Publications by authors named "Bart Deplancke"

100 Publications

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium.

PLoS Biol 2021 03 29;19(3):e3001158. Epub 2021 Mar 29.

Institute of Virology and Immunology (IVI), Bern, Switzerland.

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.
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http://dx.doi.org/10.1371/journal.pbio.3001158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032198PMC
March 2021

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

Sci Adv 2021 Jan 29;7(5). Epub 2021 Jan 29.

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud 1015, Switzerland.

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transcriptomes of ( ) and 141 Genetic Reference Panel (DGRP) lines. This comprehensive circadian gene expression atlas contains >1700 cycling genes including previously unknown central circadian clock components and tissue-specific regulators. Furthermore, >30% of DGRP lines exhibited aberrant circadian gene expression, revealing abundant genetic variation-mediated, intertissue circadian expression desynchrony. Genetic analysis of one line with the strongest deviating circadian expression uncovered a novel mutation that, as shown by protein structural modeling and brain immunohistochemistry, disrupts the light-driven flavin adenine dinucleotide cofactor photoreduction, providing in vivo support for the importance of this conserved photoentrainment mechanism. Together, our study revealed pervasive tissue-specific circadian expression variation with genetic variants acting upon tissue-specific regulatory networks to generate local gene expression oscillations.
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http://dx.doi.org/10.1126/sciadv.abc3781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846174PMC
January 2021

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression.

Elife 2021 Jan 6;10. Epub 2021 Jan 6.

Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France.

Skeletal muscles are composed of gigantic cells called muscle fibers, packed with force-producing myofibrils. During development, the size of individual muscle fibers must dramatically enlarge to match with skeletal growth. How muscle growth is coordinated with growth of the contractile apparatus is not understood. Here, we use the large flight muscles to mechanistically decipher how muscle fiber growth is controlled. We find that regulated activity of core members of the Hippo pathway is required to support flight muscle growth. Interestingly, we identify Dlg5 and Slmap as regulators of the STRIPAK phosphatase, which negatively regulates Hippo to enable post-mitotic muscle growth. Mechanistically, we show that the Hippo pathway controls timing and levels of sarcomeric gene expression during development and thus regulates the key components that physically mediate muscle growth. Since Dlg5, STRIPAK and the Hippo pathway are conserved a similar mechanism may contribute to muscle or cardiomyocyte growth in humans.
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http://dx.doi.org/10.7554/eLife.63726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815313PMC
January 2021

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity.

Trends Cell Biol 2020 12 23;30(12):937-950. Epub 2020 Oct 23.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland. Electronic address:

White adipose tissue (WAT) is a cellularly heterogeneous endocrine organ that not only serves as an energy reservoir, but also actively participates in metabolic homeostasis. Among the main constituents of adipose tissue are adipocytes, which arise from adipose stem and progenitor cells (ASPCs). While it is well known that these ASPCs reside in the stromal vascular fraction (SVF) of adipose tissue, their molecular heterogeneity and functional diversity is still poorly understood. Driven by the resolving power of single-cell transcriptomics, several recent studies provided new insights into the cellular complexity of ASPCs among different mammalian fat depots. In this review, we present current knowledge on ASPCs, their population structure, hierarchy, fat depot-specific nature, function, and regulatory mechanisms, and discuss not only the similarities, but also the differences between mouse and human ASPC biology.
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http://dx.doi.org/10.1016/j.tcb.2020.09.007DOI Listing
December 2020

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress.

Sci Rep 2020 10 27;10(1):18308. Epub 2020 Oct 27.

Laboratory of Behavioral Genetics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.

