Biology subjects

Mele, M.

Publications and source records attributed to Mele, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Disease-associated variants alter a novel physiological role of hnRNP H2 in neuronal development

Heterogeneous nuclear ribonucleoprotein H2 (hnRNP H2) is a member of the hnRNP family of RNA-binding proteins that regulate neuronal function through multiple aspects of RNA metabolism. Mutations in the nuclear localisation signal (NLS) and quasi-RNA recognition motifs (qRRMs) of hnRNP H2 have recently been linked to a severe developmental syndrome, termed HNRNPH2-related neurodevelopmental disorder. Despite its emerging importance, the physiological roles of hnRNP H2 in neuronal development and synaptic maturation, and how disease-associated variants alter these processes to drive pathology, remain poorly understood. Here, we show that hnRNP H2 is expressed in hippocampal neurons and localises to the synaptic compartment. Knockdown of hnRNP H2 revealed essential roles of the protein in the regulation of neuronal morphology, dendritic spine maturation, synaptic transmission, and cortical neuronal migration in vivo. Disease-associated hnRNP H2 variants altered protein localisation and activity-dependent synaptic recruitment, resulting in defects in neuronal morphology, in vivo cortical neuronal migration and laminar orientation, dendritic spine maturation, and synaptic function. Together, these findings establish hnRNP H2 as a critical regulator of neurodevelopment and identify a molecular basis for HNRNPH2-related neurodevelopmental disorder.

neuroscience↗

bioRxiv2026

Multi-omic dissection of reversible and persistent molecular alterations in diet-induced obesity

Diet-induced obesity drives broad molecular remodeling across host and microbial systems, but why lifestyle intervention reverses some of these alterations while others persist remains unclear. To address this, we performed a multi-omic characterization of diet-induced obese mice after a combined nutritional and exercise intervention, integrating liver transcriptomics, epigenomics, metabolomics and metallomics with gut metagenomics and metallomics. Multi-omics factor analysis resolved two dominant axes of variation. The first captured a broadly reversible response (~72% of altered variables), restored by dietary restriction and exercise, involving coordinated remodeling of hepatic metal homeostasis, epigenetic regulation, and immune and cell-turnover pathways. The second comprised persistent alterations resistant to intervention and driven primarily by microbial functional profiles: notably, functional diversity remained reduced despite substantial taxonomic recovery. Using germ-free mice to define the microbiota-responsive hepatic space, we found that a significant fraction of the persistent liver features fell within it, enriched in lipid metabolism (PPAR signaling, steroid and cholesterol biosynthesis, peroxisomal activity) and retinol metabolism. Sequential correlation analysis traced these changes to the loss of specific low-abundance taxa and their biosynthetic capacities, particularly vitamin (folate, biotin, cobalamin, pantothenate, thiamine) and cofactor metabolism, implicating microbiota-derived vitamin metabolism in sustained hepatic dysfunction. Cobalt was the sole essential element that remained persistently dysregulated and tracked dietary cobalt content, suggesting a diet--microbiota route to the persistent phenotype. These findings establish a dual regulatory framework in which metabolic plasticity is governed by reversible host-intrinsic and persistent microbiota-dependent processes, providing a systems-level explanation for obesogenic memory.

systems biology↗

bioRxiv2026

The D2-mdx mouse as a preclinical model for Duchenne muscular dystrophy: a natural history study across two independent sites

