Biology subjects

Narayan, P.

Publications and source records attributed to Narayan, P..

11 recordsLinked to original sources

bioRxiv2026

Profiling of Aggregated Amyloid β42-induced Proteomic Alterations in KOLF2.1J Induced Pluripotent Stem Cell-derived Neurons

Amyloid[beta]; (A[beta];) plaques are a hallmark of Alzheimer[prime]s disease (AD). A human cellular neuronal model that recaptures A[beta];-induced pathology is critical for advancing AD research. However, comprehensive proteomic profiling of A[beta];-induced cellular model remains elusive. In this study, we investigated the proteomic changes in induced pluripotent stem cell (iPSC)-derived neurons (iNs) exposed to synthetic A[beta]; (1-42) peptides (A[beta];42A) to improve our understanding of the cellular responses of A[beta]; aggregates and to establish a human-related platform for AD research. A[beta];42A formed extracellular aggregates around neuronal soma and neurites, impaired neurite outgrowth, and induced the expression of multiple AD-associated genes, such as APOE, BACE1, ADAM10. To define the molecular landscape of A[beta];-induced neuronal dysfunction, we performed proteomic analyses of whole-cell lysates as well as soma- and neurite-enriched fractions. Proteomic profiling revealed extensive gene alterations in pathways associated with synaptic function, neuronal maintenance, and AD pathogenesis, such as the upregulation of APOE. Importantly, the A[beta];42A-iNs system recapitulated molecular signatures observed in AD brain tissue and cerebrospinal fluid. Representative protein changes, including APOE upregulation and its colocalization with A[beta]; aggregates, were further validated in postmortem human AD brain tissue. Together, these findings manifest that the A[beta];42A-iNs system reproduces multiple cellular and molecular features of AD and exhibits strongly consensus with clinical observations. It provides a valuable platform for investigating A[beta];-driven neurodegeneration and for the discovery of therapeutic targets for AD.

neuroscience↗

bioRxiv2026

Yin Yang Interactomes Drive the Metabolic Dysfunction-Associated Liver Disease Continuum to Hepatocellular Carcinoma

