Biology subjects

Rajagopalan, P.

Publications and source records attributed to Rajagopalan, P..

10 recordsLinked to original sources

bioRxiv2026

Distributed Genetic Effects on Human Brain Structure Emerge Across Multiple Spatial Scales

Genome-wide association studies (GWAS) have identified hundreds of common genetic variants associated with regional brain volumes, enabling the construction of polygenic scores (PGS) that summarize genetic predisposition for variation in specific neuroanatomical traits. To investigate how these genetic influences are exerted spatially throughout the brain, we computed PGS for ten brain volume phenotypes, including nine major subcortical structures and intracranial volume. Each locus was weighted by its estimated GWAS effect size on regional volume in the original GWAS. In an independent, non-overlapping sample of 2,830 UK Biobank participants, we performed whole-brain voxel-based morphometry (VBM) analyses of 3D volumetric brain MRI to reveal voxel-wise associations between each PGS and modulated gray matter volume (GMV). To probe genetic effects across multiple spatial scales, analyses were repeated across Gaussian smoothing kernels ranging from 2-mm to 12-mm full-width at half-maximum (FWHM). Several PGS demonstrated highly significant associations with GMV, including localized effects in the hippocampus, amygdala, thalamus, and basal ganglia, whereas the brainstem PGS showed more widespread associations throughout the brain. For most of the PGS, the fraction of voxels surviving the false discovery rate (FDR) correction increased with increasing FWHM. Peak voxel-wise significance was often strongest at intermediate smoothing levels. Hippocampal significance maps showed progressively larger regions of significant signal at higher smoothing levels, and subsampling showed that detectable signal remained present even with substantial reductions in sample size. These findings suggest that genetic influences on brain morphology are expressed across multiple spatial scales, with consequences that may help to guide the design of deep learning methods to discover genomic loci associated with brain structure and brain diseases.

neuroscience↗

bioRxiv2026

Mapping Focal and Generalized Effects of Common Genetic Variants on Human Brain Structure

Genome-wide association studies (GWAS) have advanced the quest to understand how specific genetic variants influence human brain structure and function. Recent work has identified hundreds of common variants associated with subcortical brain volumes, sparking interest in how these genetic markers overlap across brain networks. While this can be estimated by hierarchical clustering of the genetic correlation matrix to identify modular patterns of shared architecture, no brain-wide maps of these effects are available. To address this, we computed polygenic scores (PGS) from loci associated with ten brain volume regions of interest (ROIs): nine major subcortical structures and intracranial volume, with each locus weighted by its association with regional volume. In an independent sample from the discovery GWAS, we performed large-scale segmentation of 3D volumetric T1-weighted MRI scans using voxel-based morphometry (VBM) to map 3D profile of regions where gray matter volume (GMV) was associated with each PGS. We found statistically significant, localized effects for PGS defined for the amygdala, thalamus, and basal ganglia, but PGS for brainstem volume was associated with widespread differences throughout the brain. These brain-wide maps reveal patterns consistent with both localized and distributed genetic influences, offering a novel approach to interpret the genomic architecture of brain structure.

neuroscience↗

bioRxiv2026

Structural brain alterations in autism: A large-scale voxel-based morphometry mega-analysis

BackgroundPrevious large-scale structural MRI analyses of the brain in autism have identified gray matter (GM) differences when using region-of-interest analyses based on gross anatomical regions. However, such analyses have limited spatial specificity and may obscure subtle focal differences. Whole brain voxel-based morphometry (VBM) analyses enable greater spatial precision to identify and localize previously undetected neuroanatomical alterations. PurposeTo rigorously identify voxel-wise GM and white matter (WM) volume differences in autism in the largest VBM mega-analysis to date. Materials and MethodsThis retrospective mega-analysis included structural 3D volumetric T1-weighted MRI brain scans from 3,051 participants (15.0 {+/-} 8.2 yrs; 76.8% male; 1,519 autism; 1,532 neurotypicals) collected across 51 sites/scanners. Voxel-wise GM and WM volumes were quantified using the ENIGMA CAT12 VBM pipeline. Linear mixed-effects regression was performed at each voxel to evaluate the association between diagnostic group and voxel-wise volume while adjusting for standard nuisance covariates ResultsAutism was associated with widespread lower GM volume involving cortical, subcortical, and cerebellar regions (peak t=7.39, peak {beta}=0.13); such GM differences were most notably detected in the bilateral orbitofrontal cortex, amygdala, thalamus, and posterior lobes of the cerebellum. WM volume was lower in autism across major projection, commissural, association, and cerebellar/brainstem tracts (peak t=6.74, peak {beta}=0.08), including the corona radiata, internal capsule, corpus callosum, and cerebellar peduncles. These findings remained consistent in sensitivity analyses, including covarying for full-scale IQ and the application of increasingly strict motion exclusion criteria. ConclusionAutism is associated with smaller voxel-wise GM and WM volume involving widespread cortical, subcortical, and cerebellar regions. This high-resolution identification and localization of structural brain differences support the involvement of distributed neural systems in autism that underlie reward processing, sensory integration, and motor functioning in autism. Summary statementIn the largest voxel-based morphometry study of autism to date, widespread smaller gray and white matter volumes were identified across distributed brain regions implicated in reward and sensorimotor function. Key ResultsO_LIOur largest voxel-based morphometry mega-analysis to date in autism (N=3,051), identified widespread gray and white matter alterations (peak t=7.39, peak {beta}=0.13). C_LIO_LIWe reveal novel associations within thalamic mediodorsal nuclei by leveraging finer voxel-wise volumetric analyses. C_LIO_LIAdditional associations in orbitofrontal cortex, amygdala, and cerebellum, along with extensive white matter alterations across projection, commissural, association fibers, reinforce reward-processing, sensory and motor development theories in autism. C_LI