Mitochondrial dysfunction was highlighted as a crucial vulnerability factor for the development of depression. However, systemic studies assessing stress-induced changes in mitochondria-associated genes in brain regions relevant to depression symptomatology remain scarce. Here, we performed a genome-wide transcriptomic study to examine mitochondrial gene expression in the prefrontal cortex (PFC) and nucleus accumbens (NAc) of mice exposed to multimodal chronic restraint stress. We identified mitochondria-associated gene pathways as most prominently affected in the PFC and with lesser significance in the NAc. A more detailed mitochondrial gene expression analysis revealed that in particular mitochondrial DNA-encoded subunits of the oxidative phosphorylation complexes were altered in the PFC. The comparison of our data with a reanalyzed transcriptome data set of chronic variable stress mice and major depression disorder subjects showed that the changes in mitochondrial DNA-encoded genes are a feature generalizing to other chronic stress-protocols as well and might have translational relevance. Finally, we provide evidence for changes in mitochondrial outputs in the PFC following chronic stress that are indicative of mitochondrial dysfunction. Collectively, our work reinforces the idea that changes in mitochondrial gene expression are key players in the prefrontal adaptations observed in individuals with high behavioral susceptibility and resilience to chronic stress.
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http://dx.doi.org/10.1038/s41598-020-75326-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591539PMC
October 2020

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.

BMC Biol 2020 09 19;18(1):129. Epub 2020 Sep 19.

Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.

Background: The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum. Hypotheses to explain this hourglass pattern have focused on purifying the selection of gene regulation. Here, we propose an alternative-genes are regulated in different ways at different stages and have different intrinsic capacities to respond to perturbations on gene expression.

Results: To eliminate the influence of natural selection, we quantified the expression variability of isogenetic single embryo transcriptomes throughout fly Drosophila melanogaster embryogenesis. We found that the expression variability is lower at the phylotypic stage, supporting that the underlying regulatory architecture in this stage is more robust to stochastic variation on gene expression. We present evidence that the phylotypic stage is also robust to genetic variations on gene expression. Moreover, chromatin regulation appears to play a key role in the variation and evolution of gene expression.

Conclusions: We suggest that a phylum-level pattern of embryonic conservation can be explained by the intrinsic difference of gene regulatory mechanisms in different stages.
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http://dx.doi.org/10.1186/s12915-020-00842-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502200PMC
September 2020

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons.

Sci Adv 2020 Aug 28;6(35):eaba3200. Epub 2020 Aug 28.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influence this process is largely unknown. We identify ZNF417 and ZNF587 as primate-specific KZFPs repressing HERVK (human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (ESCs). Expressed in specific regions of the human developing and adult brain, ZNF417/587 keep controlling TEeRS in ESC-derived neurons and brain organoids, secondarily influencing the differentiation and neurotransmission profile of neurons and preventing the induction of neurotoxic retroviral proteins and an interferon-like response. Thus, evolutionarily recent KZFPs and their TE targets partner up to influence human neuronal differentiation and physiology.
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http://dx.doi.org/10.1126/sciadv.aba3200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455193PMC
August 2020

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel.

Nat Metab 2019 12 9;1(12):1226-1242. Epub 2019 Dec 9.

Laboratory of Systems Biology and Genetics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype-phenotype relationship studies.
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http://dx.doi.org/10.1038/s42255-019-0147-3DOI Listing
December 2019

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors.

Proc Natl Acad Sci U S A 2020 06 27;117(24):13828-13838. Epub 2020 May 27.

School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland;

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2 h), has a wide dynamic range (from 10 to 500 cells), is scalable and parallelized, and supports antibody- or sample-multiplexed ChIP on both histone marks and transcription factors. In addition, FloChIP's interconnected design allows for straightforward chromatin reimmunoprecipitation, which allows this technology to also act as a microfluidic sequential ChIP-seq system. Finally, we ran FloChIP for the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing insights into the main factors driving collaborative DNA binding of MEF2A and into its role in B cell-specific gene regulation. Together, our results validate FloChIP as a flexible and reproducible automated solution for individual or sequential ChIP-seq.
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http://dx.doi.org/10.1073/pnas.1913261117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306797PMC
June 2020

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses.

