Biology subjects

Lehmann, N.

Publications and source records attributed to Lehmann, N..

7 recordsLinked to original sources

bioRxiv2024

Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells

Targeted kinase inhibitors are a cornerstone of cancer therapy, but their success is often hindered by the complexity of cellular signaling networks that can lead to resistance. Overcoming this challenge necessitates a deep understanding of cellular signaling responses. While standard global phosphoproteomics offers extensive insights, lengthy processing times, the complexity of data interpretation, and frequent omission of crucial phosphorylation sites limit its utility. Here, we combine data-independent acquisition (DIA) with spike-in of synthetic heavy stable isotope-labeled phosphopeptides to facilitate the targeted detection of particularly informative phosphorylation sites. Our spike-in enhanced detection in DIA (SPIED-DIA) approach integrates the improved sensitivity of spike-in-based targeted detection with the discovery potential of global phosphoproteomics into a simple workflow. We employed this method to investigate synergistic signaling responses in colorectal cancer cell lines following MEK inhibition. Our findings highlight that combining MEK inhibition with growth factor stimulation synergistically activates JNK signaling in HCT116 cells. This synergy emphasizes the therapeutic potential of concurrently targeting MEK and JNK pathways, as evidenced by the significantly impaired growth of HCT116 cells when treated with both inhibitors. Our results demonstrate that SPIED-DIA effectively identifies synergistic signaling responses in colorectal cancer cells, presenting a valuable tool for uncovering new therapeutic targets and strategies in cancer treatment.

systems biology↗

bioRxiv2023

Online stimulation of the prefrontal cortex during practice increases motor variability and modulates later cognitive transfer: a randomized, double-blinded and sham-controlled tDCS study

BackgroundThe benefits of learning a motor skill extend to improved task-specific cognitive abilities. The mechanistic underpinnings of this motor-cognition relationship potentially rely on overlapping neural resources involved in both processes, an assumption lacking causal evidence. ObjectivesWe hypothesize that interfering with prefrontal networks would affect concurrent motor skill performance, long-term learning and associated cognitive functions dependent on similar networks (transfer). MethodsWe conducted a randomized, double-blinded, sham-controlled brain stimulation study using transcranial direct current stimulation (tDCS) in young adults spanning over three weeks to assess the role of the prefrontal regions in learning a complex balance task and long-term cognitive performance. ResultsBalance training combined with active tDCS led to higher performance variability in the trained task as compared to the sham group, without affecting the learning rate. Furthermore, active tDCS also positively impacted performance in untrained motor and cognitive tasks. ConclusionThe findings of this study help ascertaining the networks directly involved in learning a complex motor task and its implications on cognitive function. Hence, opening up the possibility of harnessing the observed frontal networks involved in resource mobilization in instances of aging, brain lesion/injury or dysfunction.

neuroscience↗

bioRxiv2023

Better long-term learning ability is predicted by higher surface folding of the human premotor cortex

The capacity to learn enabled the human species to adapt to various challenging environmental conditions and pass important achievements on to the next generation. A growing body of research suggests links between neocortical folding and numerous aspects of human behaviour, but their impact on enhanced human learning capacity remains unexplored. Here we leverage multiple training cohorts to demonstrate that higher levels of premotor cortical folding reliably predict individual long-term learning gains in a challenging new motor task, above and beyond initial performance differences. Individual folding-related predisposition to motor learning was found to be independent of cortical thickness and several intracortical microstructural parameters, but dependent on larger cortical surface area. We further show that learning-relevant features of cortical folding occurred in close spatial proximity to practice-induced structural plasticity and were primarily localized in hominoid-specific frontal tertiary sulci. Our results suggest a new link between neocortical surface folding and human behavioural adaptability.

neuroscience↗

bioRxiv2023

Axon onset remodeling in response to network activity in mouse cortical neurons

In certain subtypes of pyramidal neurons, axons originate from basal dendrites, resulting in an axon-carrying dendrite branch with unique functional characteristics (AcD cells). The number of AcD cells increases during development, however, it is so far unclear whether neurons remodel their axon emergence throughout their lifetime in response to changes in network activity. To test our hypothesis of such large-scale morphological plasticity, we utilized in vitro and in vivo strategies in mouse primary somatosensory cortex to test whether network activity impacts axon onset. Based on data obtained by immunofluorescence, confocal microscopy and/or live-cell imaging, we show that neurons are indeed capable of changing the onset of their axon origin from somatic to dendritic and vice versa within a few days in vitro and that peripheral whisker manipulation and thus changes in sensory input drives large-scale morphological plasticity in vivo.

