Biology subjects

Clement, K.

Publications and source records attributed to Clement, K..

At least 19 recordsLinked to original sources

bioRxiv2026

A Weight Loss Fibrotic Response in Visceral Fat Is Driven by Defective Lysosome-Dependent Collagenolysis

Obesity induces pathological remodeling of white adipose tissue (WAT), including chronic inflammation and fibrosis, which drive metabolic dysfunction. Although weight loss (WL) is the cornerstone of obesity treatment and improves systemic metabolic health, its impact on WAT remodeling remains incompletely understood. Using a mouse model of diet-induced obesity followed by nutritional weight loss, we show that visceral WAT (vWAT) fails to fully recover despite normalization of body weight and marked metabolic improvment. Notably, vWAT fibrosis persists and continues to progress after WL. This occurs while extracellular matrix (ECM) production by adipose progenitor cells is markedly reduced following WL, explaining why pharmacological inhibition of ECM synthesis fails to prevent fibrosis during WL. Instead, we observed impaired collagen degradation by both progenitor cells and macrophages, along with lysosomal dysfunction, during WL. This suggests that defective ECM degradation, rather than continued ECM production, underlies fibrosis persistence and aggravation during WL. Together, these findings identify impaired collagenolysis as a critical barrier to adipose tissue recovery after WL and suggest that enhancing ECM clearance, rather than inhibiting ECM synthesis, may represent a more effective therapeutic strategy to restore adipose tissue function.

pathology↗

bioRxiv2026

The chemorepellent effect of metformin limits bacterial penetration into mammalian mucus by altering bacterial motility

Metformin improves metabolic health and remodels the intestinal microbiota, yet how these microbial changes contribute to therapeutic benefits remains incompletely understood. We combined human metagenomics, quantitative analyses of bacterial behavior and ex vivo mucus models to investigate how metformin modulates host-microbiota interactions. Human metagenomics revealed metformin-associated enrichment of chemotaxis- and motility-related genes. At millimolar concentrations, metformin acted as a bacterial chemorepellent, an effect abolished by deletion of the chemotaxis regulator CheY and dependent on the chemoreceptor Tsr. Direct metformin exposure or fecal water from metformin-treated individuals reduced bacterial penetration into mucin, an effect reproduced in intestinal mucus from pigs fed a moderate-fat diet. Metformin treatment was further associated with reduced fecal flagellin activity and increased anti-flagellin IgA. Together, these findings identify bacterial chemotaxis as a target of metformin and reveal a mechanism by which metformin may limit bacterial access to the intestinal mucus barrier.

microbiology↗

bioRxiv2025

Disruption of IgA-mediated aggregation at weaning favors mucus encroachment by commensal bacteria

Disruption of the gut mucus barrier is a critical step in the development of infec-tious or chronic inflammatory diseases. However, there are no clear links between developmental stages, diet, and the mechanical and biochemical properties of mucus. The transition from suckling to weaning is a pivotal stage in the devel-opment of the mucus barrier in mammals, with significant implications for the health and morbidity of mammalian infants. Here, using a novel microfluidic device, we investigate the penetration and organizational properties of motile Escherichia coli bacteria at the mucus interface using purified intestinal mucus collected from cohorts of piglets before and after weaning. In weaned piglets, E. coli penetrate more than 100 {micro}m into the mucus, a distance greater than the physiological thickness of the mucus layer in vivo. In contrast, for suckling piglets significant bacterial aggregation is observed at the interface, hindering the pene-tration process. Using the supernatant obtained from purified mucus of suckling piglets, we were able to restore bacterial aggregation in weaned piglet mucus and limit penetration. Interestingly, we also achieved the same result using purified human breast milk immunoglobulin A (IgA), which is known to promote bacterial aggregation. Our results emphasize the importance of mucosal immunoglobulin A (IgA) specificity in relation to the mothers immunological history, which is primarily transmitted through breast milk and lost during weaning. This also might explain why the suckling/weaning transition is, among other issues, a crit-ical window associated with a high incidence of gastrointestinal infections, before autologous IgA-mediated definite protection is acquired. Studying bacterial pen-etration in complex fluids using this new in vitro microfluidic device will pave the way for future research and the development of predictive tools for use in medical research trials.

microbiology↗

bioRxiv2025

A Singular Base Editing Platform for Polyfunctional Multiplex Engineering of Immune Cells