IntroductionThe quality of preclinical studies for rare diseases, such as Duchenne muscular dystrophy (DMD), relies on the availability of comprehensive natural disease history data. In addition to the classic BL10-mdx mouse, in recent years, the D2-mdx model has increasingly been used as an alternative model due to its reportedly more severely impaired phenotype. To improve our understanding of disease progression in these two DMD models, we conducted a comprehensive natural history study. Materials and MethodsThis involved a cross-sectional analysis of key in vivo and ex vivo outcome measures performed in two independent laboratories, using the same study setup in compliance with TREAT-NMD Standard Operating Procedures (SOPs), while also taking advantage of site-specific expertise. Globally, largely comparable results were obtained across the two study sites. ResultsBody composition showed pronounced differences between the strains, with BL10-mdx mice displaying a hypertrophic and D2-mdx mice displaying an atrophic phenotype. Dystrophic mice of each strain exhibited significant alterations of disease-relevant indices related to muscle functionality and integrity, mostly worsening with age, in comparison to their wildtypes. Cardiac function was affected earlier and more severely in D2-mdx mice. DiscussionNotably, for some parameters, genetic-background related differences were observed, emphasizing the need to include control groups with matching genetic backgrounds in experimental designs. ConclusionsCollectively, our natural history study provides benchmark data for these two mdx mouse strains to guide model selection for preclinical DMD studies, allowing accurate data interpretation. HighlightsO_LIDistinct body composition phenotypes: BL10-mdx mice exhibit pseudohypertrophy while D2-mdx mice display pronounced atrophy. C_LIO_LIEarlier cardiac dysfunction in D2-mdx: D2-mdx mice develop reduced ejection fraction and stroke volume from 28 weeks, while BL10-mdx only at 52 weeks. C_LIO_LIGenetic background-dependent variations: Intrinsic deficits in wildtype D2 mice demonstrate that genetic background influences outcome measures independent of dystrophic pathology. C_LIO_LIComparable ex vivo muscle physiology: Despite divergent in vivo phenotypes, isolated muscle contractile parameters show similar impairment in both dystrophic models. C_LIO_LIMulti-site standardized validation: Cross-sectional study at two independent laboratories following harmonized TREAT-NMD Standard Operating Procedures. C_LI

pharmacology and toxicology↗

bioRxiv2026

Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations

Humans exhibit substantial interindividual variation in their immune responses to infection, yet the contribution of transcript usage --the relative abundance of gene isoforms-- to this variation remains poorly understood. Here, we generate the first single-cell atlas of transcript usage variation during early responses to influenza A virus and SARS-CoV-2 across 160 individuals of African and European ancestry. We show that viral stimulation induces widespread remodelling of transcript usage across all major immune lineages, with changes that are largely lineage-restricted and frequently undetected at the gene expression level. We further find that ancestry-associated effects on transcript usage are predominantly cell type-specific and contribute to population differences in antiviral responses. In addition, the genetic regulation of transcript usage during stimulation differs between influenza A and SARS-CoV-2, pointing to virus-dependent regulatory architectures. Together, our findings establish transcript usage as a dynamic regulatory layer shaping responses to viral infection across immune cell types and human populations, providing new insights into the molecular basis of variation in human antiviral immunity.

immunology↗

bioRxiv2025

Multimodal data analysis reveals asynchronous aging dynamics across female reproductive organs

Female reproductive aging is a complex process with profound systemic health implications, yet the molecular and structural dynamics of aging across reproductive organs and tissues remain largely unexplored. Here, we integrate deep learning-based analysis of 1,112 histological images with RNA-seq data from 659 samples across seven reproductive organs in 304 female donors aged 20-70 years. We show that female reproductive organs and tissues have asynchronous aging dynamics: while the ovary and vagina age gradually, the uterus undergoes an abrupt transcriptional and cellular transition around the age of menopause. Tissue segmentation highlights that the myometrium in the uterine wall is the most age-affected tissue, marked by extracellular matrix remodeling and immune activation. Across reproductive organs, the epithelial tissue is also strongly affected by age, with the vaginal epithelium showing a unique sharp menopausal transition. Integration via multi-omics factor analysis links these tissue-specific histological transformations to specific molecular shifts, many with nonlinear expression trajectories and enriched in heritable reproductive traits such as pelvic organ prolapse and age at menarche. These findings position menopause as a key inflection point in female aging and provide insights with tissue-specific focus to support healthier menopausal transitions and reduce age-related disease risk.