neuroscience↗

bioRxiv2023

Live imaging of excitable axonal microdomains in ankyrin-G-GFP mice

The axon initial segment (AIS) constitutes not only the site of action potential initiation, but also a hub for activity-dependent modulation of output generation. Recent studies shedding light on AIS function used predominantly post-hoc approaches since no robust murine in vivo live reporters exist. Here, we introduce a reporter line in which the AIS is intrinsically labeled by an ankyrin-G-GFP fusion protein activated by Cre recombinase, tagging the native Ank3 gene. Using confocal, superresolution, and two-photon microscopy as well as whole-cell patch-clamp recordings in vitro, ex vivo, and in vivo, we confirm that the subcellular scaffold of the AIS and electrophysiological parameters of labeled cells remain unchanged. We further uncover rapid AIS remodeling following increased network activity in this model system, as well as highly reproducible in vivo labeling of AIS over weeks. This novel reporter line allows longitudinal studies of AIS modulation and plasticity in vivo in real-time and thus provides a unique approach to study subcellular plasticity in a broad range of applications.

neuroscience↗

bioRxiv2021

Neocortical pyramidal neurons with axons emerging from dendrites are frequent in non-primates, but rare in monkey and human

The canonical view of neuronal function is that inputs are received by dendrites and somata, become integrated in the somatodendritic compartment and upon reaching a sufficient threshold, generate axonal output with axons emerging from the cell body. The latter is not necessarily the case. Instead, axons may originate from dendrites. The terms "axon carrying dendrite" (AcD) and "AcD neurons" have been coined to describe this feature. Here, we report on the diversity of axon origins in neocortical pyramidal cells. We found that in non-primates (rodent, cat, ferret, pig), 10-21% of pyramidal cells of layers II-VI had an AcD. In marked contrast, in macaque and human, this proportion was lower, and it was particularly low for supragranular neurons. Unexpectedly, pyramidal cells in the white matter of postnatal cat and aged human cortex exhibit AcDs to much higher percentages. In rodent hippocampus, AcD cells are functionally privileged, since inputs here can circumvent somatic integration and lead to immediate action potential initiation in the axon. Our findings expand the current knowledge regarding the distribution and proportion of AcD cells in neocortial regions of non-primate taxa, which strikingly differs from primates where these cells are mainly found in deeper layers and white matter.

neuroscience↗

bioRxiv2021

Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSCore sequencing facilities produce huge amounts of sequencing data that need to be analysed with automated workflows to ensure reproducibility and traceability. Eoulsan is a versatile open-source workflow engine meeting the needs of core facilities, by automating the analysis of a large number of samples. Its core design separates the description of the workflow from the actual commands to be run. This originality simplifies its usage as the user does not need to handle code, while ensuring reproducibility. Eoulsan was initially developed for bulk RNA-seq data, but the transcriptomics applications have recently widened with the advent of long-read sequencing and single-cell technologies, calling for the development of new workflows. ResultWe present Eoulsan 2, a major update that (i) enhances the workflow manager itself, (ii) facilitates the development of new modules, and (iii) expands its applications to long reads RNA-seq (Oxford Nanopore Technologies) and scRNA-seq (Smart-seq2 and 10x Genomics). The workflow manager has been rewritten, with support for execution on a larger choice of computational infrastructure (workstations, Hadoop clusters, and various job schedulers for cluster usage). Eoulsan now facilitates the development of new modules, by reusing wrappers developed for the Galaxy platform, with support for container images (Docker or Singularity) packaging tools to execute. Finally, Eoulsan natively integrates novel modules for bulk RNA-seq, as well as others specifically designed for processing long read RNA-seq and scRNA-seq. Eoulsan 2 is distributed with ready-to-use workflows and companion tutorials. Availability and implementationEoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL and CeCILL-C licenses at: http://outils.genomique.biologie.ens.fr/eoulsan/. The source code and sample workflows are available on GitHub: https://github.com/GenomicParisCentre/eoulsan. A GitHub repository for modules using the Galaxy tool XML syntax is further provided at: https://github.com/GenomicParisCentre/eoulsan-tools Contacteoulsan@bio.ens.psl.eu

bioinformatics↗