Nucleic Acids Res 2020 07;48(W1):W403-W414

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed with increasingly complex analytical processes and rapidly evolving methods. To render these processes and approaches more accessible, we developed the web-based, collaborative portal ASAP (Automated Single-cell Analysis Portal). Our primary goal is thereby to democratize single-cell omics data analyses (scRNA-seq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline. ASAP is freely available at https://asap.epfl.ch.
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http://dx.doi.org/10.1093/nar/gkaa412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319583PMC
July 2020

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.

Mol Biol Evol 2020 09;37(9):2661-2678

The European Drosophila Population Genomics Consortium (DrosEU).

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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http://dx.doi.org/10.1093/molbev/msaa120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475034PMC
September 2020

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow.

Micromachines (Basel) 2020 Mar 20;11(3). Epub 2020 Mar 20.

Laboratory of Life Sciences Electronics, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, CH, Switzerland.

Hydrodynamic-based microfluidic platforms enable single-cell arraying and analysis over time. Despite the advantages of established microfluidic systems, long-term analysis and proliferation of cells selected in such devices require off-chip recovery of cells as well as an investigation of on-chip analysis on cell phenotype, requirements still largely unmet. Here, we introduce a device for single-cell isolation, selective retrieval and off-chip recovery. To this end, singularly addressable three-dimensional electrodes are embedded within a microfluidic channel, allowing the selective release of single cells from their trapping site through application of a negative dielectrophoretic (DEP) force. Selective capture and release are carried out in standard culture medium and cells can be subsequently mitigated towards a recovery well using micro-engineered hybrid SU-8/PDMS pneumatic valves. Importantly, transcriptional analysis of recovered cells revealed only marginal alteration of their molecular profile upon DEP application, underscored by minor transcriptional changes induced upon injection into the microfluidic device. Therefore, the established microfluidic system combining targeted DEP manipulation with downstream hydrodynamic coordination of single cells provides a powerful means to handle and manipulate individual cells within one device.
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http://dx.doi.org/10.3390/mi11030322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143322PMC
March 2020

Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes.

Genome Biol 2020 01 17;21(1). Epub 2020 Jan 17.

Laboratory of Integrative Systems Physiology, Institue of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

Background: RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females from classical Drosophila melanogaster strains as well as 38 inbred lines.

Results: We find that infection leads to extensive differences in isoform ratios, which results in a more diverse transcriptome with longer 5' untranslated regions (5'UTRs). We establish a role for genetic variation in mediating inter-individual splicing differences, with local splicing quantitative trait loci (local-sQTLs) being preferentially located at the 5' end of transcripts and directly upstream of splice donor sites. Moreover, local-sQTLs are more numerous in the infected state, indicating that acute stress unmasks a substantial number of silent genetic variants. We observe a general increase in intron retention concentrated at the 5' end of transcripts across multiple strains, whose prevalence scales with the degree of pathogen virulence. The length, GC content, and RNA polymerase II occupancy of these introns with increased retention suggest that they have exon-like characteristics. We further uncover that retained intron sequences are enriched for the Lark/RBM4 RNA binding motif. Interestingly, we find that lark is induced by infection in wild-type flies, its overexpression and knockdown alter survival, and tissue-specific overexpression mimics infection-induced intron retention.

Conclusion: Our collective findings point to pervasive and consistent RNA splicing changes, partly mediated by Lark/RBM4, as being an important aspect of the gut response to infection.
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http://dx.doi.org/10.1186/s13059-019-1918-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966827PMC
January 2020

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.

Genome Biol 2020 01 17;21(1). Epub 2020 Jan 17.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited.

Results: To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression.

Conclusions: Our collective findings point to a large number of infection-specific cis- and trans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.
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http://dx.doi.org/10.1186/s13059-019-1912-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966807PMC
January 2020

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning.