The risk for hepatocellular carcinoma (HCC) arising from metabolic dysfunction- associated steatotic liver disease (MASLD)-related cirrhosis exceeds the risk for cancer developing in the kidney, heart, or lung as a consequence of end-stage disease in those organs. Both experimental and clinical studies support the existence of circulating biomarkers whose elevated expression is associated with, and supports the diagnosis of, HCC. We posit the existence of oncogenic HCC biomarkers under regulation by tumor-suppressive microRNAs (miRs), and that reduced tumor-suppressive miR expression leads to increased oncogenic biomarker expression. By interrogating the MASLD-HCC miR interactome and miRs known to regulate HCC biomarkers, we identified hsa-miR-577, hsa-miR-9500, hsa-miR-101-3p, miR-206, hsa- miR-219a-1-3p, and hsa-miR-613 as tumor-suppressive miRs whose expression is reduced across multiple cancers. Their target genes, osteopontin, Golgi protein-73, and Dickkopf-related protein 1, exhibit increased expression in HCC and display oncogenic activity. Collectively, dysregulated expression of these miRs and their downstream gene products may contribute to progression along the MASLD continuum toward HCC. HighlightsWe identified tumor suppressive miRs, hsa-miR-577, hsa-miR-9500, hsa-miR-101-3p, miR-206, hsa-miR-219a-1-3p, and hsa-miR-613 with potentially reduced expression levels in HCC. Their gene products, osteopontin, Golgi protein-73, and Dickkopf-related protein 1, exhibit oncogenic properties and increased expression levels in HCC. These miR-gene product interactions may drive the MASLD continuum to HCC. Mechanistic insights should illuminate therapies. Identification of therapeutics that interrupt these interactions may represent a therapeutic pillar for patients with MASLD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/698028v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1892140org.highwire.dtl.DTLVardef@1e61677org.highwire.dtl.DTLVardef@cd0488org.highwire.dtl.DTLVardef@1e48d8a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigureC_FLOATNO MASLD-related HCC. The intersection set between the MASLD-HCC miR interactome and the set of miRs regulating biomarkers diagnostic for HCC was interrogated and tumor suppressive miRs regulating HCC biomarkers with oncogenic activity were identified. Increased risk for HCC in patients with MASLD and MASLD-cirrhosis may arise from interactions between these dysregulated miRs and their downstream gene products. C_FIG PrologueMetabolic Dysfunction-Associated Liver Disease (MASLD), the leading cause of hepatocellular carcinoma (HCC) in Sweden, is now taking epidemic proportions in South Asia. In India, there is a relatively high prevalence of pre-diabetes, diabetes and insulin resistance; body mass indices > 35 are being observed. Each of these and/or their combinations represent risk factors for MASLD. Nevertheless, both patients and providers are largely oblivious to this disease, both from a lack of general awareness and the asymptomatic nature of MASLD, at least early within its continuum. Diagnosis is often made late, and by exclusion, when presentation may include fatigue, drowsiness, mild encephalopathy (MASLD-pituitary feedback loop), prominent hepatomegaly and asciites, and with liver-specific test demonstrating stiffness, scarring and even HCC. Societal awareness and effective management of this disease are urgent needs. A strategy akin to the 4 pillars for treatment of type 2 diabetes and chronic kidney disease (CKD) needs to be implemented for treatment of patients with MASLD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=30 SRC="FIGDIR/small/698028v1_ufig2.gif" ALT="Figure 2"> View larger version (11K): org.highwire.dtl.DTLVardef@89a77org.highwire.dtl.DTLVardef@d50c15org.highwire.dtl.DTLVardef@10c6964org.highwire.dtl.DTLVardef@1db2cfa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigureC_FLOATNO Four-pillar Strategy for MASLD. A strategy akin to the one in place for treatment of type 2 diabetes and CKD needs to be implemented for treatment of patients with MASLD. Aspects of this strategy, viz. SGLT2i and GLP-1{+/-}GIP agonists, are already approved in MASLD. C_FIG

bioinformatics↗

bioRxiv2025

Boolean Logic Coupled with Overrepresentation Analysis Reveals Activation of the Platelet-derived Growth Factor Receptor Beta Pathway in a Model of Oliguric Acute Kidney Injury; Implications for Transition to Chronic Kidney Disease

Acute Kidney Injury (AKI) can occur secondary to insults including sepsis, ischemia and contrast dye administration. A time-sensitive increase in serum creatinine (SCr) or reduction in urine output (UO) has been used to define AKI and stage its severity. Oliguria or significantly reduced UO in AKI or oliguric AKI can have a major impact on outcomes including a transition to chronic kidney disease (CKD). We used Boolean logic coupled with overrepresentation analysis to identify the pathway activation signature associated with oliguric AKI in a published study of rat kidney-ischemia reperfusion. In the reperfused kidney, bulk transcriptomic analysis revealed 1068 differentially expressed genes (DEGs). Those DEGs that correlated with UO and SCr were submitted to gene ontology biological process overexpression analysis. The pathway activation signature associated with oliguric AKI included positive regulation of profibrotic platelet-derived growth factor receptor beta signaling (fold-enrichment >44) driven by src, hip1 and hip1r. Together these findings not only suggest that oliguric AKI may be associated with activation of a pathway leading to fibrosis and CKD but also informs an array of targets to potentially mitigate transition to CKD. HighlightsMechanistic insights should illuminate therapies. A model of rat kidney-ischemia reperfusion injury was queried by correlating kidney transcriptomics with kidney function to identify the pathway activation signature of oliguric AKI. The most striking feature associated with oliguric AKI was positive regulation of platelet-derived growth factor receptor {beta} driven by src, hip1, and hip1r. The pathway activation signature in oliguric AKI informs not only the sequel to injury but also an array of targets to mitigate the potential transition to kidney fibrosis and CKD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/680804v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@121edc1org.highwire.dtl.DTLVardef@80383borg.highwire.dtl.DTLVardef@1ebc25dorg.highwire.dtl.DTLVardef@1258145_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Random forest model improves annotation and discovery of variants of uncertain significance in Alzheimer's and other neurological disorders