Current methods to engineer antigen-specific receptors rely on randomly integrating vectors or double-strand break induced targeted integration, both of which pose safety risks. To implement an all-in-one tool for multiplex knockout (KO) and knock in (KI), we expand the use of cytosine and adenine base editor (ABE) nickase activity to stimulate homology-directed repair (HDR) and insert clinically relevant chimeric antigen receptors (CARs) into specific loci. Through a novel sgRNA design strategy and a recombinant adeno-associated virus (rAAV) delivered DNA template, we enhanced the efficiency of ABE8e-stimulated HDR in human T cells. By combining KI of CD19-, CD33-, or mesothelin-targeting CARs with >95% quadplex gene KO (B2M/CD3{varepsilon}/PDCD1/CISH), we achieve single-step generation of highly functional off-the-shelf CAR T cell products with enhanced function. Importantly, we found no detectable translocations or significant off-target edits and demonstrated efficacy against multiple cancer lines, and a suppressive 3D spheroid culture model. This efficient engineering process of Iterative Nicking for Synchronous Engineered Reprogramming of T cells (INSERT) establishes a safe, simplified platform for advanced therapeutic CAR T engineering.

bioengineering↗

bioRxiv2025

Spatial characterization of microbiota profiles along the gut in a widely used mouse model: effects of high-fat diet and fructooligosaccharides

The intestinal microbiota plays a pivotal role in regulating metabolic processes, and its imbalance is linked to metabolic disorders. Modulating the gut microbiota composition and function through prebiotic supplementation has been repeatedly shown to improve host metabolism. While most studies have focused on the fecal microbiota due to the ease of sampling, fecal samples do not reflect the microbial dynamics throughout the gastrointestinal tract, as regional environmental conditions shape distinct microbiota composition. Given the metabolic significance of the proximal intestine and the potential influence of microbiota on these processes, we characterized the microbiota composition along the gastrointestinal tract in a widely used model for studying host-microbiota interactions: C57Bl6J male mice fed a high-fat diet (HFD) with or without prebiotics supplementation (FOS, fructooligosaccharides). The microbiota composition, determined by long-read Nanopore sequencing, was markedly altered by HFD and FOS supplementation not only in feces but also in the jejunum, ileum and caecum. In contrast to previous observations made in humans, obesity in mice was associated with a decrease in microbiome diversity in the small intestine, highlighting species-specific microbial responses to metabolic challenges. Additionally, the pronounced bifidogenic effect of FOS supplementation in the ileum suggests FOS fermentation in the small intestine in mice, contrary to what has been previously described in humans. Finally, we report a relative homogeneity of microbiome composition along the digestive tract, possibly due to the coprophagic behavior of mice. These findings challenge the translational relevance of rodent models for studying the role of the small intestinal microbiota in human metabolic disease.

microbiology↗

bioRxiv2024

Scalable assessment of genome editing off-targets associated with genetic variants

Genome editing with RNA-guided DNA binding factors carries risk of off-target editing at homologous sequences. Genetic variants may introduce sequence changes that increase homology to a genome editing target, thereby increasing risk of off-target editing. Conventional methods to verify candidate off-targets rely on access to cells with genomic DNA carrying these sequences. However, for candidate off-targets associated with genetic variants, appropriate cells for experimental verification may not be available. Here we develop a method, Assessment By Stand-in Off-target LentiViral Ensemble with sequencing (ABSOLVE-seq), to integrate a set of candidate off-target sequences along with unique molecular identifiers (UMIs) in genomes of primary cells followed by clinically relevant gene editor delivery. Gene editing of dozens of candidate off-target sequences may be evaluated in a single experiment with high sensitivity, precision, and power. We provide an open-source pipeline to analyze sequencing data. This approach enables experimental assessment of the influence of human genetic diversity on specificity evaluation during gene editing therapy development.

genomics↗

bioRxiv2023

Obesity-elicited macrophages shape CD9hi progenitor fate to promote adipose tissue fibrosis and dysfunction

Obesity is a life-threatening condition characterized by a maladaptive remodeling of the visceral white adipose tissue (vWAT), including fibrosis, that drives vWAT metabolic alterations. We previously identified CD9hi adipose tissue progenitors as the main drivers of vWAT fibrosis in mice and humans. However, how their functions are controlled, especially by macrophages, remains largely unknown. We found that obesity-elicited monocyte-derived macrophages (obeMac) accumulation was considerably elevated in mice prone to obesity-induced vWAT fibrosis. Limiting obeMac build-up decreased the numbers and fibrogenic activation of CD9hi progenitors, leading to decreased vWAT fibrosis and improved glucose homeostasis. In patients with obesity, we identified macrophages similar to mouse obeMacs that were associated with accumulation of CD9hi progenitors in the vWAT and loss of glycemic control. Finally, intercellular communication analysis identified mediators produced by obeMacs that control the fibrogenic potential of CD9hi progenitors. Together, we uncovered an obeMac-CD9hi progenitors axis controlling vWAT fibrosis and dysfunction.

