further highlighted the need for a systematic investigation of this pathway in lower invertebrates. Structural comparison of the dmEiger-dmGrnd complex with the canonical 3:3 ligand-receptor configuration observed in human TNFSF-TNFRSF signaling suggests either conservation of this signaling modality since before the bilaterian split or convergent evolution of a similar architecture in both branches. The recent explosion in high-quality proteomes spanning diverse phyla, together with advances in protein-complex prediction using AlphaFold-multimer, now enables large-scale exploration of ligand-receptor evolution across invertebrates. Here, we analyzed 148 near-complete proteomes spanning major invertebrate phyla and identified 290 TNFSF, 336 wengen (wgn), and 115 grindelwald (grnd) homologs, including homologs from lower invertebrates. Structural characterization of 140 selected complexes using AlphaFold and AlphaFold-multimer revealed several key findings: (i) TNFSF and TNFRSF homologs are present in majority of the phyla under invertebrates (ii) the canonical 3:3 ligand-receptor signaling configuration is conserved across invertebrates; (iii) orthologs of 25 out of the 26 genes implicated in TNF signaling pathways are present in lower invertebrates; and (iv) signaling through grnd-like receptors containing a single cysteine-rich domain with CXXCXXXC signature is the predominant signaling mode in invertebrates and becomes highly prevalent in Arthropoda. We also elaborate a hypothesize on the evolutionary trajectories toward a genetically parsimonious signaling by this complex system before functional expansion in vertebrates and species diversification in Arthropoda.

bioinformatics↗

bioRxiv2024

Evidence for low affinity of GABA at the vesicular monoamine transporter VMAT2. Implications for transmitter co-release from dopamine neurons

Background and PurposeMidbrain dopamine (DA) neurons comprise a heterogeneous population of cells. For instance, some DA neurons express the vesicular glutamate transporter VGLUT2 allowing these cells to co-release DA and glutamate. Additionally, GABA may be co-released from DA neurons. However, most cells do not express the canonical machinery to synthesize GABA or the vesicular GABA transporter VGAT. Instead, GABA seems to be taken up into DA neurons by a plasmalemmal GABA transporter (GAT1) and stored in synaptic vesicles via the vesicular monoamine transporter VMAT2. Yet, it remains unclear whether GABA indeed interacts with VMAT2, or whether another transmitter could be responsible for the observed inhibitory effects attributed to GABA. Experimental ApproachWe used radiotracer flux measurements in VMAT2 expressing HEK-293 cells and synaptic vesicles from rodents to determine whether GABA qualifies as substrate at VMAT2. mRNA in situ hybridization was employed to determine expression of VMAT2 and GAT1 transcripts in DA neurons of mouse and in human midbrains. Key ResultsWe found that GABA reduced uptake of VMAT2 substrates in rodent synaptic vesicle preparations from striatum and cerebellum at millimolar concentrations but had no effect in VMAT2-expressing cells indicating that key components are missing in a non-neuronal system. Roughly 60 % of murine and human DA neurons in the substantia nigra express VMAT2 and GAT1 suggesting that many may be capable of co-releasing DA and GABA. Conclusion and ImplicationOur experiments suggest that GABA is a low-affinity substrate at VMAT2 with potential implications for basal ganglia physiology and disease. Bullet point summaryO_ST_ABSWhat is already knownC_ST_ABSO_LISubpopulations of dopamine neurons co-release glutamate and/or GABA. C_LIO_LIWhile glutamate is loaded into vesicles by VGLUT2, GABA co-release depends on GAT1 and VMAT2. C_LI What this study addsO_LIThe relative affinity of GABA at VMAT2 was found to be in the millimolar range. C_LIO_LIHuman midbrain dopamine neurons express GAT1. C_LI Clinical significanceO_LIGABA co-release from midbrain dopamine neurons may also occur in humans. C_LIO_LIGABA co-release from dopamine neurons may play a role in neuropsychiatric diseases C_LI

