Biology subjects

Kathuria, A.

Publications and source records attributed to Kathuria, A..

5 recordsLinked to original sources

bioRxiv2026

The Neural Impact Score benchmarks drugs in Multi-Region Brain Organoids

Only about 10 percent of drugs that clear animal testing succeed in humans, and central nervous system programs carry an even steeper translational gap. Human-relevant NAMs are gaining global regulatory and funding support, creating an urgent need for interpretable preclinical systems that can generate comparable, decision-ready evidence across assays, models, and species. Yet the multimodal treatment-response data produced by these systems are still evaluated assay by assay, with no unified metric showing whether a compound moves neural tissue toward a desirable or undesirable state. Here we present the Neural Impact Score (NIS), a framework that translates multimodal CNS drug-response data into a bidirectional score across four predefined biological categories: neurodevelopment, neuroinflammation, neurodegeneration, and longevity. A positive score indicates a desirable shift, whereas a negative score indicates the opposite, placing compounds on a single scale across assays, model systems, and species. To demonstrate NIS, we analyzed a vascularized human day-200 multi-region brain organoid (MRBO) composed of cortical, endothelial, and brainstem lineages and mimicking a mid-gestational cortical window (GW18-GW22). We tested five compounds with distinct mechanisms of action: a glucagon-like peptide-1 receptor agonist (GLP-1RA), a norepinephrine-dopamine reuptake inhibitor (NDRI), a selective serotonin reuptake inhibitor (SSRI), a sphingosine-1-phosphate receptor modulator, and an Akt activator. We profiled responses using single-nucleus RNA sequencing, bulk RNA sequencing, proteomics, and multi-electrode array electrophysiology. NIS integrated these readouts into category-specific and composite scores, separating beneficial from adverse effects for each compound and sorting compounds into interpretation tiers. Applying the same framework to independent human and rodent datasets without retraining, we recovered conserved human antidepressant responses despite near-chance gene-level agreement between human MRBO and rat brain, and identified an endothelial-dependent, human-specific GLP-1 response absent from the murine dorsal vagal complex. NIS therefore provides a human-relevant framework for drug evaluation and cross-species benchmarking, with a design extensible to other neural systems.

bioengineering↗

bioRxiv2026

Dual Transcriptomic and Epigenomic Signatures of THC Exposure in Human Prefrontal Cortex Development

Prenatal cannabis use is increasing globally, with estimates up to 35% in North America. Fetal exposure to {Delta}9-tetrahydrocannabinol (THC) has been linked to neurodevelopmental deficits. Yet mechanistic understanding remains limited because animal models incompletely recapitulate human fetal development, and human-relevant in vitro platforms are scarce. To address this gap, we generated human iPSC-derived prefrontal cortex organoids (PFCOs) and used an integrated multi-omics approach combining bulk RNA-seq, whole-genome bisulfite sequencing (WGBS), and electrophysiology to characterize early molecular and functional responses to acute THC exposure at a developmentally relevant stage. THC induced a rapid, transient shift toward excitatory and neurodevelopmental gene expression programs while simultaneously suppressing extracellular matrix and adhesion pathways critical for structural support. Concurrent epigenetic remodeling selectively targeted synaptic assembly, postsynaptic organization, and axonal guidance genes, creating a mismatch between early activation of neuronal programs and epigenetic repression of the scaffolding required for their proper integration. Functionally, these disruptions manifested as delayed but reversible increases in burst duration at 24 hours, indicating altered coordination of network activity. Transcriptional and epigenetic responses converged on autism spectrum disorder (ASD) associated gene networks, with strong enrichment among high-confidence and strong-candidate ASD risk genes, suggesting that THC preferentially perturbs neurodevelopmentally vulnerable pathways. Together, these findings define a mechanistic framework in which THC disrupts early human cortical development through a cycle of transient excitatory activation, compromised structural support, and persistent epigenetic alterations, which are features specifically revealed by human PFCOs.

