Biology subjects

Mark, M.

Publications and source records attributed to Mark, M..

11 recordsLinked to original sources

bioRxiv2026

Functional relevance of mobile and clustered CaV2.1 channels in central synapses

Reliable neurotransmitter release critically depends on the spatial relationship between voltage- gated calcium channels (VGCCs) and presynaptic release sites. Single particle tracking of endogenous CaV2.1 channels at glutamatergic synapses of hippocampal neurons revealed that apart from CaV2.1 channels aggregated in stable nanodomain clusters, a substantial fraction of Cav2.1 channels remained mobile, raising the question of whether these dispersed channels contribute to synaptic function. Mathematical modelling predicted that dispersed Cav2.1 channels cooperatively enhance release reliability. Upon repetitive stimulation, mobile CaV2.1 channels enable alternative use of release sites and thereby reduce the probability of failed presynaptic release. Both optogenetic immobilisation of CaV2.1 channels per se or activation of GABAB receptors (GABABRs) alone increase the failure rate and can lead to synaptic silencing. However, optogenetic clustering CaV2.1 channels prior to GABABR activation increases the fraction of synapses that remain active even in presence of GABABR agonist. The contribution of mobile channels to reliable neurotransmitter release is frequency-dependent and is minor at stimulation frequencies 1 Hz but becomes strong at frequencies over 10 Hz. These results demonstrate that mobile presynaptic CaV2.1 channels increase the frequency range of synaptic transmission but are particularly sensitive to metabotropic GABABR-mediated inhibition in glutamatergic hippocampal synapses.

neuroscience↗

bioRxiv2025

Plasma cell identity escape drives resistance to anti-BCMA T-cell-redirecting therapy in multiple myeloma

Chimeric antigen receptor T-cell (CART) and T-cell engager (TCE) therapies targeting B-cell maturation antigen (BCMA) are transforming the treatment landscape for relapsed multiple myeloma (MM). However, despite impressive initial response rates, most patients eventually relapse. To investigate this unmet medical need, we applied whole-genome sequencing (WGS) to MM cells from cohorts of 102 relapsed patients treated with anti-BCMA CART and TCE therapies. Several genomic alterations were associated with clinical outcomes, particularly primary refractoriness, including high genomic complexity and mutations in genes regulating plasma cell identity, which predicted resistance to therapy. Single-cell RNA sequencing further revealed that MM cells from refractory patients exhibited high proliferation signatures and reduced expression of TNFRSF17 (encoding BCMA), while were less enriched for plasma cell-associated transcriptional programs, a phenomenon we term "plasma cell identity escape." This profile was strongly associated with immune dysregulation of CD8 T cells including increased activation and exhaustion. This evolution of MM toward a more proliferative and lineage-divergent state, refractory to the anti-BCMA T-cell redirecting therapies, was functionally validated in preclinical MM mouse models. Collectively, our results comprehensively define the cellular and molecular mechanisms underlying primary resistance to anti-BCMA therapies.

cancer biology↗

bioRxiv2025

Aging-Associated Microbiota Drives Treg Dysfunction via TNF Signaling

Aging is associated with a chronic, low-grade inflammatory state referred to as inflammaging, which contributes to impaired immune regulation and increased susceptibility to disease. While regulatory T (Treg) cells are key mediators of immune homeostasis, their role in the context of age-related inflammation remains poorly understood. Here we demonstrate that age-related changes in the microbiota promote impaired Treg cell function, resulting in the differentiation of inflammatory T cells. In agreement, we find that aged germ-free (GF) mice exhibited a more balanced immune profile, where the Treg cells are functional and pro-inflammatory mediators are reduced, suggesting that microbial exposure is essential for the establishment of inflammaging. Furthermore, we show that the use of old microbiota in young animals was sufficient to induce pro-inflammatory T cell responses and impaired mucosal Treg cell proliferation, while young microbiota restored Treg cell function in old animals. Mechanistically, we show that exposure to aged microbiota was associated with sustained TNF signaling, elevated oxidative stress, DNA damage, and increased expression of senescence markers such as {gamma}H2AX and p16 in Treg cells. These findings uncover a microbiota-TNF-dependent mechanism by which age-associated microbial dysbiosis drives Treg cell dysfunction and promotes immune aging, highlighting the therapeutic potential of microbiota-targeted strategies to restore immune homeostasis in the elderly.

