Biology subjects

Ghosh, P. K.

Publications and source records attributed to Ghosh, P. K..

3 recordsLinked to original sources

bioRxiv2023

p53 translational isoform {triangleup}40p53 orchestrates cellular SGSH levels via microRNA-4671-5p to modulate cell cycle

{Delta}40p53, the only translational isoform of p53, modulates the full-length p53 (FLp53) activity and independently regulates targets such as the miR-186-5p-YY1 axis. To identify additional miRNAs regulated by {Delta}40p53, we performed small RNA sequencing. We found that overexpression of {Delta}40p53, but not FLp53, significantly downregulated miR-4671-5p. Expression of both isoforms at varying ratios revealed that miR-4671-5p may be modulated by FLp53 in a {Delta}40p53-dependent manner. In silico analysis identified SGSH (N-sulfoglucosamine sulfohydrolase) as a potential miR-4671-5p target. SGSH expression showed inverse correlation with miR-4671-5p in cancer datasets and prognostic significance. SGSH mRNA and protein levels were reduced upon miR-4671-5p overexpression or si{Delta}40p53 treatment, confirming regulatory linkage. Functionally, miR-4671-5p overexpression induced intra-S-phase cell cycle arrest, implicating SGSH in cell cycle regulation. These results reveal a novel {Delta}40p53-miR-4671-5p-SGSH axis that impacts cell cycle progression and may contribute to cancer outcomes. Our findings highlight the distinct regulatory role of {Delta}40p53, independent of FLp53, in maintaining cellular and metabolic homeostasis via miRNA-mediated mechanisms.

molecular biology↗

bioRxiv2022

A machine-learning tool to identify bistable states from calcium imaging data

Mapping neuronal activation using calcium imaging in vivo during behavioral tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities since action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. While a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons (PNs) in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In this manuscript we develop a tool, CaMLSort which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analyzing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviors. Key Points SummaryCalcium imaging - the gold standard of inferring neuronal activity - does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool offers a new way of analyzing calcium imaging data from populations of bistable neurons, thereby facilitating our understanding of how these neurons carry out their functions in a circuit.

neuroscience↗

bioRxiv2022

Tumor cell-intrinsic HFE drives glioblastoma growth

BackgroundGlioblastoma (GBM) tumor cells modulate expression of iron-associated genes to enhance iron uptake from the surrounding microenvironment, driving proliferation and tumor growth. The homeostatic iron regulator (HFE) gene, encoding the iron sensing HFE protein, is upregulated in GBM and correlates with poor survival outcomes. However, the molecular mechanisms underlying these observations remain unclear. Identification of pathways for targeting iron dependence in GBM tumors is therefore a critical area of investigation. MethodsWe interrogated the impact of cell-intrinsic Hfe expression on proliferation and tumor growth through genetic loss and gain of function approaches in syngeneic mouse glioma models. We determined the expression of iron-associated genes and their relationship with survival in GBM using public datasets and identified differentially expressed pathways in Hfe knockdown cells through Nanostring transcriptional profiling. ResultsLoss of Hfe induced apoptotic cell death in vitro and inhibited tumor growth in vivo while overexpression of Hfe accelerated both proliferation and tumor growth. Analysis of iron gene signatures in Hfe knockdown cells revealed alterations in the expression of several iron-associated genes, suggesting global disruption of intracellular iron homeostasis. Analyzing differentially expressed pathways further identified oxidative stress as the top pathway upregulated with Hfe loss. Enhanced 55Fe uptake and generation of reactive oxygen species (ROS) were found with Hfe knockdown, implicating toxic iron overload resulting in apoptotic cell death. ConclusionsCollectively, these findings identify a novel role for HFE in regulating iron homeostasis in GBM tumors and provide a potential avenue for future therapeutic development. Key PointsO_LIHFE is an iron sensor that is upregulated in GBM and negatively impacts survival. C_LIO_LIHFE overexpression drives proliferation and tumor growth in vivo. C_LIO_LILoss of HFE increases production of reactive oxygen species and induces apoptosis, extending survival in vivo. C_LI Importance of StudyDysregulation of iron metabolism is an important feature of GBM contributing to tumor growth and negatively impacting survival. The identification of key iron regulators controlling this process is therefore important for therapeutic targeting. We identify HFE as an important regulator of iron homeostasis in GBM and suggest a role for sexual dimorphism in HFE-mediated tumor iron regulation that ultimately results in differential survival outcomes. Our findings demonstrate that HFE drives tumor cell proliferation and survival in GBM and may be a viable target for modulating tumor iron flux and inducing apoptosis in tumor cells.

cancer biology↗