Biology subjects

Raju, R. M.

Publications and source records attributed to Raju, R. M..

3 recordsLinked to original sources

bioRxiv2024

Maternal obesity and offspring neurodevelopment are associated with hypoxic gene expression in term human placenta

One third of women in the United States are affected by obesity during pregnancy. Maternal obesity (MO) is associated with an increased risk of neurodevelopmental and metabolic disorders in the offspring. The placenta, located at the maternal-fetal interface, is a key organ determining fetal development and likely contributes to programming of long-term offspring health. We profiled the term placental transcriptome in humans (pre-pregnancy BMI 35+ [MO condition] or 18.5-25 [lean condition]) using single-nucleus RNA-seq to compare expression profiles in MO versus lean conditions, and to reveal potential mechanisms underlying offspring disease risk. We recovered 62,864 nuclei of high quality from 10 samples each from the maternal-facing and fetal-facing sides of the placenta. On both sides in several cell types, MO was associated with upregulation of hypoxia response genes. On the maternal-facing side only, hypoxia gene expression was associated with offspring neurodevelopmental measures, in Gen3G, an independent pregnancy cohort with bulk placental tissue RNA-seq. We leveraged Gen3G to determine genes that correlated with impaired neurodevelopment and found these genes to be most highly expressed in extravillous trophoblasts (EVTs). EVTs further showed the strongest correlation between neurodevelopment impairment gene scores (NDIGSs) and the hypoxia gene score. We reanalyzed gene expression of cultured EVTs, and found increased NDIGSs associated with exposure to hypoxia. Among EVTs, accounting for the hypoxia gene score attenuated 44% of the association between BMI and NDIGSs. These data suggest that hypoxia in EVTs may be a key process in the neurodevelopmental programming of fetal exposure to MO.

genomics↗

bioRxiv2023

Benchmarking whole exome sequencing pipeline for predicting pathogenic variants of significance

Benchmarking whole exome pipelines is crucial for evaluating and comparing their performance in variant calling and clinical significance annotation. It enables researchers and clinicians to assess the accuracy, sensitivity, and specificity of different pipelines and identify the most effective and reliable ones. In this study, we evaluated and compared the performance of our in-house consensus exome pipeline with a widely recognized gold standard Genome Analysis Toolkit (GATK) pipeline. Four datasets were used for evaluation, three 1000 Genome Project (1KGP) datasets and one Prostate cancer (PCa) Sample. The consensus pipeline consistently demonstrated a higher average transition-to-transversion (Ti/Tv) ratio, indicating enhanced precision in identifying single nucleotide variant (SNV) calls. This suggests that the consensus pipeline excels in effectively discerning true genetic variations from sequencing artefacts, particularly in the context of exome sequencing. Additionally, the pipeline exhibited increased sensitivity in detecting pathogenic and likely pathogenic variants in the PCa sample, further highlighting its efficacy in identifying clinically relevant variants. We also conducted a trio exome analysis with the use of two trio pipelines, viz. VarScan Trio and GATK joint calling pipelines on our erstwhile Congenital Pouch Colon (CPC) samples from our rare disease cohort which we published earlier and found that the GATK predicted a significantly higher number of variants compared to VarScan. From our pipeline, viz. CONVEX: Consensus Variant Pipeline for Exome Analysis we developed, our study demonstrates a large potential for trio-variant calling analysis paving the way for precision medicine. We discuss the impending benchmark results using the CONVEX.

bioinformatics↗

bioRxiv2022

Social deficits induced by pervasive environmental stressors are prevented by microbial or dopaminergic modulation

Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglia and dopaminergic circuits in the brain, along with changes in the structure of the gut epithelium and microbiome. Importantly, DEP/MS-induced social deficits in males are prevented by shifting the gut microbiome by cross-fostering at birth and reversed by chemogenetic activation of the dopamine system.

neuroscience↗