Biology subjects

Varas, M.

Publications and source records attributed to Varas, M..

3 recordsLinked to original sources

bioRxiv2025

Decoding calcium oscillation frequency in transcriptional regulation

Cells continuously experience fluctuating intracellular calcium (Ca{superscript 2}) signals that orchestrate diverse processes such as transcription, proliferation, and apoptosis. Temporal features of Ca{superscript 2} dynamics, including oscillation frequency, are hypothesized to encode information, allowing cells to discriminate between relevant and stochastic signals. However, the mechanisms of frequency decoding and their transcriptional consequences remain incompletely understood. To address this, we investigated how defined Ca{superscript 2} oscillation frequencies are translated into signaling cascades and gene expression programs in human non-excitable cells. Using optogenetic control of melanopsin-mediated Ca{superscript 2} influx, we induced slow (8 mHz) or fast (15 mHz) oscillations with identical single-pulse kinetics to isolate the effect of frequency. We found that TNF and IL8 transcription via NF-{kappa}B displayed sigmoidal frequency dependence, strictly requiring regular periodic stimulation, while random or low-frequency inputs with equal cumulative Ca{superscript 2} exposure were ineffective. Bulk RNA sequencing revealed a MYC-centered transcriptional response, with 116 of 215 differentially expressed genes predicted as MYC targets, despite unchanged MYC mRNA levels. Label-free phosphoproteomics identified PRKDC, CHEK2 and ATM as the top upstream kinases, forming a network linking Ca{superscript 2} oscillations to cell cycle and stress signaling. These findings demonstrate that cells can decode Ca{superscript 2} oscillation frequency through a multi-kinase network that tunes transcription via NF-{kappa}B and MYC, providing mechanistic insight into how temporal dynamics of second messengers shape cellular decision-making.

cell biology↗

bioRxiv2024

Tumor-derived hypoxic small extracellular vesicles promote endothelial cell migration and tube formation via ALS2/Rab5/β-catenin signaling

Tumor hypoxia has been associated with cancer progression, angiogenesis, and metastasis via modifications in the release and cargo composition of extracellular vesicles secreted by tumor cells. Indeed, hypoxic extracellular vesicles are known to trigger a variety of angiogenic responses via different mechanisms. We recently showed that hypoxia promotes endosomal signaling in tumor cells via HIF-1-dependent induction of the guanine exchange factor ALS2, which activates Rab5, leading to downstream events involved in cell migration and invasion. Since Rab5-dependent signaling is required for endothelial cell migration and angiogenesis, we explored the possibility that hypoxia promotes the release of small extracellular vesicles containing ALS2, which in turn activate Rab5 in recipient endothelial cells leading to pro-angiogenic properties. In doing so, we found that hypoxia promoted ALS2 expression and incorporation as cargo within small extracellular vesicles, leading to subsequent transfer to recipient endothelial cells, promoting cell migration, tube formation and downstream Rab5 activation. Consequently, ALS2-containing small extracellular vesicles increased early endosome size and number in recipient endothelial cells, which was followed by subsequent sequestration of components of the {beta}-catenin destruction complex within endosomal compartments, leading to stabilization and nuclear localization of {beta}-catenin. These events converged in the expression of {beta}-catenin target genes involved in angiogenesis. Knockdown of ALS2 in donor-tumor cells, which precluded its incorporation into small extracellular vesicles, prevented Rab5-downstream events and endothelial cell responses, which depended on Rab5 activity and guanine exchange factor activity of ALS2. These findings indicate that vesicular ALS2, secreted in hypoxia, promotes endothelial cell events leading to angiogenesis. Finally, these events might explain how tumor angiogenesis proceeds in hypoxic conditions.

cell biology↗

bioRxiv2022

Population genomics, resistance, pathogenic potential, and mobile genetic elements of carbapenem-resistant Klebsiella pneumoniae causing infections in Chile

Multidrug and carbapenem-resistant K. pneumoniae (CR-Kp) are considered critical threats to global health and key traffickers of resistance genes to other pathogens. In Chile, although a sustained increase in CR-Kp infections has been observed, few strains have been described at the genomic level, lacking molecular details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial resistance and performed a comparative genomics analysis of ten CR-Kp isolates from the Chilean surveillance of carbapenem-resistant Enterobacteriaceae. High resistance to most of the antibiotics tested was observed among the isolates, five ST25, three ST11, one ST45, and one ST505, which harbored a total of 44 plasmids, many of them predicted to be conjugative and carrying genes conferring resistance to a variety of antibiotic, metals, and disinfectants. Ten plasmids encoding either KPC-2, NDM-1, or NDM-7 carbapenemases were characterized, including novel plasmids with increased resistance gene load and a novel genetic environment for blaKPC-2 gene. This corresponds to the first report of ST25 and ST45 Kp producing NDM-7 in South America, and of an ST505 CR-Kp worldwide, producing both NDM-7 and KPC-2. Moreover, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for the detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of K. pneumoniae in Chile and South America.

microbiology↗