immunology↗

bioRxiv2024

TGFβ determines morphology and key cellular processes of activated CD4+ T cells

During an immune response, cells are simultaneously exposed to multiple cytokine signals that collectively determine their phenotype. Transforming growth factor {beta} (TGF{beta}) is a pleiotropic cytokine acting as a key regulator of T-cell differentiation with activating and suppressive effects on their immune function. Here, we systematically analyze the cellular responses of CD4+ T cells to TGF{beta} across diverse cytokine environments in the presence or absence of TGF{beta}. We found that TGF{beta} had a profound dominant effect independent of the presence of other cytokines, modulating the expression of more than 4,000 genes. In the presence of TGF{beta}, cells exhibit lower expression of translation-related and apoptosis-related genes, accompanied by increased survival of activated T cells. Notably, cells cultured in the presence of TGF{beta} were smaller in size while preserving their proliferative ability. Accordingly, we identified a dense network of transcription factors that were modulated by TGF{beta}, suggesting a core gene set connecting TGF{beta} signaling to the regulation of T-cell size. We found N-Myc to be at the center of this network, and we directly show that TGF{beta} regulates its gene expression level, protein level, and nuclear localization. Our work provides a system to study cell size control and demonstrate the profound effect of TGF{beta} in the modulation and regulation of T-cell properties, expanding its role beyond guiding their phenotype. Significance StatementTGF{beta} is a key determinant of CD4+ T-cell differentiation; however, understanding its effect on additional aspects of T-cell state is lacking. Here, we systematically studied the role of TGF{beta} in regulating T-cell physiology. Exposing cells to diverse combinations of cytokines enabled us to distill the core effect of TGF{beta}. We found TGF{beta} to have a profound effect on multiple cellular processes critical to T-cell function. Significantly, TGF{beta} induced smaller T-cells both in vitro and in vivo, suggesting that TGF{beta} could skew the population towards tissue infiltration and residency. Furthermore, TGF{beta} can be used to fine-tune T-cell size, providing a system for studying cell size control. Overall, our findings demonstrate the profound effect of TGF{beta} in the regulation of T-cell physiology.

immunology↗

bioRxiv2024

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

immunology↗

bioRxiv2023

Performing highly parallelized and reproducible GWAS analysis on biobank-scale data

MotivationGenome-wide association studies (GWAS) in large biobanks are transforming genetic research and enable the detection of novel genotype-phenotype relationships. In the last two decades, over 60,000 genetic associations across thousands of human diseases and traits have been discovered using a GWAS approach. Due to denser genotyping and increasing sample sizes, researchers are increasingly faced with computational challenges when executing GWAS analysis. A reproducible, modular and extensible pipeline with a focus on parallelization is essential to simplify data analysis and to allow researchers to devote their time to other essential tasks such as result interpretation and downstream analysis. ResultsHere we present nf-gwas, a Nextflow pipeline to run biobank-scale GWAS analysis. The pipeline automatically performs numerous pre- and post-processing steps, integrates regression modeling from the REGENIE package and currently supports single-variant, gene-based and interaction testing. nf-gwas also includes an extensive reporting functionality that allows to inspect thousands of phenotypes and navigate interactive Manhattan plots directly in the web browser. The pipeline is extensively tested using the unit-style testing framework nf-test to ensure code maintainability, a crucial requirement in clinical and pharmaceutical settings. Furthermore, we validated the pipeline against published GWAS datasets and benchmarked the pipeline on high-performance computing and cloud infrastructures to provide cost estimations to end users. Availabilitynf-gwas is free available at https://github.com/genepi/nf-gwas. Contactlukas.forer@i-med.ac.at

bioinformatics↗

bioRxiv2023

Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex

Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular and cellular processes that disturb homeostasis of local microenvironments. Here, we applied the 10x Genomics Visium Spatial Proteogenomics (Visium-SPG) platform, which measures spatial gene expression coupled with immunofluorescence protein co-detection, in post-mortem human brain tissue from individuals with late-stage Alzheimers disease (AD) to investigate changes in spatial gene expression with respect to amyloid-{beta} (A{beta}) and hyperphosphorylated tau (pTau) pathology. We identified A{beta}-associated transcriptomic signatures in the human inferior temporal cortex (ITC) during late-stage AD, which we further investigated at cellular resolution with combined immunofluorescence and single molecule fluorescent in situ hybridization (smFISH) co-detection technology. We present a workflow for analysis of Visium-SPG data and demonstrate the power of multi-omic profiling to identify spatially-localized changes in molecular dynamics that are linked to pathology in human brain disease. We provide the scientific community with web-based, interactive resources to access the datasets of the spatially resolved AD-related transcriptomes at https://research.libd.org/Visium_SPG_AD/.

