Biology subjects

Raymond, F.

Publications and source records attributed to Raymond, F..

5 recordsLinked to original sources

bioRxiv2025

Fetal Bovine and Calf Serums Differ in Their Contents of Endocannabinoids, Unsaturated Fatty Acids, Monoacyl-Glycerols, N-Acyl-Ethanolamines, Oxylipins and Cytokines.

Cell culture relies heavily on serum supplementation, but serum composition makes it difficult to ensure reproducibility and consistency of experimental results. Consequently, research groups must test multiple batches to ensure the functionality and reproducibility of their models of their models. The commonly used serums are fetal bovine serums (FBS) and calf serums (CS), which have been recognized as crucial in modulating cellular processes. While having been utilized for decades, little information is known about their respective lipid mediator contents. This study explored the presence of several major bioactive lipids involved in the regulation of inflammation, metabolism, differentiation, immune response, neuroprotection, and vascular homeostasis. These included polyunsaturated fatty acids, monoacylglycerols (MAGs), N-acyl-ethanolamines (NAEs), and oxylipins. As compared to FBS, CS samples were enriched in most fatty acids except for arachidonic acid. The levels of the endocannabinoids 2-arachidonoyl-glycerol (2-AG) and N-arachidonoyl-ethanolamine (AEA) followed the same pattern as arachidonic acid. On the other hand, most lipoxygenase-derived mediators, including, leukotriene B4, showed higher abundance in CS. Accordingly, CS serum activated the random migration of human neutrophils to a much greater extent than FBS, an effect attenuated by the BLT1 receptor antagonist CP 105,696. These findings highlight how bovine serum lipid composition is a major determinant modulating cellular responses and might thus impact experimental reproducibility. The data presented herein will help key insights beyond conventional cell culture optimization and might represent key features to consider when planning in cellulo experiments across numerous fields, also beyond immunology.

cell biology↗

bioRxiv2020

In-vivo Transcriptomic Profiling of Systemic Aging using Cell Encapsulation

Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.

bioengineering↗

bioRxiv2018

AMPK promotes induction of a tumor suppressor FLCN through activation of TFEB independently of mTOR

AMP-activated protein kinase (AMPK) is a central energy sensor and master regulator of energy homeostasis. AMPK not only elicits acute metabolic responses, but also promotes metabolic reprogramming and adaptions in the long-term through regulation of specific transcription factors/co-activators. We performed a whole-genome transcriptome profiling in wild-type and AMPK-deficient mouse embryonic fibroblasts (MEF) and mouse primary hepatocytes that had been treated with two distinct classes of small-molecule AMPK activators, namely 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) or 991. This led to the identification of distinct compound-dependent gene expression signatures and to the discovery of several AMPK-regulated genes, including folliculin (Flcn), a gene encoding for a tumor suppressor and nutrient sensor. Gene set enrichment and pathway analyses identified the lysosomal pathway and the associated transcription factor EB (TFEB) as key transcriptional mediator responsible for AMPK-dependent gene expression changes. AMPK-induced Flcn expression was abolished in TFEB/TFE3 double knockout MEF and the promoter activity of Flcn was profoundly reduced when its putative TFEB-binding site was mutated. Mechanistically, we have found that AMPK promotes the dephosphorylation and nuclear localization of TFEB independently of mTOR activity.\n\nCollectively, we identified the AMPK-TFEB-FLCN axis as a potential key regulator for cellular and metabolic homeostasis. Moreover, data from zebrafish with physiologically and pharmacologically activated AMPK confirmed the AMPK-TFEB-FLCN cascade in vivo.

molecular biology↗

bioRxiv2018

PGC1a and Exercise Adaptations in Zebrafish

Fish species display huge differences in physical activity ranging from lethargy to migration of thousands of miles, making them an interesting model to identify determinants of physical fitness. Here, we show a remarkable plasticity of zebrafish in response to exercise and induction of PGC1 (encoded by PPARGC1A), a dominant regulator of mitochondrial biogenesis. Forced expression of human PPARGC1A induces mitochondrial biogenesis, an exercise-like gene expression signature, and physical fitness comparable to wild-type animals trained in counter-current swim tunnels. Quantifying transcriptional and proteomic changes in response to exercise or PGC1, we identify conserved exercise adaptations, including a stoichiometric induction of the electron transport chain (ETC) that re-organizes into respiratory supercomplexes in both conditions. We further show that ndufa4/ndufa4l, previously assigned to complex I, associates to free and supramolecular complex IV in vivo. Thus, zebrafish is a useful and experimentally tractable vertebrate model to study exercise biology, including ETC expression and assembly.\n\nHIGHLIGHTSO_LIPGC1 reprograms zebrafish skeletal muscle to a red fiber phenotype and increases exercise performance\nC_LIO_LIZebrafish show a high molecular plasticity in response to PGC1 and exercise\nC_LIO_LISWATH-MS proteomics show a stoichiometric induction of the electron transport chain that organizes as supercomplexes in response to PGC1 and exercise\nC_LIO_LIndufa4/ndufa4l associate to free and supramolecular complex IV in vivo\nC_LI

physiology↗

bioRxiv2018

Interpretable genotype-to-phenotype classifiers with performance guarantees

Understanding the relationship between the genome of a cell and its phenotype is a central problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with great challenges for machine learning algorithms that limit their use in this setting. The high dimensionality of the data tends to hinder generalization and challenges the scalability of most learning algorithms. Additionally, most algorithms produce models that are complex and difficult to interpret. We alleviate these limitations by proposing strong performance guarantees, based on sample compression theory, for rule-based learning algorithms that produce highly interpretable models. We show that these guarantees can be leveraged to accelerate learning and improve model interpretability. Our approach is validated through an application to the genomic prediction of antimicrobial resistance, an important public health concern. Highly accurate models were obtained for 12 species and 56 antibiotics, and their interpretation revealed known resistance mechanisms, as well as some potentially new ones. An open-source disk-based implementation that is both memory and computationally efficient is provided with this work. The implementation is turnkey, requires no prior knowledge of machine learning, and is complemented by comprehensive tutorials.

genomics↗