Cell Rep 2019 12;29(12):4099-4113.e5

Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany. Electronic address:

Recruitment of brite/beige cells, known as browning of white adipose tissue (WAT), is an efficient way to turn an energy-storing organ into an energy-dissipating one and may therefore be of therapeutic value in combating obesity. However, a comprehensive understanding of the regulatory mechanisms mediating WAT browning is still lacking. Here, we exploit the large natural variation in WAT browning propensity between inbred mouse strains to gain an inclusive view of the core regulatory network coordinating this cellular process. Combining comparative transcriptomics, perturbation-based validations, and gene network analyses, we present a comprehensive gene regulatory network of inguinal WAT browning, revealing up to four distinct regulatory modules with key roles for uncovered transcriptional factors, while also providing deep insights into the genetic architecture of brite adipogenesis. The presented findings therefore greatly increase our understanding of the molecular drivers mediating the intriguing cellular heterogeneity and plasticity of adipose tissue.
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http://dx.doi.org/10.1016/j.celrep.2019.11.053DOI Listing
December 2019

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle.

Elife 2019 12 3;8. Epub 2019 Dec 3.

Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
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http://dx.doi.org/10.7554/eLife.50087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890464PMC
December 2019

Sex-dependent and sex-independent regulatory systems of size variation in natural populations.

Mol Syst Biol 2019 11;15(11):e9012

Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland.

Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sexual size dimorphism is mostly unknown. Here we take a multi-layered systems omics approach to study size variation in the Drosophila wing. We show that expression levels of many critical growth regulators such as Wnt and TGFβ pathway components significantly differ between sexes but not between lines exhibiting size differences within each sex, suggesting a primary role of these regulators in sexual size dimorphism. Only a few growth genes including a receptor of steroid hormone ecdysone exhibit association with between-line size differences. In contrast, we find that between-line size variation is largely regulated by genes with a diverse range of cellular functions, most of which have never been implicated in growth. In addition, we show that expression quantitative trait loci (eQTLs) linked to these novel growth regulators accurately predict population-wide, between-line wing size variation. In summary, our study unveils differential gene regulatory systems that control wing size variation between and within sexes.
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http://dx.doi.org/10.15252/msb.20199012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878047PMC
November 2019

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress.

iScience 2019 Sep 2;19:436-447. Epub 2019 Aug 2.

Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France. Electronic address:

Eukaryotic genomes encode several buffering mechanisms that robustly maintain invariant phenotypic outcome despite fluctuating environmental conditions. Here we show that the Drosophila gut-associated commensals, represented by a single facultative symbiont, Lactobacillus plantarum (Lp), constitutes a so far unexpected buffer that masks the contribution of the host's cryptic genetic variation (CGV) to developmental traits while the host is under nutritional stress. During chronic under-nutrition, Lp consistently reduces variation in different host phenotypic traits and ensures robust organ patterning during development; Lp also decreases genotype-dependent expression variation, particularly for development-associated genes. We further provide evidence that Lp buffers via reactive oxygen species (ROS) signaling whose inhibition impairs microbiota-mediated phenotypic robustness. We thus identified a hitherto unappreciated contribution of the gut facultative symbionts to host fitness that, beyond supporting growth rates and maturation timing, confers developmental robustness and phenotypic homogeneity in times of nutritional stress.
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http://dx.doi.org/10.1016/j.isci.2019.07.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6704380PMC
September 2019

Multilevel regulation of the glass locus during Drosophila eye development.

PLoS Genet 2019 07 12;15(7):e1008269. Epub 2019 Jul 12.

Department of Biology, University of Fribourg, Fribourg, Switzerland.

Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control identity of photoreceptor as well as non-photoreceptor cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintenance of differentiated tissues. The molecular mechanisms that control expression of glass, however, remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alternative small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible Glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but is able to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is largely unaffected by targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.
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http://dx.doi.org/10.1371/journal.pgen.1008269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6655844PMC
July 2019

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Nat Commun 2019 04 18;10(1):1809. Epub 2019 Apr 18.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revealed that KFZPs contribute to a wide variety of other biological processes. Using murine and human in vitro and in vivo models, we demonstrate here that one poorly studied KZFP, ZFP30, promotes adipogenesis by directly targeting and activating a retrotransposon-derived Pparg2 enhancer. Through mechanistic studies, we further show that ZFP30 recruits the co-regulator KRAB-associated protein 1 (KAP1), which, surprisingly, acts as a ZFP30 co-activator in this adipogenic context. Our findings provide an understanding of both adipogenic and KZFP-KAP1 complex-mediated gene regulation, showing that the KZFP-KAP1 axis can also function in a non-repressive manner.
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http://dx.doi.org/10.1038/s41467-019-09803-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472429PMC
April 2019

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.