genomics↗

bioRxiv2025

rDNAcaller: a fast and robust pipeline to call ribosomal DNA variants

Ribosomal DNA (rDNA) genes are essential components of the ribosome, organized as tandem repeats on the mammalian genomes. Extensive genetic and copy number variation in rDNA has been reported both within and between individuals, contributing to phenotypic diversity. However, previous rDNA variant calling strategies have relied on methods designed for diploid regions and have not been systematically benchmarked. With the recent availability of a telomere-to-telomere (T2T) genome assembly, rDNA regions have been fully assembled for the first time, enabling benchmarking and optimization of rDNA variant calling strategies. We developed a customized simulator that replicates real intra- and inter-individual rDNA variation based on the T2T assembly to benchmark the performance of commonly used variant callers, including GATK, Mutect2, and Lofreq. Additionally, we optimized the preprocessing and mapping steps to remove pseudogenes and significantly improve accuracy. Based on these optimizations, we introduce rDNAcaller, a novel pipeline for accurate rDNA variant detection using short-read whole-genome sequencing. rDNAcaller integrates optimized preprocessing with the top-performing variant caller and achieves 94% precision on experimental data from the T2T cell line. Applying our pipeline to data from the 1000 Genomes Project, we identify 5,607 novel rDNA variant positions across human populations, with African individuals showing the highest number of variants. Overall, rDNAcaller is a robust and versatile tool for analyzing rDNA variation, addressing the limitations of existing methods in handling high ploidies. By enabling accurate detection of rDNA variants, it facilitates deeper exploration of rDNAs role in phenotypic diversity, supporting future genomic studies and broadening our understanding of rDNA biology in health and disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/653643v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@148419borg.highwire.dtl.DTLVardef@cb3b42org.highwire.dtl.DTLVardef@9fa802org.highwire.dtl.DTLVardef@1cf4ff0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

The impact of sex, age, and genetic ancestry on DNA methylation across tissues

Understanding the consequences of individual DNA methylation variation is crucial for advancing our knowledge of human biology and disease. Yet, the collective impact of individual traits on DNA methylation and their downstream effects on gene expression across human tissues remain poorly understood. Here, we quantify the contributions of sex, age, genetic ancestry, and BMI on autosomal DNA methylation variation across 9 human tissues and 424 individuals from the Genotype-Tissue Expression project. We show that genetic ancestry and age have a greater impact on DNA methylation than sex, with aging effects being more widespread but less pronounced. On average, less than 10% of the gene expression variation in sex, age, and ancestry are mediated by DNA methylation differences, with ancestry showing the largest proportion of mediation. We further show that ancestry-associated DNA methylation differences accumulate at CpG sites with extreme methylation states and are largely under genetic control. The female autosomal genome exhibits consistent hypermethylation across tissues at Polycomb-repressed regions. Ultimately, we show that age-related Polycomb target hypermethylation is observed across multiple tissues, but not in the gonads. Our multi-individual, multi-tissue approach defines the key drivers of human DNA methylation variation in healthy conditions, establishing a baseline for the interpretation of DNA methylation changes in disease contexts.

bioinformatics↗

bioRxiv2025

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ancestry, introducing potential biases that remain uncharacterized. Here, we generate over 800 million full-length reads with long-read RNA-seq in 43 lymphoblastoid cell line samples from eight genetically-diverse human populations and build a cross-ancestry gene annotation. We show that transcripts from non-European samples are underrepresented in reference gene annotations, leading to systematic biases in allele-specific transcript usage analyses. Furthermore, we show that personal genome assemblies enhance transcript discovery compared to the generic GRCh38 reference assembly, even though genomic regions unique to each individual are heavily depleted of genes. These findings underscore the urgent need for a more inclusive gene annotation framework that accurately represents global transcriptome diversity.

