Biology subjects

Fridman, D.

Publications and source records attributed to Fridman, D..

4 recordsLinked to original sources

bioRxiv2025

Membrane potential and feedback dynamics regulate CatSper-mediated progesterone signaling in human sperm

Activation of the sperm-specific Ca2+ channel CatSper by progesterone evokes rapid changes in intracellular Ca2+ in human sperm that are required for fertilization. However, the mechanisms regulating the progesterone-induced Ca2+ signals have remained elusive. Here, we used quantitative kinetic fluorimetry with fast voltage-sensitive fluorescent indicators to investigate how progesterone affects the membrane potential (Vm) of human sperm. Additionally, we employed the FASTM technique to simultaneously record at millisecond time resolution changes in both Vm and intracellular Ca2+. We show that progesterone evokes a rapid pulse-like depolarization and repolarization. The depolarization is caused by Ca2+ influx through CatSper, which pulls Vm away from a resting membrane potential (Vrest) of -65 mV set by the sperm-specific K+ channel Slo3. We further show that Vm- and Ca2+-dependent mechanisms limit the CatSper-mediated Ca2+ influx, thereby promoting repolarization and enabling K+ efflux through Slo3 channels to restore Vrest. Our findings demonstrate that non-genomic progesterone signaling in human sperm is regulated by negative feedback on CatSper and involves a dynamic interplay between CatSper and Slo3 in controlling Vm. We anticipate that our novel kinetic, quantitative Vm recording and Vm/Ca2+-multiplexing techniques will reveal additional molecular mechanisms underlying CatSper-mediated Ca2+ signaling in human sperm both in health and disease.

cell biology↗

bioRxiv2024

Deciphering rapid cell signaling and control of cell motility by reverse opto-chemical engineering

Cells transform complex environmental stimuli into physiological responses. For time-varying stimuli or motile cells, the perception of the environment depends on the temporal stimulus pattern and cell motion, respectively. Here we report a concept, "reverse optochemical engineering" (ROCE), that uses temporal light patterns and photo-triggers to expose cells to virtual sensory landscapes while recording in real time their physiological responses and motor behavior. We studied cyclic-nucleotide signaling in cell lines, sperm, olfactory neurons, and cardiomyocytes. The technique can be employed for remote control of motility by light. We reprogrammed sperm from a chemotactic to a phototactic cell that is attracted towards light. The method provides new opportunities to decipher the mechanisms and signaling molecules underlying rapid cellular computations, and thus reveal the wire diagram of cellular networks.

biophysics↗

bioRxiv2023

Assessing transcriptomic re-identification risks using discriminative sequence models

Gene expression data provides molecular insights into the functional impact of genetic variation, for example through expression quantitative trait loci (eQTL). With an improving understanding of the association between genotypes and gene expression comes a greater concern that gene expression profiles could be matched to genotype profiles of the same individuals in another dataset, known as a linking attack. Prior works demonstrating such a risk could analyze only a fraction of eQTLs that are independent due to restrictive model assumptions, leaving the full extent of this risk incompletely understood. To address this challenge, we introduce the discriminative sequence model (DSM), a novel probabilistic framework for predicting a sequence of genotypes based on gene expression data. By modeling the joint distribution over all known eQTLs in a genomic region, DSM improves the power of linking attacks with necessary calibration for linkage disequilibrium and redundant predictive signals. We demonstrate greater linking accuracy of DSM compared to existing approaches across a range of attack scenarios and datasets including up to 22K individuals, suggesting that DSM helps uncover a substantial additional risk overlooked by previous studies. Our work provides a unified framework for assessing the privacy risks of sharing diverse omics datasets beyond transcriptomics.

genomics↗

bioRxiv2021

Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing - RADD-Seq

Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, like cancer, and assists in monitoring their progression and prognosis. However, genome-wide maps of DNA damage distribution are challenging to produce. Here we describe the localization of DNA damage and repair loci by Repair Assisted Damage Detection sequencing - RADD-Seq. Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of oxidative DNA damage loci before and after repair. Oxidative lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and capable of identifying genomic hotspots prone to mutation.

genomics↗