Biology subjects

Rakshit, A.

Publications and source records attributed to Rakshit, A..

3 recordsLinked to original sources

bioRxiv2026

Metal homeostasis is remodeled in response to different quiescence triggers

Cells can enter a reversible non-proliferative state called quiescence either spontaneously or in response to nutrient deprivations. Metal ions are essential nutrients and play wide-ranging regulatory and signaling roles in biological processes. We previously showed that zinc is an essential nutrient for the mammalian cell cycle as zinc deprivation drives cells into quiescence, and this quiescent state is associated with changes in iron, copper, and manganese, suggesting broad remodeling of metal homeostasis. Here we examine whether metal remodeling is a general feature of quiescence by inducing quiescence via different triggers (zinc deficiency, serum starvation, and growth factor withdrawal) in MCF10A cells. Fluorescence microscopy and elemental analysis reveal significant trigger-dependent changes in the labile and total metal pools of quiescent cells. To gain insight into these differences, we carried out RNA sequencing and differential expression analysis, focusing on metal associated, metal regulatory, and metal homeostasis genes. While core quiescence pathways are shared across triggers, quiescence states remain molecularly distinct. A significant percent of 2458 metal homeostasis annotated genes are differentially expressed including 55% in starvation-induced quiescence, 50% in zinc deficiency-induced quiescence and 21% in growth factor withdrawal-induced quiescence. Our results also showed unique alteration of genes involved in major metal dependent processes including antioxidant activity, oxidative phosphorylation, heme metabolism, and chromatin accessibility in different quiescence states. Overall, this work demonstrates that metal homeostasis is systematically rewired during cellular quiescence with associated effects on genes that regulate critical biological processes. Significance StatementCells constantly evaluate their nutrient and energy status and integrate these signals into proliferation-quiescence decisions. Quiescence prevents cells from passing damage to daughter cells. Metals are essential micronutrients for biological processes. While limitation of zinc can drive cells into quiescence and alter other metals, how metals are remodeled and whether this is a common feature of quiescence was unknown. Here we examined three quiescence triggers by modifying growth media and serum, the primary source of metals. We report significant changes in labile and total Cu, Fe, Zn and Mn pools, and metal associated genes in response to distinct quiescence triggers. These changes converge on mitochondrial function, cellular antioxidant activity, and heme biosynthesis in a trigger specific manner.

cell biology↗

bioRxiv2026

OPM-FLUX: A Pipeline for OPM MEG Data Analysis

Optically pumped magnetometer-based magnetoencephalography (OPM-MEG) has recently emerged as a powerful neuroimaging approach in cognitive neuroscience, extending beyond the limitations of conventional cryogenic systems with greater experimental flexibility and wearable recording. Despite these advantages, standardised data analysis frameworks specifically tailored to OPM technology are still lacking, leading to variability in processing choices and reduced reproducibility across laboratories and hardware platforms. We introduce OPM-FLUX, a comprehensive and fully documented end-to-end analysis pipeline developed for OPM-MEG data. The pipeline defines a clear sequence of preprocessing, noise suppression, artifact handling, spectral analysis, evoked response analysis along with recommended parameter settings. It also includes source reconstruction to identify where in the brain the signals originate. In addition, OPM-FLUX supports multivariate pattern analysis (MVPA), enabling time-resolved decoding of cognitive processes from sensor level data. OPM-FLUX is implemented in MNE-Python and distributed as interactive Jupyter Notebooks that combine executable code with detailed methodological explanations and graphical outputs. The pipeline further provides standardized reporting templates and a data acquisition Standard Operating Procedure to facilitate preregistration, consistent documentation, and standard practices across research sites. The workflow is demonstrated using openly available datasets acquired from both Cerca/QuSpin and FieldLine OPM systems during a visuospatial attention paradigm that modulates alpha, beta, and gamma oscillations and elicits event-related responses. By supporting multiple OPM platforms and promoting consistent methodological choices, OPM-FLUX enhances transparency, comparability, and replication in OPM-MEG research. The pipeline also serves as an educational resource for students and researchers entering the field and is designed to evolve alongside ongoing technological and methodological advances in OPM-based brain imaging.

neuroscience↗

bioRxiv2025

Systematic characterization of zinc in a series of breast cancer cell lines reveals significant changes in zinc homeostasis

An optimal amount of labile zinc (Zn2+) is essential for proliferation of human cells, where Zn2+ levels that are too high or too low cause cell cycle exit. Tumors of the breast have been characterized by high levels of total Zn2+. Given the role of Zn2+ in proliferation of human cells and elevation of zinc in breast cancer tumors, we examined the concentration of total and labile Zn2+ across a panel of 5 breast cancer cell lines, compared to the normal MCF10A cell line. We found that three cell lines (MDA-MB-231, MDA-MB-157, and SK-Br-3) showed elevated labile Zn2+ in the cytosol, while T-47D showed significantly lower Zn2+, and MCF7 showed no change compared to MCF10A cells. There was no change in total Zn2+ across the cell lines, as measured by ICP-MS, but we did observe a difference in the cells ability to accumulate Zn2+ when Zn2+ in the media was elevated. Therefore, we examined how proliferation of each cell line was affected by increases and decreases in the media. We found striking differences, where three cancer cell lines (MDA-MB-231, MDA-MB-157, and MCF7) showed robust proliferation in high Zn2+ at concentrations that killed MCF10A, T-47D, and SK-Br-3 cells. We also discovered that 4 of the 5 cancer cell lines demonstrate compromised proliferation and increased cell death in low Zn2+, suggesting these cells may be addicted to Zn2+. Overall, our study suggests significant differences in Zn2+ homeostasis and regulation in different types of breast cancer cells, with consequences for both proliferation and cell viability.

cell biology↗