Biology subjects

Louis, S.

Publications and source records attributed to Louis, S..

5 recordsLinked to original sources

bioRxiv2026

The DGKK mRNA is a primary target of the Prader-Willi syndrome-associated snoRNA SNORD116

Box C/D small nucleolar RNAs (SNORDs) classically guide site-specific modification of ribosomal RNAs through antisense elements located upstream of their D[prime] and D boxes, termed ASE1 and ASE2. Yet many orphan SNORDs have no established primary targets, including the paternally expressed multicopy SNORD116 family implicated in Prader-Willi syndrome. Our previous comparative analysis identified the DGKK/Dgkk interaction as the most evolutionarily persistent candidate involving the highly conserved SNORD116 ASE1 sequence and showed that SNORD116 depletion increases DGKK RNA abundance in human cells. Here, we re-evaluated this interaction alongside a focused set of recently published candidates and asked whether evolutionary persistence was accompanied by independent evidence of regulation. DGKK/Dgkk showed reproducible increases following transient SNORD116 loss across human iPSC-derived neural cells and in brain tissues from Snord116-knockout mice. Its predicted SNORD116 interaction site combined a marked local depletion of human sequence variation with an overlapping cis-regulatory interval identified in mouse. SNORD116 deficiency was also associated with increased endogenous DGK[kappa]; protein across several mouse brain regions, including the hypothalamus. More broadly, comparison across the candidate set showed that evolutionary persistence, duplex stability and expression response did not systematically align, indicating that sequence-based properties alone do not allow reliable prediction of responses to SNORD116 loss. Together, these data support DGKK/Dgkk as the best-supported primary regulatory target of SNORD116 to date and establish it as a model for dissecting the regulatory mechanism of this orphan snoRNA family.

molecular biology↗

bioRxiv2026

Chemical Probing of Diacylglycerol Dynamics at Lipid Droplets

Diacylglycerols (DAGs) are central intermediates in lipid metabolism and signaling, yet their trafficking and persistence within lipid droplets (LDs) remain incompletely understood due to the lack of chemically stable, DAG-mimetic imaging tools. Here, we report the development of a family of solvatochromic fluorescent lipid analogs, termed DONDI, designed to probe DAG-associated dynamics at LDs. These probes are based on a 1,8-naphthalimide scaffold conjugated to modified aminoglycerol backbones bearing oleoyl chains to mimic native glycerolipids. Biophysical characterization and atomistic molecular dynamics simulations revealed probe-specific membrane insertion and hydrogen-bonding behaviors consistent with distinct lipid-mimetic properties. Live-cell imaging in NIH 3T3 fibroblasts demonstrated that DONDI probes were efficiently internalized and selectively accumulated within lipid droplets. Structure-function analysis identified DONDI-5 as the closest mimic of 1,2-diacylglycerol, displaying rapid uptake, strong LD enrichment, and prolonged intracellular retention without detectable relocalization to other cellular membranes. These properties enabled sustained visualization of LD-associated DAG pools over extended time scales. Collectively, this work establishes DONDI-5 as a chemically stable DAG-mimetic probe and provides direct experimental support that DAGs can be transported to and transiently stored within lipid droplets without prior conversion to triacylglycerols.

biochemistry↗

bioRxiv2025

Generation of apical-out nasal organoids to facilitate viral infection and drug screening

Advanced culture systems such as organoids can serve as powerful platforms to study epithelial physiology, as they recapitulate the organisation and many key functions of the tissue of origin. The nasal epithelium is the first respiratory epithelium that is exposed to inhaled airborne pathogens. As a result, it is crucial to model host-pathogen interactions occurring in this tissue. To facilitate the efficient modelling of these interactions, we have developed a method to generate de novo apical-out nasal organoids from nasal epithelial cell aggregates. Optimisation of this method revealed a stark tissue-specific effect of the culture temperature, as apical-out nasal organoids were generated in much higher efficiency at 32.5 {degrees}C, compared to more widely used temperatures of 37{degrees}C. These organoids are composed of ciliated, basal and goblet cells and are produced in a completely standardised and scalable manner, devoid of any extracellular matrix hydrogel. Moreover, they displayed high homogeneity in size and cellular composition, as well as susceptibility to viral infections and capability to model antiviral drug responses. Here, we describe a method for the efficient and reproducible generation of apical-out nasal organoids with high potential to be utilised in host-pathogen interaction studies and personalised medicine from easy-to-access nasal swabs.

cell biology↗

bioRxiv2024

Inflammation in Areas of Fibrosis Precedes Loss of Kidney Function in Lupus Nephritis