pathology↗

bioRxiv2023

Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells

Gene editing the BCL11A erythroid enhancer is a validated approach to fetal hemoglobin (HbF) induction for {beta}-hemoglobinopathy therapy, though heterogeneity in edit allele distribution and HbF response may impact its safety and efficacy. Here we compared combined CRISPR-Cas9 endonuclease editing of the BCL11A +58 and +55 enhancers with leading gene modification approaches under clinical investigation. We found that combined targeting of the BCL11A +58 and +55 enhancers with 3xNLS-SpCas9 and two sgRNAs resulted in superior HbF induction, including in engrafting erythroid cells from sickle cell disease (SCD) patient xenografts, attributable to simultaneous disruption of core half E-box/GATA motifs at both enhancers. We corroborated prior observations that double strand breaks (DSBs) could produce unintended on- target outcomes in hematopoietic stem and progenitor cells (HSPCs) such as long deletions and centromere-distal chromosome fragment loss. We show these unintended outcomes are a byproduct of cellular proliferation stimulated by ex vivo culture. Editing HSPCs without cytokine culture bypassed long deletion and micronuclei formation while preserving efficient on-target editing and engraftment function. These results indicate that nuclease editing of quiescent hematopoietic stem cells (HSCs) limits DSB genotoxicity while maintaining therapeutic potency and encourages efforts for in vivo delivery of nucleases to HSCs.

genetics↗

bioRxiv2023

Novel mechanism of MYC deregulation in Multiple Myeloma

MYC deregulation occurs in 67% of multiple myeloma (MM) cases and associates with progression and worse prognosis in MM. Enhanced MYC expression is known to be driven by translocation or amplification events, but it only occurs in 40% of MM patients. Here, we describe a new mechanism of MYC regulation, whereby epigenetic regulation of MYC by increased accessibility of a cell-type specific enhancer leads to increased MYC expression. We found enhancer activity does not associate with enhancer hijacking events. We identified specific binding of c-MAF, IRF4, and SPIB transcription factors to the enhancer can activate MYC. In addition, we discovered focal amplification of this specific enhancer in approximately 4% of MM patients. Together, our findings define a new epigenetic mechanism of MYC deregulation in MM beyond known translocations or amplifications and point to the importance of non-coding regulatory elements and their associated transcription factor networks as drivers of MM progression.

cancer biology↗

bioRxiv2023

Dietary fibers benefits on glucose homeostasis require type 2 conventional dendritic cells in mice fed a high-fat diet

Diet composition impacts metabolic health and is now recognized to shape the immune system, especially in the intestinal tract. Nutritional imbalance and increased caloric intake are induced by high-fat diet (HFD) in which lipids are enriched at the expense of dietary fibers. Such nutritional challenge alters glucose homeostasis as well as intestinal immunity. Here, we observed that short-term HFD induced dysbiosis, glucose intolerance and decreased intestinal ROR{gamma}t+ CD4 T cells, including peripherally-induced Tregs and IL17-producing (Th17) T cells. However, dietary fiber supplementation of HFD-fed animals was sufficient to maintain ROR{gamma}t+ CD4 T cell subsets and microbial species known to induce them, alongside having a beneficial impact on glucose tolerance. Dietary fiber-mediated normalization of Th17 cells and amelioration of glucose handling required the cDC2 dendritic cell subset in HFD-fed animals, while IL-17 neutralization limited fibers impact on glucose tolerance. Overall, we uncover a novel and pivotal role of cDC2 in the control of the immune and metabolic effects of dietary fibers in the context of HFD feeding.

immunology↗

bioRxiv2020

Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to graft-versus-leukemia

Resistance to the graft-versus-leukemia (GvL) effect remains the major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis of GvL resistance for advanced lymphoid malignancies remains incompletely understood. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell-intrinsic features shape GvL outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post- HSCT relapse are shaped by distinct molecular dynamics and suggest that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for HLA loss was observed, even when present in pre-transplant subpopulations. Regardless of post-transplant relapse kinetics, gain of stem cell modules was a common signature associated with leukemia relapse. These data elucidate the biological pathways that underlie GvL resistance and post-transplant relapse. One Sentence SummaryWe find that the clinical kinetics of chronic lymphocytic leukemia relapse after stem cell transplant are underwritten by distinct genetic and epigenetic evolutionary trajectories and suggest that the selection pressures of the post-transplant, immunologic bottleneck are unlike those imposed by chemotherapy.

