Biology subjects

Benes, V.

Publications and source records attributed to Benes, V..

50 records · Page 3Linked to original sources

bioRxiv2020

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection

Human intestinal epithelial cells form a primary barrier protecting us from pathogens, yet only limited knowledge is available about individual contribution of each cell type to mounting an immune response against infection. Here, we developed a pipeline combining single-cell RNA-Seq and highly-multiplex RNA imaging and applied it to human intestinal organoids infected with human astrovirus, a model human enteric virus. We found that interferon controls the infection and that astrovirus infects all major cell types and lineages with a preferential infection of proliferating cells. Intriguingly, each intestinal epithelial cell lineage has a unique basal expression of interferon-stimulated genes and, upon astrovirus infection, undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes. These findings suggest that in the human intestinal epithelium, each cell lineage plays a unique role in resolving virus infection. Our pipeline can be applicable to other organoids and viruses, opening new avenues to unravel roles of individual cell types in viral pathogenesis.

systems biology↗

bioRxiv2020

Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo

Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements. Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we advance Single Molecule Footprinting to detect individual molecular interactions of transcription factors and nucleosomes with DNA at mouse cis-regulatory elements. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that for most types of transcription factors high DNA co-occupancy can occur in absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy for binding cooperativity. These findings elucidate the binding cooperativity mechanism used by transcription factors in absence of strict organisation of their binding motifs, a characteristic feature of most of enhancers.

genomics↗

bioRxiv2020

A temperature-dependent translational switch controls biofilm development in Vibrio cholerae

The gastrointestinal pathogen Vibrio cholerae frequently forms biofilms during its life cycle. Biofilm formation is vital for protection against environmental stresses and is thought to facilitate intestinal colonization. Adaptation to temperature is crucial for V. cholerae survival, as the pathogen is exposed to seasonal temperature variations in the aquatic environment, and temperature fluctuations during host-environment transitions. Here, we show that V. cholerae strains naturally lacking the master biofilm transcriptional regulator HapR are unable to develop colony rugosity at low temperatures. We find that BipA, a ribosome-associated GTPase, accounts for this temperature-dependent control of biofilm formation by repressing translation of the primary biofilm transcriptional activators VpsR and VpsT at low temperatures. In vitro studies demonstrate that low temperatures influence BipA structural conformation and decrease its sensitivity to proteolysis. Proteomic analyses reveal that BipA exerts temperature-dependent control over >200 proteins in V. cholerae involved in a multitude of cell processes, including biofilm assembly. Our study reveals a remarkable new facet of the complex V. cholerae biofilm regulatory cascade and suggests that combined transcriptional-translational control could be a common mechanism by which bacteria adapt to environmental flux.

microbiology↗

bioRxiv2020

DNA damage independent inhibition of NF-κB transcription by anthracyclines

Anthracyclines are among the most used and effective anticancer drugs. Their activity has been attributed to DNA double-strand breaks resulting from topoisomerase II poisoning and to eviction of histones from select sites in the genome. Here we show that the extensively used anthracyclines Doxorubicin, Daunorubicin and Epirubicin, decrease the transcription of nuclear factor kappa B (NF-{kappa}B)-dependent gene targets, but not interferon responsive genes. Using an NMR-based structural approach, we demonstrate that anthracyclines disturb the complexes formed between the NF-{kappa}B subunit RelA and its DNA binding sites. The variant anthracyclines Aclarubicin, Doxorubicinone and the newly developed Dimethyl-doxorubicin, which share anticancer properties with the other anthracyclines but do not induce DNA damage, also suppressed inflammation, thus uncoupling DNA damage from the effects on inflammation. These findings have implications for anticancer therapy and for the development of novel anti-inflammatory drugs with limited side effects for life-threatening conditions such as sepsis.

immunology↗

bioRxiv2020

Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. In BriefIn budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/065920v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@19b86f4org.highwire.dtl.DTLVardef@1b923f3org.highwire.dtl.DTLVardef@1e74f69org.highwire.dtl.DTLVardef@10e787f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIYeast cells have thousands of short NAD-RNAs related to the 5-ends of mRNAs C_LIO_LIRNA polymerase II prefers a YAAG promoter motif for NAD incorporation into RNA C_LIO_LINAD-RNA is strongly guarded against by Rai1, Dxo1, and Npy1 decapping enzymes at different subcellular sites C_LIO_LIIn vitro, NAD-mRNAs are rejected from translation C_LI

cell biology↗

bioRxiv2020

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung.

The complexity of the lung microenvironment together with changes in cellular composition during disease progression make it exceptionally hard to understand the molecular mechanisms leading to the development of chronic lung diseases. Although recent advances in cell type resolved and single-cell sequencing approaches hold great promise for studying complex diseases, their implementation greatly relies on local access to fresh tissue, as traditional methods to process and store tissue do not allow viable cell isolation. To overcome these hurdles, we developed a novel, versatile workflow that allows long-term storage of human lung tissue with high cell viability, permits thorough sample quality check before cell isolation, and is compatible with next generation sequencing-based profiling, including single-cell approaches. We demonstrate that cryopreservation is suitable for isolation of multiple cell types from different lung locations and is applicable to both healthy and diseased tissue, including COPD and tumor samples. Basal cells isolated from cryopreserved airways retain the ability to differentiate, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for -omics profiling of human lung cells. In addition, we obtained high-quality single-cell RNA sequencing data of cells isolated from cryopreserved human lung, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our cryopreservation workflow is well-suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to human tissue.