neuroscience↗

bioRxiv2026

Determination of GLP-1 Secretion Potential of Dead and Live Akkermansia muciniphila Using Human L-cells

Background/ObjectivesGlucagon-Like Peptide-1 (GLP-1) is a key incretin hormone that regulates glucose homeostasis and energy metabolism. Impaired GLP-1 signaling contributes to the development of obesity, metabolic syndrome, and type 2 diabetes. Emerging evidence indicates that gut microbiota-derived components can influence GLP-1 secretion, highlighting the therapeutic potential of microbial modulators. Akkermansia muciniphila, a next-generation probiotic associated with improved metabolic health, remains underexplored for its capacity to stimulate GLP-1 release. This study aimed to investigate the GLP-1- stimulatory effects of live and pasteurized (dead) A. muciniphila strains in human enteroendocrine cells. MethodsHuman enteroendocrine L-cells (NCI-H716) were treated with varying doses of live and dead A. muciniphila from Vidya Herbss proprietary VHAKM strain and a commercially available marketed strain (dead form). Following incubation, GLP-1 levels were quantified from culture supernatants using enzyme-linked immunosorbent assay (ELISA). Comparative analyses assessed differences in GLP-1 secretion between strains and treatment forms. ResultsBoth live and pasteurized VHAKM strains significantly increased GLP-1 secretion compared to untreated controls. The live VHAKM strain exhibited higher GLP-1 stimulatory activity than its pasteurized counterpart and the marketed strain. The results suggest a strain-specific and viability-dependent modulation of GLP-1 secretion in human L-cells. ConclusionsThis study demonstrates that A. muciniphila VHAKM enhances GLP-1 secretion in a strain- and form-dependent manner, with live cells showing superior efficacy. These findings provide foundational insights for developing microbiome-targeted interventions to boost endogenous GLP-1 levels and improve metabolic health outcomes.

microbiology↗

bioRxiv2025

Multi-Cellular Human Liver Organoids Enable Complete Maturation of Induced Pluripotent Hepatocyte-like Cells Through Purely Endogenous Signals

Induced pluripotent stem cells (iPSCs) require further maturation before they can substitute primary human cells. Induced pluripotent stem cell hepatocyte-like cells (iHLCs) exhibit significantly lower hepatic functions than primary human hepatocytes (PHHs). Maturation of iHLCs has relied unsuccessfully on administering chemical cocktails in widely differing temporal patterns that are 106-fold higher in concentration than in vivo. Hence, there is no reproducible approach for iHLC maturation. We report the assembly of a multicellular 3D human liver organoid that recapitulates the in vivo hepatic microenvironment. Intra-and intercellular signaling between human hepatic cells and iHLCs results in their maturation. Within seven-days, iHLCs in organoids expressed markers of hepatocyte maturation that were statistically similar to PHHs including alphafetoprotein (AFP), hepatic nuclear factor (HNF)-4, and albumin. Ki67+ iHLCs decreased by 2-fold from Days 1 to 14. Expression of two cytochrome P450 (CYP) enzymes, CYP3A4 and CYP2E1, in iHLCs were statistically similar to PHHs by Days 7 and 14, respectively. Biotransformation of acetaminophen and ethanol were statistically similar to PHHs by Day 14. On Day 1, the concentration of endogenously secreted prostaglandin E2 (PGE2) was identical to values reported in adult humans. Over the 14-day culture, the concentrations of endogenously secreted hepatocyte growth factor (HGF) and Oncostatin M (OSM) increased until they were 26-36% of in vivo values. The organoids are secreting critically important maturation molecules that are similar to levels reported in healthy humans. These trends demonstrate how closely the multi-cellular organoids are emulating in vivo-like behavior while undergoing further maturation.

