Biology subjects

Anders, S.

Publications and source records attributed to Anders, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Control of Golgi Architecture Through Three Centrosome Cohesion Pathways

Centrosome cohesion mechanisms link the two interphase centrosomes into a single microtubule-organizing center that is closely associated with the Golgi apparatus. The contribution of cohesion mechanisms to Golgi organization and function remains unclear. Here, we show that rootletin-CEP68 filaments, the C-Nap1-ninein linker, and microtubules derived from subdistal appendages, all of which promote centrosome cohesion, regulate the Golgi through distinct mechanisms while acting synergistically to maintain its organization and function. Centrosome-anchored rootletin-CEP68 filaments associate with AKAP450 through periodic binding of its PACT domain to CEP68 and extend into the Golgi, thereby establishing a physical connection between both organelles. The rootletin-CEP68-AKAP450 linkage even functions in cell types in which rootletin and AKAP450 do not mediate centrosome cohesion, suggesting that Golgi organization is the basic function of these filaments. Knockout analyses demonstrate that the three centrosome cohesion mechanisms collectively regulate Golgi morphology, positioning, and reassembly as well as cell migration. Each mechanism contributes distinctly to the overall process, indicating that they operate as a multifaceted system.

cell biology↗

bioRxiv2026

Inflammatory injury drives CIN and STING loss in polyploidpancreatic acinar cells

Epidemiological studies link pancreatic inflammation to increased cancer risks with elevated levels of chromosomal instability (CIN), yet the underlying cause remains unclear. The exocrine pancreas and lactating mammary gland harbor polyploid cells to boost secretory efficiency. Using organoid and in vivo models of pancreatic injury, we show that polyploid acinar cells contribute to regeneration via acinar-to-ductal metaplasia. The metaplasia induced cell size reduction is associated with crowding and spindle misorientation, leading to mitotic errors such as lagging chromosomes, chromatin bridges, and micronuclei. Micronucleated cells are not always eliminated or arrested in the cell cycle but can continue to proliferate and expand. Polyploid cells in post-lactational mammary gland organoids equally exhibited proliferation-related CIN. Single-cell proteomics of acinar cells shows STING1 loss and increased ATR levels in polyploid cells, enabling continued proliferation. These findings uncover physiological links between polyploidy, tissue repair, and CIN, offering new insights into cancer risks after tissue remodeling.

cell biology↗

bioRxiv2024

Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods

Advanced deep-learning methods, such as foundation models, promise to learn representations of biology that can be employed to predict in silico the outcome of unseen experiments, such as the effect of genetic perturbations on the transcriptomes of human cells. To see whether current models already reach this goal, we benchmarked five foundation models and two other deep learning models against deliberately simplistic linear baselines. For combinatorial perturbations of two genes for which only the individual single perturbations had been seen, we find that the deep learning-based approaches did not perform better than a simple additive model. For perturbations of genes that had not yet been seen, the deep learning-based approaches did not outper-form the baseline of predicting the mean across the training perturbations. We hypothesize that the poor performance is partially because the pre-training data is observational; we show that a simple linear model reliably outperforms all other models when pre-trained on another perturbation dataset. While the promise of deep neural networks for the representation of biological systems and prediction of experimental outcomes is plausible, our work highlights the need for clear setting of objectives and for critical benchmarking to direct research efforts. Contactconstantin.ahlmann@embl.de