Genome Biol 2019 04 19;20(1):71. Epub 2019 Apr 19.

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.
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http://dx.doi.org/10.1186/s13059-019-1671-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474054PMC
April 2019

A Comprehensive Drosophila melanogaster Transcription Factor Interactome.

Cell Rep 2019 04;27(3):955-970.e7

Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation.
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http://dx.doi.org/10.1016/j.celrep.2019.03.071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485956PMC
April 2019

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Lab Chip 2019 04;19(9):1610-1620

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biomedical research by enabling the in-depth analysis of cell-to-cell heterogeneity of tissues with unprecedented resolution. One of the catalyzing technologies is single cell droplet microfluidics, which has massively increased the overall cell throughput, routinely allowing the analysis of thousands of cells per experiment at a relatively low cost. Among several existing droplet-based approaches, the Drop-seq platform has emerged as one of the most widely used systems. Yet, this has surprisingly not incentivized major refinements of the method, thus restricting any lab implementation to the original Drop-seq setup, which is known to suffer from up to 80% bead loss during the process. In this study, we present a systematic re-engineering and optimization of Drop-seq: first, we re-designed the original dropleting device to be compatible with both air-pressure systems and syringe pumps, thus increasing the overall flexibility of the platform. Second, we devised an accompanying chip for post-encapsulation bead processing, which simplifies and massively increases Drop-seq's cell processing efficiency. Taken together, the presented optimization efforts result in a more flexible and efficient Drop-seq version.
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http://dx.doi.org/10.1039/c9lc00014cDOI Listing
April 2019

The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance.

Cell Stem Cell 2019 03;24(3):405-418.e7

Service and Central Laboratory of Hematology, Departments of Oncology and of Laboratories, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.

It has been recently shown that increased oxidative phosphorylation, as reflected by increased mitochondrial activity, together with impairment of the mitochondrial stress response, can severely compromise hematopoietic stem cell (HSC) regeneration. Here we show that the NAD-boosting agent nicotinamide riboside (NR) reduces mitochondrial activity within HSCs through increased mitochondrial clearance, leading to increased asymmetric HSC divisions. NR dietary supplementation results in a significantly enlarged pool of progenitors, without concurrent HSC exhaustion, improves survival by 80%, and accelerates blood recovery after murine lethal irradiation and limiting-HSC transplantation. In immune-deficient mice, NR increased the production of human leucocytes from hCD34+ progenitors. Our work demonstrates for the first time a positive effect of NAD-boosting strategies on the most primitive blood stem cells, establishing a link between HSC mitochondrial stress, mitophagy, and stem-cell fate decision, and unveiling the potential of NR to improve recovery of patients suffering from hematological failure including post chemo- and radiotherapy.
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http://dx.doi.org/10.1016/j.stem.2019.02.012DOI Listing
March 2019

Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases?

Lab Chip 2018 12;18(24):3903-3912

Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

Emulsion drops are frequently used as vessels, for example, to conduct biochemical reactions in small volumes or to perform screening assays at high throughputs while consuming minimal sample volumes. These applications typically require drops that do not allow exchange of reagents such that no cross-contamination occurs. Unfortunately, in many cases, reagents are exchanged between emulsion drops even if they have a low solubility in the surrounding phase, resulting in cross-contaminations. Here, we investigate the mechanism by which hydrophilic reagents are transported across an oil phase using water-oil-water double emulsion drops as a model system. Remarkably, even large objects, including 11 000 base pair double-stranded circular DNA are transported across oil shells. Importantly, this reagent transport, that is to a large extent caused by aqueous drops that spontaneously form at the water-oil interface, is not limited to double emulsions but also occurs between single emulsion drops. We demonstrate that the uncontrolled reagent transport can be decreased by at least an order of magnitude if appropriate surfactants that lower the interfacial tension only moderately are employed or if the shell thickness of double emulsions is decreased to a few hundreds of nanometers.
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http://dx.doi.org/10.1039/c8lc01000eDOI Listing
December 2018

A stromal cell population that inhibits adipogenesis in mammalian fat depots.