Variants of uncertain significance (VUS) are a bottleneck for genetic discovery and complicate clinical decision-making in Alzheimers disease and related neurological disorders (ADRD). We developed MoVUS: Model for Variants of Unknown Significance, a random-forest approach that integrates functional predictors to classify missense VUS. MoVUS leverages a balanced random forest model trained on dbNSFP v5.1a with high-confidence ClinVar and HGMD labels, using harmonized functional prediction rankscores. MoVUS produced confident, explainable calls, with [~]98% accuracy (AUC [~]0.998), prioritizing potentially pathogenic candidates and down-ranked likely benign variants on independent validation sets of ClinVar-only and HGMD-only variants. In our discovery analyses on ADRD-implicated variants in dbNSFP and from independent collaborator cohorts, we achieved high-confidence classifications on a majority of the unknown variants (average of 55% of discovery variants). We also had access to medical records and family trees for some variants, further validating our findings. Across held-out and external datasets, MoVUS reports high accuracy alongside confidence scores and helps prioritize actionable candidates, and reduces bias by considering multiple scores for each variant. To facilitate use, we developed a web app for users to browse across 100+ ADRD genes. MoVUS provides transparent, reproducible triage for research follow-up by pairing consensus predictors with SHAP-based visualizations and explanations.

genetics↗

bioRxiv2025

INTERLEUKIN-18 AS A THERAPEUTIC TARGET FOR WESTERN DIET-INDUCED CARDIOMYOPATHY

BackgroundA diet high in saturated fats and sugars (Western diet-WD) promotes obesity and left ventricular dysfunction in the mouse, which is, at least in part, mediated by pro-inflammatory cytokine Interleukin-18 (IL-18). Therefore, we hypothesized that a blocking recombinant-murine IL-18 binding protein (IL-18BP) would rescue cardiac function in WD-fed mice. MethodsIn this 9-week study, 10-week-old adult C57BL/6J mice were assigned to standard diet (SD) or a WD. After 7 weeks of WD feeding, the mice were assigned to two groups: WD+IL-18BP (0.5 mg/kg daily, intraperitoneal injections) or WD control for the last 2 weeks of the study. Food intake, body weight, and glucose tolerance were assessed. Cardiac systolic and diastolic function were measured by Doppler echocardiography at baseline, 5 weeks, and 9 weeks. IL-18 plasma levels were quantified with ELISA. ResultsWD induced a significant increase in body weight, significantly worsened glucose tolerance, and significantly increased (worsening) in diastolic function (isovolumetric relaxation time -IRT- and myocardial performance index -MPI-) compared to SD. Rescue with IL-18BP in WD-fed mice resulted in a significant improvement in IRT and MPI, without significant changes in food intake, weight gain, or glucose tolerance. ConclusionsIL-18BP rescued cardiac function in mice with WD-induced diastolic dysfunction, independent of weight gain and glucose tolerance. These results confirm the central and independent role of IL-18 in cardiac dysfunction associated with diet-induced obesity.

physiology↗

bioRxiv2025

Temporal dynamics of proteome and phosphorproteome during neuronal differentiation in the reference KOLF2.1J iPSC line