genomics↗

bioRxiv2024

Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence

Immunosenescence, or immune aging, is characterized by both changes in cell type abundance and a decline in cellular function, leading to increased susceptibility to immune-related diseases. Yet, the extent to which sex influences the dynamic composition of immune cells during immunosenescence remains unknown. Here, we use single-cell RNA sequencing in peripheral blood mononuclear cells from 982 donors to uncover the sex-specific immune aging dynamics. We reveal that aging drives sexually dimorphic compositional and transcriptional shifts, with females showing stronger immune remodeling. Female-specific shifts include the expansion of three cytotoxic CD8+ T effector memory subpopulations and inflammatory monocytes. In addition, female CD4+ central memory T cells exhibit abundance shifts in subpopulations involved in autoimmunity alongside age-associated transcriptional signatures enriched for autoimmune-related pathways. Conversely, males show an age-related expansion of a B cell subpopulation associated with an asymptomatic precursor state to chronic lymphocytic leukemia. These sex-biased, functionally distinct immune subpopulations represent sex-specific hallmarks of immune aging. Our work underscores the complexity and sexual dimorphism of immunosenescence and supports the development of sex-specific strategies to promote healthy aging. Highlights- A single-cell transcriptomic atlas of >1 million PBMCs from 982 donors uncovers sex-specific immune aging trajectories. - Aging females show greater cellular remodeling and stronger transcriptional shifts than males. - Female-specific expansions with age of cytotoxic CD8+ T effector memory cells, inflammatory monocytes, and CD4+ T helper 22 cells reflect a systemic shift toward a pro-inflammatory, self-reactive immune state. - Male-specific B cell shifts reveal expansion of CD5+ clonal subpopulations linked to leukemic precursor states. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/622096v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@161b6b1org.highwire.dtl.DTLVardef@214d55org.highwire.dtl.DTLVardef@5c3ee8org.highwire.dtl.DTLVardef@263227_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Synaptic accumulation of GluN2B-containing NMDA receptors mediates the effects of BDNF-TrkB signalling on synaptic plasticity and in epileptogenesis

Brain-derived neurotrophic factor (BDNF) is a key mediator of synaptic plasticity and memory formation in the hippocampus. However, the BDNF-induced alterations in the glutamate receptors coupled to the plasticity of glutamatergic synapses in the hippocampus have not been elucidated. In this work we investigated the putative role of GluN2B-containing NMDA receptors in the plasticity of glutamatergic synapses induced by BDNF. Stimulation of hippocampal synaptoneurosomes with BDNF led to a significant time-dependent increase in the synaptic surface expression of GluN2B-containing NMDA receptors as determined by immunocytochemistry with colocalization with pre- (vesicular glutamate transporter) and post-synaptic markers (PSD95). Similarly, BDNF induced the synaptic accumulation of GluN2B-containing NMDA receptors at the synapse in cultured hippocampal neurons, by a mechanism sensitive to the PKC inhibitor G[O]6983. The effects of PKC may be mediated by phosphorylation of Pyk2, as suggested by western blot experiments analyzing the phosphorylation of the kinase on Tyrosine 402. GluN2B-containing NMDA receptors mediated the effects of BDNF in the facilitation of the early phase of long-term potentiation (LTP) of hippocampal CA1 synapses induced by {theta}-burst stimulation, since the effect of the neurotrophin was abrogated in the presence of the GluN2B inhibitor Co 101244. In the absence of BDNF, the GluN2B inhibitor did not effect LTP. Surface accumulation of GluN2B-containing NMDA receptors was also observed in hippocampal synaptoneurosomes isolated from rats subjected to the pilocarpine model of temporal lobe epilepsy, after reaching Status epilepticus, an effect that was inhibited by administration of the TrkB receptor inhibitor ANA-12. Together, these results show that the synaptic accumulation of GluN2B-containing NMDA receptors mediate the effects of BDNF in the plasticity of glutamatergic synapses in the hippocampus.

neuroscience↗

bioRxiv2024

Activation of the proteasome 20S Core particle prevents neuronal death induced by oxygen- and glucose deprivation in cultured neurons

AbstractNeuronal damage in brain ischemia is characterized by a disassembly of the proteasome and a decrease in its proteolytic activity. However, to what extent these alterations are coupled to neuronal death is controversial since proteasome inhibitors were shown to provide protection in different models of stroke in rodents. This question was addressed in the present work using cultured rat cerebrocortical neurons subjected to transient oxygen- and glucose-deprivation (OGD) as a model for in vitro ischemia. Under the latter conditions there was a time-dependent loss in the proteasome activity, determined by cleavage of the Suc-LLVY-AMC fluorogenic substrate, and the disassembly of the proteasome, as assessed by native-polyacrylamide gel electrophoresis followed by western blot against Psma2 and Rpt6, which are components of the catalytic core and regulatory particle, respectively. Immunocytochemistry experiments against the two proteins also showed differential effects on their dendritic distribution. OGD also downregulated the protein levels of Rpt3 and Rpt10, two components of the regulatory particle, by a mechanism dependent on the activity of NMDA receptors and mediated by calpains. Activation of the proteasome activity, using an inhibitor of USP14, a deubiquitinase enzyme, inhibited OGD-induced cell death, and decreased calpain activity as determined by analysis of spectrin cleavage. Similar results were obtained in the presence of two oleic amide derivatives (B12 and D3) which directly activate the 20S proteasome. Together, these results show that proteasome activation prevents neuronal death in cortical neurons subjected to in vitro ischemia, indicating that inhibition of the proteasome is a mediator of neuronal death in brain ischemia.