cell biology↗

bioRxiv2019

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

Long read sequencing is increasingly being used to determine eukaryotic genomes. We used nanopore technology to generate chromosome-level assemblies for 3 different strains of Drechmeria coniospora, a nematophagous fungus used extensively in the study of innate immunity in Caenorhabditis elegans. One natural geographical isolate demonstrated high stability over decades, whereas a second isolate, not only had a profoundly altered genome structure, but exhibited extensive instability. We conducted an in-depth analysis of sequence errors within the 3 genomes and established that even with state-of-the-art tools, nanopore methods alone are insufficient to generate eukaryotic genome sequences of sufficient accuracy to merit inclusion in public databases.

genomics↗

bioRxiv2019

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. The challenge to systematically discover SVs in single cells remains unsolved, with copy-neutral and complex variants typically escaping detection. We developed single cell tri-channel-processing (scTRIP), a computational framework that jointly integrates read depth, template strand and haplotype phase to comprehensively discover SVs in single cells. We surveyed SV landscapes of 565 single cell genomes, including transformed epithelial cells and patient-derived leukemic samples, and discovered abundant SV classes including inversions, translocations and large-scale genomic rearrangements mediating oncogenic dysregulation. We dissected the molecular karyotype of the leukemic samples and examined their clonal structure. Different from prior methods, scTRIP also enabled direct detection and discrimination of SV mutational processes in individual cells, including breakage-fusion-bridge cycles. scTRIP will facilitate studies of clonal evolution, genetic mosaicism and somatic SV formation, and could improve disease classification for precision medicine.

genomics↗

bioRxiv2019

Host-dependent induction of disease tolerance to infection by tetracycline antibiotics

Synergy of resistance and disease tolerance mechanisms is necessary for an effective immune response leading to survival and return to homeostasis when an organism is challenged by infection. Antibiotics are used for their resistance enhancement capabilities by decreasing pathogen load, but several classes have long been known to have beneficial effects that cannot be explained strictly on the basis of their capacity to control the infectious agent. Here we report that tetracycline antibiotics, a class of ribosome-targeting drugs, robustly protects against sepsis by inducing disease tolerance, independently from their direct antibiotic properties. Mechanistically, we find that mitochondrial inhibition of protein synthesis perturbs the electron transfer chain and leads to improved damage repair in the lung and fatty acid oxidation and glucocorticoid sensitivity in the liver. Using a partial and acute deletion of CRIF1 in the liver, a critical mitoribosomal component for protein synthesis, we find that mice are protected against bacterial sepsis, an observation which is phenocopied by the transient inhibition of complex I of ETC by phenformin. Together, we demonstrate that ribosome-targeting antibiotics are beneficial beyond their antibacterial activity and that mitochondrial protein synthesis inhibition leading to ETC perturbation is a novel mechanism for the induction of disease tolerance.

immunology↗

bioRxiv2019

Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish

During heart regeneration in the zebrafish, fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre-existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here, using sox10 genetic fate mapping, we identified a subset of pre-existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively after cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration.

developmental biology↗

bioRxiv2019

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

Microbial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.

microbiology↗

bioRxiv2018

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development

The endothelial to haematopoietic transition (EHT) is the process whereby haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). The intermediary steps of this process are unclear, in particular the identity of endothelial cells that give rise to HSPCs is unknown. Using single-cell transcriptome analysis and antibody screening we identified CD44 as a new marker of EHT enabling us to isolate robustly the different stages of EHT in the aorta gonad mesonephros (AGM) region. This allowed us to provide a very detailed phenotypical and transcriptional profile for haemogenic endothelial cells, characterising them with high expression of genes related to Notch signalling, TGFbeta/BMP antagonists (Smad6, Smad7 and Bmper) and a downregulation of genes related to glycolysis and the TCA cycle. Moreover, we demonstrated that by inhibiting the interaction between CD44 and its ligand hyaluronan we could block EHT, identifying a new regulator of HSPC development.

developmental biology↗

bioRxiv2017

Single-cell RNA-sequencing redefines blood cell type classification in mosquitoes

Mosquito blood cells are ancestral immune cells that help control infection by vector-borne pathogens. Despite their importance, little is known about mosquito blood cell biology beyond the ambiguous morphological and functional criteria used for their classification. Here we combined the power of single-cell RNA-sequencing, imaging flow cytometry and single-molecule RNA hybridization to analyze blood cells of the malaria mosquito Anopheles gambiae. By demonstrating that blood cells express nearly half of the mosquito transcriptome, our dataset represents an unprecedented view into their transcriptional machinery. Analyses of differentially expressed genes identified transcriptional signatures of two distinct cell types that challenge the current morphology-based classification of these cells. We further demonstrated an active transfer of a cellular marker between blood cells that confounds their identity. We propose that cell-to-cell exchange is broadly relevant for cell type classification and may account for the remarkable cellular diversity observed in nature.

immunology↗

bioRxiv2017

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues

Animal bodies comprise a diverse array of tissues and cells. To characterise cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii1-4. We identify five transcriptionally distinct groups of differentiated cells that are spatially coherent, as revealed by spatial mapping5. Besides somatic musculature, ciliary bands and midgut, we find a group of cells located at the apical tip of the animal, comprising sensory-peptidergic neurons, and another group composed of non-apical neural and epidermal cells covering the rest of the body. These data establish a basic subdivision of the larval body surface into molecularly defined apical versus non-apical tissues, and support the evolutionary conservation of the apical nervous system as a distinct part of the bilaterian brain6.

evolutionary biology↗