bioengineering↗

bioRxiv2022

Evaluation of Transfer Learning Methods for Detecting Alzheimer's Disease with Brain MRI

Deep neural networks show great promise for classifying brain diseases and making prognostic assessments based on neuroimaging data, but large, labeled training datasets are often required to achieve high predictive accuracy. Here we evaluated a range of transfer learning or pre-training strategies to create useful MRI representations for downstream tasks that lack large amounts of training data, such as Alzheimers disease (AD) classification. To test our proposed pre-training strategies, we analyzed 4,098 3D T1-weighted brain MRI scans from the Alzheimers Disease Neuroimaging Initiative (ADNI) cohort and independently validated with an out-of-distribution test set of 600 scans from the Open Access Series of Imaging Studies (OASIS3) cohort for detecting AD. First, we trained 3D and 2D convolutional neural network (CNN) architectures. We tested combinations of multiple pre-training strategies based on (1) supervised, (2) contrastive learning, and (3) self-supervised learning - using pre-training data within versus outside the MRI domain. In our experiments, the 3D CNN pre-trained with contrastive learning provided the best overall results - when fine-tuned on T1-weighted scans for AD classification - outperformed the baseline by 2.8% when trained with all of the training data from ADNI. We also show test performance as a function of the training dataset size and the chosen pre-training method. Transfer learning offered significant benefits in low data regimes, with a performance boost of 7.7%. When the pre-trained model was used for AD classification, we were able to visualize an improved clustering of test subjects diagnostic groups, as illustrated via a uniform manifold approximation (UMAP) projection of the high-dimensional model embedding space. Further, saliency maps indicate the additional activation regions in the brain scan using pre-training, that then maximally contributed towards the final prediction score.

neuroscience↗

bioRxiv2022

Cancer type-specific prioritization strategy for targetable dependencies developed from the DepMap profile of head and neck cancer

ObjectivesThe DepMap genome-wide loss of function CRISPR screens offer new insight into gene dependencies in HPV(-) head and neck squamous cell carcinoma (HNSCC) cell lines. We aimed to leverage this data to guide preclinical studies by cataloging novel targetable dependencies that are predicted to offer a useful therapeutic window. We also aimed to identify targets potentially representing synthetic lethalities by testing for associations between genetic alterations and gene dependency profile. MethodsDepMap was queried for gene probability and effect scores in cell lines from 87 tumors, including 63 HPV(-) HNSCCs plus 24 esophageal squamous cell carcinomas (ESCCs), which have comparable etiology, tissue or origin, and genetic profile to HNSCC. A probability score of [≥] 0.5 was used as the threshold for essentiality. Essential genes were selected for analysis by 4 criteria: (1) presence in [≥]10% cell lines, (2) lack of common essential designation by DepMap, (3) lack of predicted dependency in normal cell lineages, and (4) designation as druggable by the Drug-Gene Interaction Database. ResultsThe 143 genes meeting selection criteria had a median gene effect score of 0.56. Selection criteria captured targets of standard therapeutic agents of HNSCC including TYMS (5-FU), tubulin genes (taxanes), EGFR (cetuximab), plus additional known oncogenes like PIK3CA and ERBB3. Functional classification analysis showed enrichment of tyrosine kinases, serine/threonine kinases, RNA-binding proteins, and mitochondrial carriers. 90% of the 143 dependencies were not known oncogenes in the OncoKB Database. 10% of targets had inhibitors previously used in a non-HNSCC phase II trial, including 8 that have not yet been tested in cancer. The 13 genes with median gene effect scores greater than of PIK3CA and not well-studied in HNSCC were assigned highest priority, including DHRSX, MBTPS1, TDP2, FARS2, TMX2, RAB35, CFLAR, GPX4, SLC2A1, TP63, PKN2, MAP3K11, and TIPARP. A novel association was found between NOTCH1 mutation and increased TAP1 dependency. ConclusionsThe DepMap CRISPR screens capture well-studied targets in HNSCC as well as numerous genes without known roles in HNSCC or malignancy in general. Several of these targets have well-developed inhibitors that provide resources to guide preclinical studies. Association of some of the dependencies with known molecular subgroups in HNSCC may enhance use of cell line models to guide personalization of therapy.

cancer biology↗

bioRxiv2022

Human papilloma virus E6 regulates therapy responses in oropharyngeal cancer by repressing the PGC-1α/ERRα axis