neuroscience↗

bioRxiv2024

Cigarette smoking drives accelerated aging across human tissues

Tobacco smoke is the main cause of preventable mortality worldwide. Smoking increases the risk of developing many diseases and has been proposed as an aging accelerator. Yet, the molecular mechanisms driving smoking-related health decline and aging acceleration in most tissues remain unexplored. Here, we characterize gene expression, alternative splicing, DNA methylation and histological alterations induced by cigarette smoking across human tissues. We show that smoking impacts tissue architecture and triggers systemic inflammation. We find that in many tissues, the effects of smoking significantly overlap those of aging in the same direction. Specifically, both age and smoking upregulate inflammatory genes and drive hypomethylation at enhancers. In addition, we observe widespread smoking-driven hypermethylation at target regions of the Polycomb repressive complex, which is a well-known aging effect. Smoking-induced epigenetic changes overlap causal aging CpGs, suggesting that these methylation changes may directly mediate aging acceleration observed in smokers. Finally, we find that smoking effects that are shared with aging are more persistent over time. Overall, our multi-tissue and multi-omic analysis of the effects of cigarette smoking provides an extensive characterization of the impact of tobacco smoke across tissues and unravels the molecular mechanisms driving smoking-induced tissue homeostasis decline and aging acceleration.

bioinformatics↗

bioRxiv2022

TransCistor reveals the landscape of cis-regulatory long noncoding RNAs

A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such cis-lncRNAs are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistors simple and conservative statistical models are compatible with functionally-defined target gene maps generated by existing and future technologies. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Known cis-lncRNAs are correctly identified, including XIST, LINC00240 and UMLILO, and predictions are consistent across analysis methods, perturbation types and independent experiments. Our results indicate that cis-activity is detected in a minority of lncRNAs, primarily involving activators over repressors. Cis-lncRNAs are detected by both RNA interference and antisense oligonucleotide perturbations. Mechanistically, cis-lncRNA transcripts are observed to physically associate with their target-genes, and are weakly enriched with enhancer-elements. In summary, TransCistor establishes a quantitative foundation for cis-lncRNAs, opening a path to elucidating their molecular mechanisms and biological significance.

genomics↗

bioRxiv2022

Deterioration of the human transcriptome with age due to increasing intron retention and spurious splicing

Adult aging is characterized by a progressive deterioration of biological functions at physiological, cellular and molecular levels, but its damaging effects on the transcriptome are not well characterized. Here, by analyzing splicing patterns in [~]1,000 human subjects sampled across multiple tissues, we found that splicing fidelity declines with age. Most prominently, genuine introns fail to be spliced out, manifesting as a broad surge in intron retention, and this is exacerbated by the increase in diverse spurious exon-exon junctions with age. Both of these effects are prominently detected in the majority of human tissues. Collectively, they result in the progressive deterioration of the active transcriptome, wherein functional mRNAs are increasingly diluted with non-functional splicing isoforms. We discuss the concept of "splicing damage" and formulate methods to quantify it. Using these tools, we show that splicing damage increases both with age and with the incidence of diseases. Altogether, this work uncovers transcriptome damage as a critical molecular indicator of human aging and healthspan.