cancer biology↗

bioRxiv2020

Mechanism of monoallelic expression and allelic rheostat role of DNA methylation

In diploid cells, maternal and paternal copies of genes usually have similar transcriptional activity. Mammalian allele-specific epigenetic mechanisms such as X-chromosome inactivation (XCI) and imprinting were historically viewed as rare exceptions to this rule. The discovery of mitotically stable monoallelic autosomal expression (MAE) a decade ago revealed an additional allele-specific mode regulating thousands of mammalian genes. However, despite its prevalence, the mechanistic basis of MAE remains unknown. To uncover the mechanism of MAE maintenance, we devised a small-molecule screen for reactivation of silenced alleles across multiple loci using targeted RNA sequencing. Contrary to previous reports, we identified DNA methylation as a key mechanism of MAE mitotic maintenance. In contrast with the binary choice of the active allele in XCI, stringent transcriptome-wide analysis revealed MAE as a regulatory mode with tunable control of allele-specific expression, dependent on the extent of DNA methylation. In a subset of MAE genes, allelic imbalance was insensitive to changes in DNA methylation, implicating additional mechanisms in MAE maintenance in these loci. Our findings identify a key mechanism of MAE maintenance, reveal tunability of this mode of gene regulation, and provide the essential platform for probing the biological role of MAE in development and disease.

genomics↗

bioRxiv2020

Macrophage Scavenger Receptor 1 mediates lipid-induced inflammation in non-alcoholic fatty liver disease

Obesity-associated inflammation is a key player in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). However, the exact mechanisms remain incompletely understood. Here we demonstrate that macrophage scavenger receptor 1 (MSR1, CD204) expression is associated with the occurrence of hepatic lipid-laden foamy macrophages and correlates with the degree of steatosis and steatohepatitis in a cohort of 170 NAFLD patients. Mice lacking Msr1 are protected against high fat-cholesterol diet (HFD)-induced metabolic disorder, showing fewer hepatic lipid-laden foamy macrophages, less hepatic inflammation, improved dyslipidemia and glucose tolerance, while showing a change in hepatic lipid metabolism. We show that MSR1 induces a pro-inflammatory response via the JNK signaling pathway upon triggering by saturated fatty acids. In vitro blockade of the receptor prevented the accumulation of lipids in primary macrophages which inhibited the switch towards a pro-inflammatory phenotype and the release of cytokines such as TNFa. Targeting MSR1 using monoclonal antibody therapy in an obesity-associated NAFLD mouse model and ex vivo human liver slices resulted in the prevention of foamy macrophage formation and liver inflammation. Moreover, we identified that rs41505344, a polymorphism in the upstream transcriptional region of MSR1, was associated with altered serum triglycerides and aspartate transaminase levels in a cohort of over 400,000 patients. Taken together, our data suggest a critical role for MSR1 in lipid homeostasis and a potential therapeutic target for the treatment of NAFLD. One Sentence SummaryThe immunometabolic role of MSR1 in human NAFLD.

immunology↗

bioRxiv2020

The brain's hedonic valuation system's resting-state connectivity predicts weight loss and correlates with leptin

Weight gain is often associated with the pleasure of eating foods rich in calories and lack of willpower to reduce such food cravings, but empirical evidence is sparse. Here we investigated the role that connectivity within the brains hedonic valuation system (BVS, the ventral striatum and the ventromedial prefrontal cortex) at rest plays (1) to predict weight gain or loss over time and (2) for homeostatic hormone regulation. We found that intrinsic connectivity within the BVS at rest (RSC) predicted out-of-sample weight changes over time in lean and obese participants. Counterintuitively, such BVS RSC was higher in lean versus obese participants before the obese participants underwent a drastic weight loss intervention (Roux-en-Y gastric bypass surgery, RYGB). The RYGB surgery increased BVS RSC in the obese after surgery. The obese participants increase in BVS RSC correlated with decreases in fasting state systemic leptin, a homeostatic hormone signalling satiety that has been previously linked to dopamine functioning. Taken together, our results indicate a first link between brain connectivity in reward circuits in a more tonic state at rest, homeostatic hormone regulation involved in dopamine functioning and ability to lose weight. Significance statementWith obesity rates on the rise, advancing our understanding of what factors drive peoples ability to lose and gain weight is crucial. This research is the first to link what we know about the brains hedonic valuation system (BVS) to weight loss and homeostatic hormone regulation. We found that connectivity at rest (RSC) within the BVS system predicted changes in weight, differentiated between lean and obese participants, and increased after a weight loss intervention (gastric bypass surgery). Interestingly, the extent to which BVS RSC improved after surgery correlated to decreases in circulating levels of the satiety hormone leptin. These findings are the first to reveal the neural and hormonal determinants of weight loss, combining hedonic and homeostatic drivers of (over-)eating.