Nature 2018 07 20;559(7712):103-108. Epub 2018 Jun 20.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Adipocyte development and differentiation have an important role in the aetiology of obesity and its co-morbidities. Although multiple studies have investigated the adipogenic stem and precursor cells that give rise to mature adipocytes, our understanding of their in vivo origin and properties is incomplete. This is partially due to the highly heterogeneous and unstructured nature of adipose tissue depots, which has proven difficult to molecularly dissect using classical approaches such as fluorescence-activated cell sorting and Cre-lox lines based on candidate marker genes. Here, using the resolving power of single-cell transcriptomics in a mouse model, we reveal distinct subpopulations of adipose stem and precursor cells in the stromal vascular fraction of subcutaneous adipose tissue. We identify one of these subpopulations as CD142 adipogenesis-regulatory cells, which can suppress adipocyte formation in vivo and in vitro in a paracrine manner. We show that adipogenesis-regulatory cells are refractory to adipogenesis and that they are functionally conserved in humans. Our findings point to a potentially critical role for adipogenesis-regulatory cells in modulating adipose tissue plasticity, which is linked to metabolic control, differential insulin sensitivity and type 2 diabetes.
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http://dx.doi.org/10.1038/s41586-018-0226-8DOI Listing
July 2018

Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation.

Cell Metab 2018 08 14;28(2):282-288.e3. Epub 2018 Jun 14.

Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8549, USA. Electronic address:

Adipose tissue in the mammary gland undergoes dramatic remodeling during reproduction. Adipocytes are replaced by mammary alveolar structures during pregnancy and lactation, then reappear upon weaning. The fate of the original adipocytes during lactation and the developmental origin of the re-appearing adipocyte post involution are unclear. Here, we reveal that adipocytes in the mammary gland de-differentiate into Pdgfrα preadipocyte- and fibroblast-like cells during pregnancy and remain de-differentiated during lactation. Upon weaning, de-differentiated fibroblasts proliferate and re-differentiate into adipocytes. This cycle occurs over multiple pregnancies. These observations reveal the potential of terminally differentiated adipocytes to undergo repeated cycles of de-differentiation and re-differentiation in a physiological setting.
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http://dx.doi.org/10.1016/j.cmet.2018.05.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535147PMC
August 2018

The Human Cell Atlas.

Elife 2017 12 5;6. Epub 2017 Dec 5.

National Institute of Biomedical Genomics, Kalyani, India.

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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http://dx.doi.org/10.7554/eLife.27041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762154PMC
December 2017

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells.

Cell Chem Biol 2018 01 22;25(1):51-56.e6. Epub 2017 Nov 22.

Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. Electronic address:

The regulation of fundamental processes such as gene expression or cell differentiation involves chromatin states, demarcated by combinatorial histone post-translational modification (PTM) patterns. The subnuclear organization and dynamics of chromatin states is not well understood, as tools for their detection and modulation in live cells are lacking. Here, we report the development of genetically encoded chromatin-sensing multivalent probes, cMAPs, selective for bivalent chromatin, a PTM pattern associated with pluripotency in embryonic stem cells (ESCs). cMAPs were engineered from a set of PTM-binding (reader) proteins and optimized using synthetic nucleosomes carrying defined PTMs. Applied in live ESCs, cMAPs formed discrete subnuclear foci, revealing the organization of bivalent chromatin into local clusters. Moreover, cMAPs enabled direct monitoring of the loss of bivalency upon treatment with small-molecule epigenetic modulators. cMAPs thus provide a versatile platform to monitor chromatin state dynamics in live cells.
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http://dx.doi.org/10.1016/j.chembiol.2017.10.008DOI Listing
January 2018