Induced pluripotent stem cell (iPSC)-derived neurons have emerged as a powerful model to investigate both neuronal development and neurodegenerative diseases. Although transcriptomics and imaging have been applied to characterize neuronal development signatures, comprehensive datasets of protein and post-translational modifications (PTMs) are not readily available. Here, we applied quantitative proteomics and phosphoproteomics to profile the differentiation of the KOLF2.1J iPSC line, the first reference line of the iPSC Neurodegenerative Disease Initiative (iNDI) project. We developed an automated workflow enabling high-coverage enrichment of proteins and phosphoproteins. Our results revealed molecular signatures across proteomic and phosphoproteomic landscapes during differentiation of iPSC-derived neurons. Proteomic data highlighted distinct changes in mitochondrial pathways throughout the course of differentiation, while phosphoproteomics revealed specific regulatory dynamics in GTPase signaling pathways and microtubule proteins. Additionally, phosphosite dynamics exhibited discordant trends compared to protein expression, particularly in processes related to axon functions and RNA transport. Furthermore, we mapped the kinase dynamic changes that are critical for neuronal development and maturation. We developed an interactive Web app (https://niacard.shinyapps.io/Phosphoproteome/) to visualize temporal landscape dynamics of protein and phosphosite expression. By establishing baselines of proteomic and phosphoproteomic profiles for neuronal differentiation, this dataset offers a valuable resource for future research into neuronal development and neurodegenerative diseases using this reference iPSC line. HighlightsO_LITemporal dynamics of proteome and phosphoproteome profiles in KOLF2.1J iPSC derived neurons. C_LIO_LIPhosphoproteomics highlights GTPase signaling and microtubule regulation in neuronal differentiation. C_LIO_LIKinome mapping reveals a shift in kinase activity patterns from early to late differentiation. C_LIO_LIShinyapp for visualizing the trajectory of protein and phosphosite expression during neuronal differentiation. C_LI

neuroscience↗

bioRxiv2025

UNCONVENTIONAL INTERLEUKIN-1 SIGNALING IN CARDIAC DYSFUNCTION

Interleukin-1{beta} (IL-1{beta}) is an apical pro-inflammatory cytokine that has also been shown to negatively modulate cardiac contractility. Whether IL-1{beta} effects on systemic inflammation and cardiac function are intertwined and associated with each other, or whether they are independent of each other, is unknown. An unconventional signaling of the IL-1 receptor type I through the phosphoinositide-3 kinase{gamma} (PI3K{gamma}), at least in part independent of the proinflammatory signaling, has been characterized in inflammation and cancer. We hypothesized that IL-1{beta} would increase the expression of PI3K p110{gamma} in cardiomyocytes, which in turn results in selective induction of p87 co-signaling and cardiac dysfunction through a scaffolding function on phosphodiesterase 3B (PDE3B). Using genetically modified mice, we show that a kinase-independent PI3K p110{gamma} mechanism mediates IL-1-induced cardiac dysfunction. This may have compelling implications for the understanding and treatment of heart failure with reduced ejection fraction.

immunology↗

bioRxiv2023

Spinal neural tube formation and regression in human embryos

Formation of the nervous system in the spinal region of higher vertebrates involves primary and secondary neurulation, in which the neural tube forms by closure and canalisation respectively. These processes are incompletely understood in humans, in part due to the challenge of accessing neurulation-stage embryos (3-7 weeks post-conception). Here we present findings on completion of primary neurulation and formation of the secondary body (including secondary neurulation) in 108 human embryos that span Carnegie Stages (CS) 10 to 18. Several outstanding questions on low spinal development in humans are addressed: we show that primary neurulation is completed at the human posterior neuropore with a pattern of neural plate bending similar to that in the mouse. There is no evidence of a transition zone to secondary neurulation, which proceeds from CS13 with formation of a single lumen as in mouse, not coalescence of multiple lumens as has been claimed based on chick neurulation. Secondary neural tube splitting is seen in the more proximal tail regions of 60% of human embryos. A somite is formed every 7 h in human, compared with 2 h in mice and a 5 h segmentation clock in human organoids. Termination of axial elongation occurs after downregulation of WNT3A and FGF8 in the CS15 embryonic tailbud, with a burst of apoptosis that may remove the neuro-mesodermal progenitors. We conclude that low spinal neurulation and secondary body formation follow a similar pattern in humans as in mammalian model systems such as mouse and rat. Investigators are now attempting to recapitulate events of neurulation in organoids derived from human stem cells, and our findings provide normative data for interpretation of such in vitro results.