neuroscience↗

bioRxiv2019

Microbiome Determinants and Physiological Effects of the Benzoate-Hippurate Microbial-Host Co-Metabolic Pathway

ObjectiveGut microbial products are involved in type 2 diabetes, obesity and insulin resistance. In particular, hippurate, a hepatic phase 2 conjugation product of microbial benzoate metabolism, has been associated with a healthy phenotype. This study aims to identify metagenomic determinants and test protective effects of hippurate. DesignWe profiled the urine metabolome by 1H Nuclear Magnetic Resonance (NMR) spectroscopy to derive associations with metagenomic sequences in 271 middle-aged Danish individuals to identify dietary patterns in which urine hippurate levels were associated with health benefits. We follow up with benzoate and hippurate infusion in mice to demonstrate causality on clinical phenotypes. ResultsIn-depth analysis identifies that the urine hippurate concentration is associated with microbial gene richness, microbial functional redundancy as well as functional modules for microbial benzoate biosynthetic pathways across several enterotypes. Through dietary stratification, we identify a subset of study participants consuming a diet rich in saturated fat in which urine hippurate, independently of gene richness, accounts for links with metabolic health that we previously associated with gene richness. We then demonstrate causality in vivo through chronic subcutaneous infusions of hippurate or benzoate (20 nmol/day) resulting in improved glycemic control in mice fed a high-fat diet. Hippurate improved insulin secretion through increased {beta}-cell mass and reduced liver inflammation and fibrosis, whereas benzoate treatment resulted in liver inflammation. ConclusionOur translational study shows that the benzoate-hippurate pathway brings a range of metabolic improvements in the context of high-fat diets, highlighting the potential of hippurate as a mediator of metabolic health.

systems biology↗

bioRxiv2019

Assessment of computational methods for the analysis of single-cell ATAC-seq data

BackgroundRecent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges. scATAC-seq experiments sample DNA, which, due to low copy numbers (diploid in humans) lead to inherent data sparsity (1-10% of peaks detected per cell) compared to transcriptomic (scRNA-seq) data (20-50% of expressed genes detected per cell). Such challenges in data generation emphasize the need for informative features to assess cell heterogeneity at the chromatin level.\n\nResultsWe present a benchmarking framework that was applied to 10 computational methods for scATAC-seq on 13 synthetic and real datasets from different assays, profiling cell types from diverse tissues and organisms. Methods for processing and featurizing scATAC-seq data were evaluated by their ability to discriminate cell types when combined with common unsupervised clustering approaches. We rank evaluated methods and discuss computational challenges associated with scATAC-seq analysis including inherently sparse data, determination of features, peak calling, the effects of sequencing coverage and noise, and clustering performance. Running times and memory requirements are also discussed.\n\nConclusionsThis reference summary of scATAC-seq methods offers recommendations for best practices with consideration for both the non-expert user and the methods developer. Despite variation across methods and datasets, SnapATAC, Cusanovich2018, and cisTopic outperform other methods in separating cell populations of different coverages and noise levels in both synthetic and real datasets. Notably, SnapATAC was the only method able to analyze a large dataset (> 80,000 cells).

bioinformatics↗

bioRxiv2018

Interpretable and accurate prediction models for metagenomics data

Biomarker discovery using metagenomic data is becoming more prevalent for patient diagnosis, prognosis and risk evaluation. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes. Moreover, they seldom generalize well when learned on small datasets. Here, we introduce an original approach that focuses on three models inspired by microbial ecosystem interactions: the addition, subtraction, and ratio of microbial taxon abundances. While being extremely simple, their performance is surprisingly good and compares to or is better than Random Forest, SVM or Elastic Net. Such models besides being interpretable, allow distilling biological information of the predictive core-variables. Collectively, this approach builds up both reliable and trustworthy diagnostic decisions while agreeing with societal and legal pressure that require explainable AI models in the medical domain.

bioinformatics↗

bioRxiv2018

Analysis and comparison of genome editing using CRISPResso2

Genome editing technologies are rapidly evolving, and analysis of deep sequencing data from target or off-target regions is necessary for measuring editing efficiency and evaluating safety. However, no software exists to analyze base editors, perform allele-specific quantification or that incorporates biologically-informed and scalable alignment approaches. Here, we present CRISPResso2 to fill this gap and illustrate its functionality by experimentally measuring and analyzing the editing properties of six genome editing agents.

bioinformatics↗