Biology subjects

Cools, M.

Publications and source records attributed to Cools, M..

3 recordsLinked to original sources

bioRxiv2025

Vsb1, Ypq1 and Ypq2 control dynamic cationic amino acid storage in the yeast vacuole

Although the yeast vacuole plays a crucial role in storing and mobilizing cationic amino acids (CAA), CAA transport at the vacuolar membrane remains poorly understood. Here, by combining analysis of CAA pools, uptake and permeabilization assays, we establish Vsb1 as the principal vacuolar lysine transporter, enabling its strong accumulation in the vacuole while mitigating its toxicity. We further show that, although Ypq1 can mediate proton-independent vacuolar lysine import, it mainly functions as a lysine exporter necessary for lysine mobilization under conditions of lysine scarcity and downregulated as lysine stores are exhausted. Using quantitative models based on dynamic metabolic labeling, we further show that, surprisingly, in growing cells, CAA rapidly exchange between vacuolar and cytosolic compartments, a process involving the export activity of Ypq1 and its paralogue Ypq2, specific for lysine and arginine, respectively. Together, our findings reveal the unexpectedly complex function of Vsb1 and Ypq1/2 as the key transporters mediating dynamic vacuolar CAA storage. 40-word summaryZaremba et al. characterize Vsb1 as the main yeast vacuolar lysine importer and Ypq1/2 as bi- directional vacuolar transporters of lysine and arginine. Their study highlights the role of vacuolar transporters in regulating cationic amino acid homeostasis under fluctuating nutrient availability.

cell biology↗

bioRxiv2025

A laser capture microdissection-based method for high-sensitivity transcriptomics from archived FFPE tissue slides with single-cell resolution using LCM-FFPEseq

Understanding gene expression within its spatial context is essential for unravelling biological processes. Laser Capture Microdissection (LCM) has emerged as a transformative technology, enabling targeted isolation of individual cells or regions from tissue sections while preserving spatial context. However, its application to formalin-fixed, paraffin-embedded (FFPE) tissues has been limited by RNA degradation, leaving the vast repository of clinical FFPE samples underutilized. To address this, we introduce LCM-FFPEseq, a novel method combining LCM with the advanced Smart-seq3xpress protocol and FFPE-specific adaptations for spatial transcriptomics of FFPE sections. Unlike traditional protocols requiring thousands of cells to generate high-quality libraries, LCM-FFPEseq achieves high sensitivity, reproducibility, and transcript coverage. With as few as 30 FFPE-embedded K562 cells and Sertoli cells, we detected over 14,000 protein-coding genes per sample, with no substantial gains when a higher number of cells were isolated. Even individual LCM-isolated cells yielded an average of 7,353 or 6,490 protein-coding genes per K562 or Sertoli single cell, respectively. To demonstrate its clinical utility, we applied LCM-FFPEseq to archived testicular FFPE samples from transgender females receiving gender-affirming hormone therapy. Transcriptomic profiling of isolated seminiferous tubules revealed tubular hyalinization to be associated with greater upregulation of extracellular matrix remodelling and inflammatory pathways, alongside stronger downregulation of spermatogenesis-associated pathways. These findings suggest that testicular fibrosis and/or tubular hyalinization may contribute to germ cell loss following inappropriate hormonal exposure. By enabling high-resolution transcriptomics in archived FFPE samples, LCM-FFPEseq unlocks new possibilities for investigating rare cell types, spatial heterogeneity, and therapy-induced tissue remodelling in vast FFPE repositories.

genomics↗

bioRxiv2025

Dynamic Causal White Matter Atlas of Auditory and Visual Speech Networks at Millisecond Resolution: Intracranial Evidence from 125 Patients

Background and ObjectivesSince the era of Penfield, invasive neurophysiology has laid a lasting foundation for functional neuroscience by elucidating brain regions necessary for speech. However, whole-brain investigations have yet to distinguish the millisecond-scale dynamics and specific white matter pathways that support rapid naming in the auditory and visual domains. MethodsIn this observational study, we constructed a whole-brain Dynamic Causal Tractography atlas using intracranial neurophysiological data from 125 neurosurgical patients. The resulting video atlas captured local cortical high-gamma activity and cortico-cortical coactivation via white matter tracts during rapid and delayed auditory and picture naming. Direct electrical stimulation was employed to assess the causal significance of the observed neural dynamics. ResultsThe atlas revealed white matter coactivation intensity patterns at specific 5-millisecond time windows that best aligned with sensorimotor and language symptoms elicited by electrical stimulation (Spearmans {rho} = 0.58-0.91; p = 4.8 x 10cc to 1.6 x 10c{superscript 2}c). Rapid auditory naming was associated with deactivation of the right rostral middle frontal gyrus and increased coactivation along the left arcuate fasciculus, linked to stimulation-induced receptive and expressive aphasia. In contrast, delayed auditory naming correlated with a late surge in bifrontal coactivation. Rapid picture naming involved early coactivation between cortices connected via the bilateral inferior longitudinal fasciculi--associated with stimulation-induced visual distortions--coinciding with transient co-inactivation of Brocas area. DiscussionThese findings delineate dissociable white matter-mediated mechanisms supporting rapid naming in the auditory and visual domains. Reduced inhibitory monitoring by the right dorsolateral prefrontal cortex may facilitate efficient lexical retrieval via left perisylvian pathways during auditory naming. In contrast, excessive bifrontal interaction may underlie delayed auditory naming. Rapid visual object recognition appears to rely on early occipitotemporal coactivation with minimal involvement of Brocas area. The resulting atlas--accompanied by a publicly available dataset (61.2 GB) and analysis code--serves as a valuable resource for students and trainees studying the network dynamics underlying speech, as well as for presurgical language mapping in patients undergoing cortical or subcortical intervention.

neuroscience↗