bioinformatics↗

bioRxiv2024

Two distinct chromatin modules regulate proinflammatory gene expression

Various mechanisms have been proposed to explain gene activation and co-regulation, including enhancer-promoter interactions via chromatin looping and the enrichment of transcription factors into hubs or condensates. However, these conclusions often stem from analyses of individual loci, and genome-wide studies exploring mechanistic differences with coupled gene expression are lacking. In this study, we dissected the proinflammatory gene expression program induced by TNF in primary human endothelial cells using NGS- and imaging-based techniques. Our findings, enabled by our novel RWireX approach for single-cell ATAC-seq analysis, revealed two distinct regulatory chromatin modules: autonomous links of co-accessibility (ACs) between separated sites, and domains of contiguous co-accessibility (DCs) with increased local transcription factor binding. Genes in ACs and DCs exhibited different transcriptional bursting kinetics, highlighting the existence of two structurally and functionally distinct regulatory chromatin modules in the proinflammatory response. These findings provide a novel mechanistic framework for understanding how cells achieve rapid and precise gene expression control. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/606159v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1f5f7e8org.highwire.dtl.DTLVardef@166b4d7org.highwire.dtl.DTLVardef@1ea9206org.highwire.dtl.DTLVardef@118d534_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITwo distinct, non-mutually exclusive chromatin modules, ACs and DCs, that regulate proinflammatory gene expression were identified based on deep scATAC-seq. C_LIO_LIACs represent long-range genomic interactions with regulation occurring more by transcription burst frequency. C_LIO_LIDCs are regions of increased local transcription factor binding that can modulate transcription burst size. C_LIO_LIThe AC/DC model integrates sequencing-based evidence for chromatin looping with microscopy observations of transcription factor hubs/condensates into a unified model. C_LIO_LIOur findings provide a novel framework for understanding how cells achieve rapid and precise gene expression control. C_LI

genomics↗

bioRxiv2023

Identification of astrocyte-driven pseudolineages reveals clinical stratification and therapeutic targets in Glioblastoma

The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data forecast how tumor cells organize to sustain growth and identifies rate of activation as the main predictor of growth. Accordingly, patients with a higher quiescence fraction exhibit improved outcomes. Further, DNA methylation arrays enable ASA-related patient stratification. Comparison of healthy and malignant gene expression dynamics reveals dysregulation of the Wnt-antagonist SFRP1 at the quiescence to activation transition. SFRP1 overexpression renders GBM quiescent and increases overall survival of tumor-bearing mice. Surprisingly, it does so through reprogramming the tumors stem-like methylome into an astrocyte-like one. Our findings offer a novel patient stratification with clinical impact, new biomarkers and therapeutic avenues to halt GBM progression.

cancer biology↗

bioRxiv2023

The bromodomain inhibitor JQ1 is a molecular glue targeting centromeres

Centromeres are the position on each chromosome that orchestrates the accurate partitioning of the genome during cell division. Centromere-dependent cell-cycle checkpoints are maintained by cancer cells to prevent catastrophic chromosome segregation defects in dividing cells1, 2, making centromeric chromatin a valuable target for anti-cancer therapeutics. However, no compounds have been identified that specifically target centromeric chromatin using standard drug discovery approaches. Here we develop a big-data approach to identify the protein composition of repetitive DNA loci, including centromeres, and screen candidate small molecules that act on centromeric chromatin composition. We discover that the BET bromodomain protein BRD4 localises to centromeres and regulates centromeric cohesion. We further show that the bromodomain inhibitor JQ1 affects centromeric BRD4 by stabilising a direct interaction between BRD4 and Centromere Protein B (CENP-B), acting as a molecular-glue that promotes centromere cohesion in a CENP-B-dependent manner. Strikingly, CENP-B transitions from a non-essential protein in JQ1-sensitive cells to the most significant determinant of cell-proliferation in JQ1-resistant cells. Our observations demonstrate a completely overlooked role for BRD4 and JQ1 in directly targeting the centromere, with important consequences for JQ1-derivatives currently entering clinical use3.

molecular biology↗

bioRxiv2022

Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/499860v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@149fe11org.highwire.dtl.DTLVardef@c71902org.highwire.dtl.DTLVardef@13ae945org.highwire.dtl.DTLVardef@a8d37e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Lung endothelium instructs dormancy of susceptible metastatic tumour cells

During metastasis, cancer cells hijack blood vessels and travel via the circulation to colonize distant sites1,2. Due to the rarity of these events, the immediate cell fate decisions of arrested circulating tumour cells (aCTC) are poorly understood and the role of the endothelium, as the interface of dissemination, remains elusive3,4. Here, we developed a novel strategy to specifically enrich for aCTC subpopulations capturing all cell states of the extravasation process and, in combination with single cell RNA-sequencing, provide a first blueprint of the transcriptional basis of early aCTC decisions. Upon their arrest at the metastatic site, tumour cells either started proliferating intravascularly or extravasated and preferably reached a state of quiescence. Endothelial-derived angiocrine Wnt factors were found to drive this bifurcation by inducing a mesenchymal-like phenotype in aCTCs instructing them to follow the extravasation-dormancy branch. Surprisingly, homogenous tumour cell pools showed an unexpected baseline heterogeneity in Wnt signalling activity and epithelial-to-mesenchyme-transition (EMT) states. This heterogeneity was established at the epigenetic level and served as the driving force of aCTC behaviour. Hypomethylation enabled high baseline Wnt and EMT activity in tumour cells leading them to preferably follow the extravasation-dormancy route, whereas methylated tumour cells had low activity and proliferated intravascularly. The data identify the pre-determined methylation status of disseminated tumour cells as a key regulator of aCTC behaviour in the metastatic niche. While metastatic niche-derived factors per default instruct the acquisition of quiescence, aCTCs unwind a default proliferation program and only deviate from it if hypomethylation in key gene families renders them responsive towards the microenvironment.