Therapy with radiation plus cisplatin kills human papilloma virus-related (HPV+) oropharyngeal squamous cell carcinomas (OPSCCs) by increasing reactive oxygen species beyond cellular antioxidant capacity. To explore why some patients fail these standard treatments, we evaluated whether the variation in HPV oncoprotein levels among HPV+ OPSCCs impacts mitochondrial metabolism, a source of antioxidant capacity. In cell line and patient-derived xenograft models, levels of HPV full-length E6 (fl-E6) inversely correlated with oxidative phosphorylation, antioxidant capacity, and therapy resistance, and fl-E6 was the only HPV oncoprotein to display such correlation. Ectopically expressing fl-E6 in models with low levels reduced mitochondrial mass, depleted antioxidant capacity, and sensitized to therapy. In this setting, fl-E6 repressed the PGC-1/ERR pathway for mitochondrial biogenesis by reducing p53-dependent PGC-1 transcription. Concordant observations were made in three clinical cohorts, where expression of mitochondrial components was higher in tumors of patients with reduced survival. These tumors contained the lowest fl-E6 levels, highest p53 target gene expression, and an activated PGC-1/ERR pathway. Our findings demonstrate that E6 can potentiate treatment responses by depleting mitochondrial antioxidant capacity and provide evidence for low E6 negatively impacting patient survival. E6s interaction with the PGC-1/ERR axis has implications for predicting and targeting treatment resistance in OPSCC.

cancer biology↗

bioRxiv2021

A critical role for E2-p53 interaction during the human papillomavirus 16 life cycle

Human papillomaviruses (HPV) are causative agents in ano-genital and oral cancers; HPV16 is the most prevalent type detected in human cancers. The HPV16 E6 protein targets p53 for proteasomal degradation to facilitate proliferation of the HPV16 infected cell. However, in HPV16 immortalized cells E6 is predominantly spliced (E6*) and unable to degrade p53. Here we demonstrate that human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), and HPV16 positive oropharyngeal cancers, retain significant expression of p53. In addition, p53 levels can be increased in HPV16+ head and neck cancer cell lines following treatment with cisplatin. Introduction of full-length E6 into HFK+HPV16 resulted in attenuation of cellular growth (in hTERT immortalized HFK, E6 expression promoted enhanced proliferation). An understudied interaction is that between E2 and p53 and we investigated whether this was important for the viral life cycle. We generated mutant genomes with E2 unable to interact with p53 resulting in profound phenotypes in primary HFK. The mutant induced hyper-proliferation, but an ultimate arrest of cell growth; {beta}-galactosidase staining demonstrated increased senescence, and COMET assays showed increased DNA damage compared with HFK+HPV16 wild type cells. There was failure of the viral life cycle in organotypic rafts with the mutant HFK resulting in premature differentiation and reduced proliferation. The results indicate that the E2-p53 interaction is critical during the HPV16 life cycle, and that disruption of this interaction has anti-viral potential. We discuss potential mechanisms to explain these phenotypes. ImportanceHuman papillomaviruses are causative agents in around 5% of all cancers. There are currently no antivirals available to combat these infections and cancers, therefore it remains a priority to enhance our understanding of the HPV life cycle. Here we demonstrate that an interaction between the viral replication/transcription/segregation factor E2 and the tumor suppressor p53 is critical for the HPV16 life cycle. HPV16 immortalized cells retain significant expression of p53, and the critical role for the E2-p53 interaction demonstrates why this is the case. If the E2-p53 interaction is disrupted then HPV16 immortalized cells fail to proliferate, have enhanced DNA damage and senescence, and there is premature differentiation during the viral life cycle. Results suggest that targeting the E2-p53 interaction would have therapeutic benefits, potentially attenuating the spread of HPV16.

molecular biology↗

bioRxiv2019

Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models

Therapeutic innovation for human papilloma virus-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) is impaired by inadequate biomarkers and preclinical models. This study addressed both limitations using the largest panel of HPV+ HNSCC patient-derived xenografts (PDXs) and organoids described to date. Whole exome profiles of the PDXs were compared to those of HPV+ human tumors and cell lines, and genetic features of the models were analyzed relative to their growth properties and outcomes of their patients of origin. PDX engraftment enriched for negatively prognostic NOTCH1 mutations while preserving multiple features lost in existing cell lines, including PIK3CA mutations, TRAF3 deletion, and absence of EGFR amplification. Observation of more mutations in faster-growing models facilitated identification of an association between mutational burden and local progression in both HPV+ and HPV-HNSCCs. Reduced E7 and p16INK4A levels found in a PDX from a lethal case led to detection of a similar profile among recurrent HPV+ HNSCCs in two patient cohorts, where low E2F target gene expression downstream of E7 predicted recurrence and mortality. Our findings bridge a critical gap in preclinical models for HPV+ HNSCCs and simultaneously reveal novel applications for mutational burden and E2F target dysregulation in biomarker development.

cancer biology↗