neuroscience↗

bioRxiv2022

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.

We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Most epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains, but not with circulating human coronaviruses. Many expanding CDR3s were also present at high precursor frequency in pre-pandemic TCR repertoires. A similar set of early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the pre-infection naive repertoire. High frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection. One-Sentence SummaryHigh frequency naive precursors underly the rapid T cell response during the crucial early phases of acute viral infection.

immunology↗

bioRxiv2022

Ubiquitination occurs in the mitochondrial matrix byeclipsed targeted components of the ubiquitin machinery

Ubiquitination is a critical type of post translational modification in eukaryotic cells. It is involved in regulating nearly all cellular processes in the cytosol and nucleus. Mitochondria, known as the metabolism heart of the cell, are organelles that evolved from bacteria. Using the subcellular compartment-dependent -complementation, we detect multiple components of ubiquitination machinery as being eclipsed distributed to yeast mitochondria. Subsequently, the results with respect to MTS (mitochondrial targeting sequence) targeted HA-tagged ubiquitin demonstrate that certain ubiquitination events specifically occur in yeast mitochondria and are independent of proteasome activity in the cytosol/nucleus. Importantly, we show that the E2 Rad6 affects the pattern of protein ubiquitination in mitochondria and provides an in vivo assay for its activity in the matrix of the organelle. This study shows that ubiquitination occurs in the mitochondrial matrix by eclipsed targeted components of the ubiquitin machinery, providing a new perspective of mitochondrial and ubiquitination research.

cell biology↗

bioRxiv2021

Antigen experience relaxes the organisational structure of the T cell receptor repertoire

The creation and evolution of the T cell receptor repertoire within an individual combines stochastic and deterministic processes. We systematically examine the structure of the repertoire in different T cell subsets in young, adult and LCMV infected mice, from the perspective of variable gene usage, nucleotide sequences and amino acid motifs. Young individuals share a high level of organization, especially in the frequency distribution of variable genes and amino acid motifs. In adult mice, this structure relaxes and is replaced by idiotypic evolution of the effector and regulatory repertoire. The repertoire of CD4+ regulatory T cells was more similar to naive cells in young mice, but became more similar to effectors with age. Finally, we observed a dramatic restructuring of the repertoire following infection with LCMV. We hypothesize that the stochastic process of recombination and thymic selection initially impose a strong structure to the repertoire, which gradually relaxes following asynchronous responses to different antigens during life.

immunology↗

bioRxiv2019

Meiosis Initiates In The Fetal Ovary Of Mice Lacking All Retinoic Acid Receptor Isotypes

Gametes are generated through a specialized cell differentiation process, meiosis which, in most mammals, is initiated in ovaries during fetal life. It is widely admitted that all-trans retinoic acid (ATRA) is the molecular signal triggering meiosis initiation in mouse female germ cells, but a genetic approach in which ATRA synthesis is impaired disputes this proposal. In the present study, we investigated the contribution of endogenous ATRA to meiosis by analyzing fetuses lacking all RARs ubiquitously, obtained through a tamoxifen-inducible cre recombinase-mediated gene targeting approach. Efficient ablation of RAR-coding genes was assessed by the multiple congenital abnormalities displayed by the mutant fetuses. Unexpectedly, their germ cells robustly expressed STRA8, REC8, SYCP1 and SYCP3, showing that RAR are actually dispensable up to the zygotene stage of meiotic prophase I. Thus our study goes against the current model according to which meiosis is triggered by endogenous ATRA in the developing ovary and revives the identification of the meiosis-preventing substance synthesized by CYP26B1 in the fetal testis.

developmental biology↗