genomics↗

bioRxiv2025

Paracrine Bone-Derived Senescent Secretome Induces Spatially Patterned ECM and Biomechanical Vulnerability in Human Brain Organoids

Aging is increasingly recognized as a systemic process, yet the mechanisms by which senescent cells signal from peripheral tissues accelerate brain aging remain poorly defined. Here, we used chronic exposure of human cerebral organoids to the secretome of senescent osteocytes to investigate how peripheral aging signals reshape brain tissue architecture. We combined spatially resolved optical fiber-based interferometry nanoindentation with transcriptomic and immunofluorescence profiling, demonstrating that bone-derived senescence-associated secretory phenotype (SASP) factors induce a biphasic mechanical response, early global tissue softening, followed by the emergence of discrete hyper-stiff microdomains. This spatially heterogeneous biomechanical remodeling was accompanied by upregulation of extracellular matrix (ECM), inflammatory, and senescence pathways, and suppression of neurodevelopmental and synaptic gene networks. Our results reveal that chronic paracrine SASP exposure from senescent osteocytes drives localized ECM reorganization and mechanical vulnerability in human brain tissue, providing mechanistic insight into how peripheral cellular senescence may contribute to regional brain fragility during aging.

bioengineering↗

bioRxiv2025

Multi-Region Brain Organoid: Fusion Organoid with Cerebral, Endothelial and Mid-Hindbrain Components

Brain organoid technology has revolutionized our ability to model human neurodevelopment in vitro. However, current techniques remain limited by their reliance on simplified endothelial cell populations rather than a complete endothelial system. We engineered Multi-Region Brain Organoids (MRBOs) that integrate cerebral, mid/hindbrain, and complex endothelial organoids into one structure. Different from the earlier approaches based on isolated HUVECs, our endothelial organoids contain diverse vascular cell types, including vascular progenitors, mature endothelial cells, pericytes, proliferating angiogenic cells and stromal cells. Our strategy employs a sequential modulation of key developmental pathways to generate individual organoids, followed by optimized fusion conditions that maintain regional identities while supporting cellular integration. Single-nucleus RNA sequencing shows that MRBOs develop discrete neural populations specific to each brain region alongside specialized endothelial populations that establish paracrine signalling networks. Integration analysis with human fetal brain data shows that MRBOs contribute to 80% of cellular clusters found in human fetal brain tissue (Carnegie stages 12-16), whereas CellChat analysis identifies 13 previously uncharacterized endothelial-neural signalling interactions. Notably, we uncover endothelial-derived factors that support the persistence of intermediate progenitor populations during hindbrain development, but not during the cerebral one thereby revealing a new role for complex endothelial populations in regional brain patterning. This platform enables matching multiple developmental regions, fully incorporating the endothelial nature at the same time providing opportunities for studying neurodevelopmental disorders in which neural-endothelial interactions are disrupted. Our engineered MRBO system establishes a foundation for investigating complex neurodevelopmental processes, providing an enabling context closer to physiological relevance.

bioengineering↗

bioRxiv2018

Identifying the genetic basis of variation in cell behaviour in human iPS cell lines from healthy donors

Large cohorts of human iPSCs from healthy donors are potentially a powerful tool for investigating the relationship between genetic variants and cellular phenotypes. Here we integrate high content imaging, gene expression and DNA sequence datasets for over 100 human iPSC lines to identify the genetic basis of inter-individual variability in cell behaviour. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we identified genes that correlated in expression with intrinsic (genetic) and extrinsic (ECM) factors. However, variation in mRNA levels could not account for outlier cell behaviour. Instead, we identified rare, deleterious SNVs in the coding sequence of genes involved in ECM adhesion that occurred in cell lines that were outliers for one or more phenotypes such as cell spreading. These also correlated with altered germ layer differentiation on micropatterned surfaces. Our study thus establishes a strategy for integrating genetic and cell biological measurements for high-throughput analysis.

cell biology↗