developmental biology↗

bioRxiv2021

A reference induced pluripotent stem cell line for large-scale collaborative studies

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate iPSC lines and deeply characterised their genetic properties using whole genome sequencing, their genomic stability upon CRISPR/Cas9-based gene editing, and their phenotypic properties including differentiation to commonly-used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and hundreds of its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. SummaryThe authors of this collaborative study deeply characterized human induced pluripotent stem cell (iPSC) lines to rationally select a clonally-derived cell line that performs well across multiple modalities. KOLF2.1J was identified as a candidate reference cell line based on single-cell analysis of its gene expression in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and the efficiency with which it differentiated into multiple target cell populations. Since it is deeply characterized and can be readily acquired, KOLF2.1J is an attractive reference cell line for groups working with iPSCs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/472643v6_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@cef106org.highwire.dtl.DTLVardef@31d5d8org.highwire.dtl.DTLVardef@1ce6d8corg.highwire.dtl.DTLVardef@17a19d2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons

Fully automated proteomic pipelines have the potential to achieve deep coverage of cellular proteomes with high throughput and scalability. However, it is important to evaluate performance, including both reproducibility and ability to provide meaningful levels of biological insight. Here, we present an approach combining high field asymmetric waveform ion mobility spectrometer (FAIMS) interface and data independent acquisition (DIA) proteomics approach developed as part of the induced pluripotent stem cell (iPSC) Neurodegenerative Disease Initiative (iNDI), a large-scale effort to understand how inherited diseases may manifest in neuronal cells. Our FAIMS-DIA approach identified more than 8000 proteins per mass spectrometry (MS) acquisition as well as superior total identification, reproducibility, and accuracy compared to other existing DIA methods. Next, we applied this approach to perform a longitudinal proteomic profiling of the differentiation of iPSC-derived neurons from the KOLF2.1J parental line used in iNDI. This analysis demonstrated a steady increase in expression of mature cortical neuron markers over the course of neuron differentiation. We validated the performance of our proteomics pipeline by comparing it to single cell RNA-Seq datasets obtained in parallel, confirming expression of key markers and cell type annotations. An interactive webapp of this temporal data is available for aligned-UMAP visualization and data browsing (https://share.streamlit.io/anant-droid/singlecellumap). In summary, we report an extensively optimized and validated proteomic pipeline that will be suitable for large-scale studies such as iNDI.

neuroscience↗

bioRxiv2020

Castration delays epigenetic aging and feminises DNA methylation at androgen-regulated loci

In mammals, females generally live longer than males. Nevertheless, the mechanisms underpinning sex-dependent longevity are currently unclear. Epigenetic clocks are powerful biological biomarkers capable of precisely estimating chronological age using only DNA methylation data. These clocks have been used to identify novel factors influencing the aging rate, but few studies have examined the performance of epigenetic clocks in divergent mammalian species. In this study, we developed the first epigenetic clock for domesticated sheep (Ovis aries), and using 185 CpG sites can predict chronological age with a median absolute error of 5.1 months from ear punch and blood samples. We have discovered that castrated male sheep have a decelerated aging rate compared to intact males, mediated at least in part by the removal of androgens. Furthermore, we identified several androgen-sensitive CpG dinucleotides that become progressively hypomethylated with age in intact males, but remain stable in castrated males and females. Many of these androgen sensitive demethylating sites are regulatory in nature and located in genes with known androgen-dependent regulation, such as MKLN1, LMO4 and FN1. Comparable sex-specific methylation differences in MKLN1 also exist in mouse muscle (p=0.003) but not blood, indicating that androgen dependent demethylation exists in multiple mammalian groups, in a tissue-specific manner. In characterising these sites, we identify biologically plausible mechanisms explaining how androgens drive male-accelerated aging.

developmental biology↗