cancer biology↗

bioRxiv2022

Analyzing single-cell bisulfite sequencing data with scbs

Single-cell bisulfite sequencing (scBS) is a technique that enables the assessment of DNA methylation at single-base pair and single-cell resolution. The analysis of large datasets obtained from scBS requires preprocessing to reduce data size, improve signal-to-noise ratio, and provide interpretability. Typically, this is achieved by dividing the genome into large tiles and averaging the methylation signals within each tile. Here, we demonstrate that this coarse-graining approach can lead to signal dilution. As an alternative, we propose improved strategies to identify more informative regions for methylation quantification, and a more accurate quantitation method than simple averaging. Our approach enables better discrimination of cell types and other features of interest and reduces the need for large numbers of cells. We also present an approach to detect differentially methylated regions (DMRs) between groups of cells, and demonstrate its ability to identify biologically meaningful regions that are associated with genes involved in the core functions of specific cell types. To facilitate the analysis of scBS data, we have developed a software tool called Meth-SCAn that implements these methods and provides additional functionality.

bioinformatics↗

bioRxiv2022

R/LinkedCharts: A novel approach for simple but powerful interactive data analysis

In any research project involving data-rich assays, exploratory data analysis is a crucial step. Typically, this involves jumping back and forth between visualizations that provide overview of the whole data and others that dive into details. In data quality assessment, for example, it might be very helpful to have one chart showing a summary statistic for all samples, and clicking on one of the data points would display details on this sample in a second plot. Setting up such interactively linked charts is usually too cumbersome and time-consuming to use them in ad hoc analysis. We present R/LinkedCharts, a framework that renders this task radically simple: Producing linked charts is as quickly done as is producing conventional static plots in R, requiring a data scientist to write only very few lines of simple R code to obtain complex and general visualization. We expect that the convenience of our new tool will enable data scientists and bioinformaticians to perform much deeper and more thorough EDA with much less effort. Furthermore, R/LinkedCharts apps, typically first written as quick-and-dirty hacks, can also later be polished to provide interactive data access in publication quality, thus contributing to open science.

bioinformatics↗

bioRxiv2022

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterized the proteome and transcriptome in-depth alongside genetic and ex-vivo drug response profiling in a clinically well annotated CLL discovery cohort (n= 68). Unsupervised clustering of the proteome data revealed six subgroups. Five of these proteomic groups were associated with genetic features, while one group was only detectable at the proteome level. This new group was characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). We developed classifiers to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n= 165, n= 169) and confirmed that ASB-CLL comprises about 20 % of CLL patients. The inferior overall survival observed in ASB-CLL was independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling. Single sentence summaryWe performed the largest proteogenomic analysis of CLL, linked proteomic profiles to clinical outcomes, and discovered a new poor outcome subgroup (ASB-CLL).

cancer biology↗

bioRxiv2022

Interferon regulates stem cell output via post-transcriptional repression of Sox2 independent of its antiviral function in the brain

Stem cells show intrinsic interferon signalling, which protects them from viral infections at all ages. In the ageing brain, interferon signalling in stem cells also reduces their ability to activate. Whether these functions are linked and at what time interferons start taking on a role in stem cell functioning is unknown. Additionally, the molecular link between interferons and activation in neural stem cells and how this relates to productivity is not well understood. Here we combine single-cell transcriptomics, RiboSeq and animal models of interferon to show that this pathway is important for proper stem cell function at all ages. Interferon orchestrates cell cycle and mTOR activity to post-transcriptionally repress Sox2 and drive the exit from stem cell activation. The interferon response then decreases in the subsequent maturation states. Mathematical simulations indicate that this regulation is beneficial for the young and harmful for the old brain. Our study establishes molecular mechanisms of interferon in stem cells and interferons as genuine regulators of stem cell homeostasis and a potential therapeutic target to repair the ageing brain.