neuroscience↗

bioRxiv2024

An efficient method for immortalizing mouse embryonic fibroblasts

Mouse embryonic fibroblasts (MEFs) derived from genetically modified mice are a valuable resource for studying gene function and regulation. The MEF system can also be combined with rescue studies to characterize the function of mutant genes/proteins, such as disease-causing variants. However, primary MEFs undergo senescence soon after isolation and passaging, making long-term genetic manipulations difficult. Previously described methods for MEF immortalization are often inefficient or alter the physiological properties of the cells. Here, we describe an optimized protocol for immortalizing MEFs via CRISPR-mediated deletion of the Tp53 gene. This method is highly efficient and consistently generates immortalized MEFs, or iMEFs, within 14 days. Importantly, iMEFs closely resemble the parent cell populations, and individual iMEFs can be cloned and expanded for subsequent genetic manipulation and characterization. We envision that this protocol can be adopted to immortalize other mouse primary cell types. Key FeaturesO_LICRISPR-based knockout of the Tp53 gene enables efficient immortalization of mouse embryonic fibroblasts (MEFs) in under 2 weeks. C_LIO_LIImmortalization requires a Neon electroporator or another comparable electroporation system to transfect cells with the Tp53 CRISPR constructs. C_LI

developmental biology↗

bioRxiv2024

Monocytes Mobilized by Gut Neurons Remodel the Enteric Nervous System

The proper organization of the enteric nervous system (ENS) is critical for normal gastrointestinal (GI) physiology. Inflammatory bowel disease (IBD) dysregulates GI physiology, including bowel movements (motility), but in many IBD patients, GI motility disorders persist in remission through a poorly understood pathological process. Here we uncover that post-inflammatory GI dysmotility (PI-GID) stems from structural ENS remodeling driven by a combination of neuronal loss and neurogenesis. Enteric neurons respond to mucosal inflammation by upregulating CCL2 expression and facilitating the recruitment of CCR2+ monocytes into the neural myenteric plexus within the intestinal muscle. This is followed by the expansion of monocyte-derived macrophages and their migration into the myenteric ganglia and phagocytosis of neurons. However, excessive recruitment of monocytes results in disproportionate ENS remodeling and PI-GID. The expansion of inflammatory cells is known to promote tissue hypoxia. We find that enteric neurons become hypoxic upon colitis, but hypoxia-induced signaling via HIF1 initiates an adaptation program in enteric neurons to attenuate CCL2 expression and limit monocyte recruitment. We demonstrate that reinforcing HIF1 signaling in enteric neurons prevents PI-GID by reducing colitis-associated monocyte recruitment in the myenteric plexus and protecting against ENS remodeling. In summary, our findings unveil PI-GID pathogenesis and identify a regulatory axis for its prevention. One Sentence SummaryIntestinal mucosal inflammation engages enteric neurons in the inflammatory response leading to neurogenic recruitment of monocytes into the extra-mucosal myenteric plexus followed by pathological structural remodeling of the enteric nervous system by monocyte-derived macrophages.

immunology↗

bioRxiv2024

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

Many biomedical research projects produce large-scale datasets that may serve as resources for the research community for hypothesis generation, facilitating diverse use cases. Towards the goal of developing infrastructure to support the findability, accessibility, interoperability, and reusability (FAIR) of biomedical digital objects and maximally extracting knowledge from data, complex queries that span across data and tools from multiple resources are currently not easily possible. By utilizing existing FAIR application programming interfaces (APIs) that serve knowledge from many repositories and bioinformatics tools, different types of complex queries and workflows can be created by using these APIs together. The Playbook Workflow Builder (PWB) is a web-based platform that facilitates interactive construction of workflows by enabling users to utilize an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by an ecosystem. Via a user-friendly web-based user interface (UI), workflows can be constructed from contributed building-blocks without technical expertise. The output of each step of the workflows are provided in reports containing textual descriptions, as well as interactive and downloadable figures and tables. To demonstrate the ability of the PWB to generate meaningful hypotheses that draw knowledge from across multiple resources, we present several use cases. For example, one of these use cases sieves novel targets for individual cancer patients using data from the GTEx, LINCS, Metabolomics, GlyGen, and the ExRNA Communication Consortium (ERCC) Common Fund (CF) Data Coordination Centers (DCCs). The workflows created with the PWB can be published and repurposed to tackle similar use cases using different inputs. The PWB platform is available from: https://playbook-workflow-builder.cloud/.

bioinformatics↗