BackgroundInterstitial fibrosis in lupus nephritis (LN) is often infiltrated by immune cells but typically regarded as nonspecific "scar reaction." This study aimed to investigate the relationship between inflammatory fibrosis and kidney disease progression in LN. MethodsInterstitial fibrosis and tubular atrophy (IFTA) were scored in 124 LN kidney biopsies. Inflammation in areas of IFTA (i-IFTA) was graded 0-3 according to the Banff Classification of Allograft Pathology. Significant glomerular filtration rate (GFR) loss was defined as a decline of >15 ml/min at 3 years from biopsy. Immune cell phenotype was defined by serial immunohistochemistry (13-plex). ResultsIFTA was observed in 88/124 (71%) biopsies, and i-IFTA was identified in 76/88 (86%) cases. The distribution of i-IFTA grades was heterogenous across all IFTA grades. In patients with moderate-to-severe IFTA (>25%), the degree of i-IFTA was associated with a higher risk of significant GFR loss: 0/2 (0%), 1/3 (33%), 3/4 (75%), and 7/9 (78%) for i-IFTA grades 0, 1, 2, and 3, respectively (p = 0.028). Multiplexed histology revealed that i-IFTA was mostly composed of CD163+ macrophages and CD4 T cells, followed by CD8 T cells and granulocytes. ConclusionI-IFTA is frequently observed in LN and is dominated by macrophages and T cells. For patients with baseline IFTA >25%, the degree of i-IFTA emerged as a predictor of GFR loss. These data support the routine scoring of i-IFTA in LN due to its prognostic implications and nominate i-IFTA as a potential therapeutic target. LAY SUMMARYScar tissue often contains immune cells, but we still do not fully understand their role. In lupus nephritis (LN), this is typically dismissed as "nonspecific inflammation". However, our study analyzed kidney biopsies from 124 people with LN and found that inflammation in scarred areas may predict future kidney function loss. Specifically, we identified a type of immune cell, CD163+ macrophages, that may contribute to scarring and kidney damage. Our findings suggest that routinely assessing inflammation in scarred areas could help predict kidney health in LN patients and highlight a possible new target for therapies to prevent kidney damage.

immunology↗

bioRxiv2022

CARD9 in Neutrophils Protects from Colitis and Controls Mitochondrial Metabolism and Cell Survival

ObjectivesInflammatory bowel disease (IBD) results from a combination of genetic predisposition, dysbiosis of the gut microbiota and environmental factors, leading to alterations in the gastrointestinal immune response and chronic inflammation. Caspase recruitment domain 9 (Card9), one of the IBD susceptibility genes, has been shown to protect against intestinal inflammation and fungal infection. However, the cell types and mechanisms involved in the CARD9 protective role against inflammation remain unknown. DesignWe used dextran sulfate sodium (DSS)-induced and adoptive transfer colitis models in total and conditional CARD9 knock-out mice to uncover which cell types play a role in the CARD9 protective phenotype. The impact of Card9 deletion on neutrophil function was assessed by an in vivo model of fungal infection and various functional assays, including endpoint dilution assay, apoptosis assay by flow cytometry, proteomics and real time bioenergetic profile analysis (Seahorse). ResultsLymphocytes are not intrinsically involved in the CARD9 protective role against colitis. CARD9 expression in neutrophils, but not in epithelial or CD11c+ cells, protects against DSS-induced colitis. In the absence of CARD9, mitochondrial dysfunction in neutrophils leads to their premature death through apoptosis, especially in oxidative environment. The decrease of fonctional neutrophils in tissues could explain the impaired containment of fungi and increased susceptibility to intestinal inflammation. ConclusionThese results provide new insight into the role of CARD9 in neutrophil mitochondrial function and its involvement in intestinal inflammation, paving the way for new therapeutic strategies targeting neutrophils. Summary boxO_LIWhat is already known about this subject? O_LIInflammatory bowel disease (IBD) results from genetic predisposition, microbiota dysbiosis and environmental factors, but the alterations of the immune response leading to chronic intestinal inflammation are still not fully understood. C_LIO_LICaspase recruitment domain 9 (Card9), one of the IBD susceptibility genes, has been shown to protect against intestinal inflammation and fungal infection. C_LIO_LIHowever, the cell types and cellular mechanisms involved in the CARD9 protective role against inflammation remain unknown. C_LI C_LIO_LIWhat are the new findings? O_LICARD9 expression in neutrophils, but not in lymphocytes, epithelial cells or CD11c+ cells, protects against DSS-induced colitis. C_LIO_LIIn the absence of CARD9, mitochondrial dysfunction in neutrophils leads to their premature death through apoptosis, especially in oxidative environment. C_LIO_LIThe decrease of fonctional neutrophils in tissues could explain the impaired containment of fungi and increased susceptibility to intestinal inflammation. C_LI C_LIO_LIHow might it impact on clinical practice in the foreseeable future? O_LIThese results provide new insight into the role of CARD9 in neutrophil mitochondrial function and its involvement in intestinal inflammation. C_LIO_LIUnderstanding the role of neutrophils in chronic inflammation could lead to innovative therapeutic strategies targeting these key immune cells for various complex diseases. C_LI C_LI

immunology↗