neuroscience↗

bioRxiv2021

Cellular development and evolution of the mammalian cerebellum

The expansion of the neocortex, one of the hallmarks of mammalian evolution1,2, was accompanied by an increase in the number of cerebellar neurons3. However, little is known about the evolution of the cellular programs underlying cerebellum development in mammals. In this study, we generated single-nucleus RNA-sequencing data for [~]400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse, and the marsupial opossum. Our cross-species analyses revealed that the cellular composition and differentiation dynamics throughout cerebellum development are largely conserved, except for human Purkinje cells. Global transcriptome profiles, conserved cell state markers, and gene expression trajectories across neuronal differentiation show that the cerebellar cell type-defining programs have been overall preserved for at least 160 million years. However, we also discovered differences. We identified 3,586 genes that either gained or lost expression in cerebellar cells in one of the species, and 541 genes that evolved new expression trajectories during neuronal differentiation. The potential functional relevance of these cross-species differences is highlighted by the diverged expression patterns of several human disease-associated genes. Altogether, our study reveals shared and lineage-specific programs governing the cellular development of the mammalian cerebellum, and expands our understanding of the evolution of mammalian organ development.

evolutionary biology↗

bioRxiv2021

The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes

Protein S-palmitoylation, the addition of a long-chain fatty acid to target proteins, is among the most frequent reversible protein modification in Metazoa, affecting subcellular protein localization, trafficking and protein-protein interactions. S-palmitoylated proteins are abundant in the neuronal system and are associated with neuronal diseases and cancer. Despite the importance of this post-translational modification, it has not been thoroughly studied in the model organism Drosophila melanogaster. Here we present the palmitoylome of Drosophila S2R+ cells, comprising 198 proteins, an estimated 3.5% of expressed genes in these cells. Comparison of orthologs between mammals and Drosophila suggests that S-palmitoylated proteins are more conserved between these distant phyla than non-S-palmitoylated proteins. To identify putative client proteins and interaction partners of the DHHC family of protein acyl-transferases (PATs) we established DHHC-BioID, a proximity biotinylation-based method. In S2R+ cells ectopic expression of the DHHC-PAT dHip14-BioID in combination with Snap24 or an interaction-deficient Snap24- mutant, as a negative control, resulted in biotinylation of Snap24 but not the Snap24-mutant. DHHC-BioID in S2R+ cells using 10 different DHHC-PATs as bait identified 520 putative DHHC-PAT interaction partners of which 48 were S-palmitoylated and are therefore putative DHHC-PAT client proteins. Comparison of putative client protein/DHHC-PAT combinations indicates that CG8314, CG5196, CG5880 and Patsas have a preference for transmembrane proteins, while S-palmitoylated proteins with the Hip14-interaction motif are most enriched by DHHC-BioID variants of approximated and dHip14. Finally, we show that BioID is active in larval and adult Drosophila and that dHip14-BioID rescues dHip14 mutant flies, indicating that DHHC-BioID is non-toxic. In summary we provide the first systematic analysis of a Drosophila palmitoylome. We show that DHHC-BioID is sensitive and specific enough to identify DHHC-PAT client proteins and provide DHHC-PAT assignment for ca. 25% of the S2R+ cell palmitoylome, providing a valuable resource. In addition, we establish DHHC-BioID as a useful concept for the identification of tissue-specific DHHC-PAT interactomes in Drosophila.

biochemistry↗

bioRxiv2021

In vivo high-throughput screening of novel adeno-associated viral capsids targeting adult neural stem cells in the subventricular zone