genomics↗

bioRxiv2022

Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Recent innovations in droplet-based single-cell RNA-sequencing (scRNA-seq) have provided the technology necessary to investigate biological questions at cellular resolution. With the ability to assay thousands of cells in a single capture, pooling cells from multiple individuals has become a common strategy. Droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences, and numerous computational methods have been developed to address this problem. However, another challenge implicit with droplet-based scRNA-seq is the occurrence of doublets - droplets containing two or more cells. The inaccurate assignment of cells to individuals or failure to remove doublets contribute unwanted noise to the data and result in erroneous scientific conclusions. Therefore, it is essential to assign cells to individuals and remove doublets accurately. We present a new framework to improve individual singlet classification and doublet removal through a multi-method intersectional approach. We developed a framework to evaluate the enhancement in donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. The accuracy was assessed using scRNA-seq data of [~]1.4 million peripheral blood mononucleated cells from 1,034 unrelated individuals and [~]90,000 fibroblast cells from 81 unrelated individuals. We show that our approach significantly improves droplet assignment by separating singlets from doublets and classifying the correct individual compared to any single method. We show that the best combination of techniques varies under different biological and experimental conditions, and we present a framework to optimise cell assignment for a given experiment. We offer Demuxafy (https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/index.html) - a framework built-in Singularity to provide clear, consistent documentation of each method and additional tools to simplify and improve demultiplexing and doublet removal. Our results indicate that leveraging multiple demultiplexing and doublet detecting methods improves accuracy and, consequently, downstream analyses in multiplexed scRNA-seq experiments.

genomics↗

bioRxiv2022

In vivo single-cell profiling of lncRNAs during Ebola virus infection

Long non-coding RNAs (lncRNAs) are pivotal mediators of systemic immune response to viral infection, yet most studies concerning their expression and functions upon immune stimulation are limited to in vitro bulk cell populations. This strongly constrains our understanding of how lncRNA expression varies at single-cell resolution, and how their cell-type specific immune regulatory roles may differ compared to protein-coding genes. Here, we perform the first in-depth characterization of lncRNA expression variation at single-cell resolution during Ebola virus (EBOV) infection in vivo. Using bulk RNA-sequencing from 119 samples and 12 tissue types, we significantly expand the current macaque lncRNA annotation. We then profile lncRNA expression variation in immune circulating single-cells during EBOV infection and find that lncRNAs expression in fewer cells is a major differentiating factor from their protein-coding gene counterparts. Upon EBOV infection, lncRNAs present dynamic and mostly cell-type specific changes in their expression profiles especially in monocytes, the main cell type targeted by EBOV. Such changes are associated with gene regulatory modules related to important innate immune responses such as interferon response and purine metabolism. Within infected cells, several lncRNAs have positively and negatively correlated expression with viral load, suggesting that expression of some of these lncRNAs might be directly hijacked by EBOV to attack host cells. This study provides novel insights into the roles that lncRNAs play in the host response to acute viral infection and paves the way for future lncRNA studies at single-cell resolution.

genomics↗

bioRxiv2021

Genetic, parental and lifestyle factors influence telomere length

The average length of telomere repeats (TL) declines with age and is considered to be a marker of biological ageing. Here, we measured TL in six blood cell types from 1,046 individuals using the clinically validated Flow-FISH method. We identified remarkable cell-type-specific variations in TL. Host genetics, environmental, parental and intrinsic factors such as sex, parental age, and smoking are associated to variations in TL. By analysing the genome-wide methylation patterns, we identified that the association of maternal, but not paternal, age to TL is mediated by epigenetics. Coupling these measurements to single-cell RNA-sequencing data for 62 participants revealed differential gene expression in T-cells. Genes negatively associated with TL were enriched for pathways related to translation and nonsense-mediated decay. Altogether, this study addresses cell-type-specific differences in telomere biology and its relation to cell-type-specific gene expression and highlights how perinatal factors play a role in determining TL, on top of genetics and lifestyle.

cell biology↗

bioRxiv2020

Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics

Ebola virus (EBOV) causes epidemics with high case fatality rates, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. To better understand EBOV infection in vivo, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cell activity during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, providing insight into pathogenesis. We find that immature, proliferative monocyte-lineage cells with reduced antigen presentation capacity replace conventional circulating monocyte subsets within days of infection, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying viral RNA abundance in individual cells, we identify molecular determinants of tropism and examine temporal dynamics in viral and host gene expression. Within infected cells, we observe that EBOV down-regulates STAT1 mRNA and interferon signaling, and up-regulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating cellular pathways the virus manipulates for its replication. Overall, this study sheds light on EBOV tropism, replication dynamics, and elicited immune response, and provides a framework for characterizing interactions between hosts and emerging viruses in a maximum containment setting.

microbiology↗