Biology subjects

Sud, R.

Publications and source records attributed to Sud, R..

3 recordsLinked to original sources

bioRxiv2023

Proteomic analysis reveals APOE isoform-specific regulation of ribosomes in neural precursor cells

ApoE4 isoform contributes to increased risk for Alzheimers Disease (AD) over the life course of individuals. Much remains unknown about the biological pathways that connect APOE4 genotype with the development of pathology that eventually leads to AD, nor do we know how early in life these cellular alterations begin. To answer these questions, we derived neural precursor cells (NPCs) from induced pluripotent stem cells (IPSCs) that were CRISPR-edited at the APOE locus. We intended to characterize the protein expression landscape in the NPCs subsequent to targeted deletion of E4 from a parent IPSC line of APOE3/4 genotype. Differentially expressed proteins (DEPs) following mass spectrometric analysis were determined from the protein abundance fold change values obtained for each protein. Proteins which showed >1.5-fold difference with FDR adjusted P-value < 0.05 were considered differentially expressed. DEPs were mapped to the STRING database (v11.5) for retrieval of interacting proteins and functional enrichment. CRISPR-editing of E4 from the parent line revealed 98 differential expressed proteins. Of these, 54 were upregulated, and 44 were downregulated. Further analysis of the DEPs via STRING database showed that these changes primarily affect pathways linked to RNA processing, plasma membrane repair, and cytoskeleton organization. Indeed, we find the effects of E4 extend beyond proteins considered central to AD pathology. Knowing more about the protein interactions regulated by ApoE, in an isoform-specific manner, can reveal new mechanistic insights into development of AD.

neuroscience↗

bioRxiv2022

A replication study on key neurodevelopmental pathways affected by valproate treatment ofneural precursor cells

Adults with bipolar disorder or epileptic seizures are commonly prescribed sodium valproate. In utero exposure to this drug is linked to a multitude of defects in normal brain development, from neural tube defects to autism spectrum disorders. During the course of brain development, neural precursor cells (NPCs) give rise to neurons and glia, and therefore to understand the valproate-induced defects, it is crucial to understand its effect on NPCs. Two NPC lines, both derived from healthy individuals, were used for all experiments. Cells were treated with 0.7mM valproate for one week. Fresh media (+/- drug) was replenished every alternate day. RNA was extracted on day 7 of drug treatment, and transcriptomics performed. All experiments were performed in biological replicates. Genes that showed >1-fold difference (with FDR adjusted q-value [≤] 0.05) were considered differentially expressed. We further investigated the interacting partners of the differentially expressed genes using PINOT, as well as cellular pathways using DAVID. Our primary endpoint of analysis were genes that were differentially expressed (DEGs) with valproate treatment in both the NPC lines used. We found 21 such genes that were common in the two lines. PINOT revealed 504 interacting partners of the DEGs. Functional annotation analysis showed significant enrichment of four signaling pathways - Wnt, Notch, Rho-GTPase and PI3K-AKT. While the role of Rho-GTPase is a novel finding, we have replicated previously reported findings on Wnt, Notch and PI3K-Akt pathways, which further strengthens their role in mediating neurodevelopmental anomalies.

neuroscience↗

bioRxiv2019

Studying cellular functions in bipolar disorder: Are there specific predictors of lithium response?

BackgroundLithium is the first-line mood stabilizer for the treatment of bipolar disorder (BD). In order to interrogate cellular phenotypes related to disease and lithium treatment response, this study used neural precursor cells (NPCs) and lymphoblastoid cell lines (LCLs) from BD patients who are well characterized for clinical lithium response.\n\nMethodsBD patients diagnosed according to the DSM-IV criteria; were recruited from the outpatient services of the National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India. Clinical lithium response was assessed using the \"Alda scale\" and \"NIMH Retrospective Life chart method\". The controls were ethnically matched healthy subjects with no family history of neuropsychiatric illness. NPCs from two BD patients from the same family who clearly differed in their clinical response to lithium were chosen, and compared with healthy population controls. Whole transcriptome sequencing (RNA-Seq) and analysis were performed, with and without in vitro lithium (1mM for 7 days). In addition, mitochondrial membrane potential (MMP), cell viability and cell proliferation parameters were examined. Experiments were also performed in 25 LCLs from BD patients (16 lithium responders and 9 lithium non-responders), and 12 healthy control LCLs, to evaluate them in a system amenable to clinical translation.\n\nResultsRNA-Sequencing and analysis did not reveal differences in NPCs on in vitro lithium treatment. MMP was lower in BD, both in NPCs and LCLs; reversal with in vitro lithium happened only in LCLs and was unrelated to lithium response. Cell proliferation was higher in BD compared to controls, and there was no change on lithium addition. Cell viability assays indicated greater cell death in BD; which could only be rescued in LCLs of clinical lithium responders. The latter finding was associated with enhanced BCL2 and GSK3B expression with in vitro lithium.\n\nDiscussionOverall, our study findings indicate that there are cellular phenotypes related to the disease (mitochondrial potential, cell proliferation) in NPCs and LCLs. We also observed clinical lithium response related phenotypes (cell viability, BCL2/ GSK3B expression) in LCLs. The next step would be to evaluate a larger set of PBMCs from clinical lithium response groups of BD to derive cellular phenotypes related to direct clinical application.

neuroscience↗