The adult mammalian brain entails a reservoir of neural stem cells (NSCs) generating glial cells and neurons. However, NSCs become increasingly quiescent with age, which hampers their regenerative capacity. New means are therefore required to genetically modify adult NSCs for re-enabling endogenous brain repair. Recombinant adeno-associated viruses (AAVs) are ideal gene therapy vectors due to an excellent safety profile and high transduction efficiency. We thus conducted a high-throughput screening of 177 intraventricularly injected barcoded AAV variants profiled by RNA sequencing. Quantification of barcoded AAV mRNAs identified two synthetic capsids, AAV9_A2 and AAV1_P5, both of which transduce active and quiescent NSCs. Further optimization of AAV1_P5 by judicious selection of promoter and dose of injected viral genomes enabled labeling of 30-60% of the NSC compartment, which was validated by FACS analyses and single cell RNA sequencing. Importantly, transduced NSC readily produced neurons. The present study identifies AAV variants with a high regional tropism towards the v-SVZ with high efficiency in targeting adult NSCs, thereby paving the way for preclinical testing of regenerative gene therapy.

neuroscience↗

bioRxiv2021

Leaky wiring of the brain: local cluster of coupled synapses and extracellular signal integration

The wiring scheme of neurons is key to the function of the brain. Neurons are structurally wired by synapses and it is a long-held view that most synapses in the CNS are sufficiently isolated to avoid cross-talk to AMPA receptors of neighboring synapses. Here we report in hippocampal brain slices that quantal glutamate release activated optical reporter proteins >1.5 {micro}m distant to the releasing synapse. 2P-glutamate uncaging was used to quantitatively probe glutamate spread in the neuropil. Releasing [~]35000 molecules of glutamate ([~]5 vesicles) at a distance of 500 nm to a spine generated an uncaging EPSC reaching [~]30% of the quantal amplitude at synaptic AMPA-Rs. The same stimulus activated [~]70% of the quantal amplitude at NMDA-Rs and still generated clear current and calcium responses when applied at >= 2 {micro}m remote to the spine. Extracellular spread of glutamate on the sub-micrometer scale appeared cooperative and caused supra-additive activation of AMPA-Rs in a spine. These observations are not predicted by previously used models of glutamate diffusion in the neuropil. An extracellular glutamate scavenger system weakly reduced field potential responses but not the quantal amplitude, indicating that a cross-talk component regularly contributes to synaptic transmission. Our data suggest that slight synaptic crosstalk responses at AMPA receptors of [~]2-4 adjacent synapses may be common (>70 synapses for NMDA receptors). Such broadcasting of synaptic signals to very local neighborhoods could stabilize network learning performance and allow for integration of synaptic activity within the extracellular space.

neuroscience↗

bioRxiv2020

Single cell 3'UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism

Autism spectrum disorder (ASD) is a neurodevelopmental disease affecting social behavior. Many of the high-confident ASD risk genes relate to mRNA translation. Specifically, many of these genes are involved in regulation of gene expression for subcellular compartmentalization of proteins1. Cis-regulatory motifs that often localize to 3- and 5-untranslated regions (UTRs) offer an additional path for posttranscriptional control of gene expression. Alternative cleavage and polyadenylation (APA) affect 3UTR length thereby influencing the presence or absence of regulatory elements. However, APA has not yet been addressed in the context of neurodevelopmental disorders. Here we used single cell 3end sequencing to examine changes in 3UTRs along the differentiation from neural stem cells (NSCs) to neuroblasts within the adult brain. We identified many APA events in genes involved in neurodevelopment, many of them being high confidence ASD risk genes. Further, analysis of 3UTR lengths in single cells from ASD and healthy individuals detected longer 3UTRs in ASD patients. Motif analysis of modulated 3UTRs in the mouse adult neurogenic lineage and ASD-patients revealed enrichment of the cytoplasmic and polyadenylation element (CPE). This motif is bound by CPE binding protein 4 (CPEB4). In human and mouse data sets we observed co-regulation of CPEB4 and the CPEB-binding synaptic adhesion molecule amyloid beta precursor-like protein 1 (APLP1). We show that mice deficient in APLP1 show aberrant regulation of APA, decreased number of neural stem cells, and autistic-like traits. Our findings indicate that APA is used for control of gene expression along neuronal differentiation and is altered in ASD patients.

neuroscience↗

bioRxiv2020

Computational analysis of ligand dose range thermal proteome profiles

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. We present a statistical analysis method with reliable control of the false discovery rate and apply it to several datasets probing epigenetic drugs. We detect off-target drug engagement in unrelated protein families.

bioinformatics↗