Biology subjects

Chaoui, K.

Publications and source records attributed to Chaoui, K..

7 recordsLinked to original sources

bioRxiv2026

A generalizable normalization framework to decouple protocol and instrument effects: Application to high-sensitivity proteomics multicentric study (PME13)

Multicenter studies are essential for benchmarking analytical workflows, yet their interpretation is often confounded by the combined effects of experimental protocols and instrumentation. To address this challenge, we introduce a simple normalization-based analytical framework, the recovery metric ({rho}), designed to decouple protocol driven effects from instrument dependent variability. We applied this framework to the 13th Proteomics Multicentric Experiment (PME13), a large multicentric proteomics dataset generated across 27 laboratories using high sensitivity workflows and varying sample preparation protocols. By leveraging a common digested reference sample, {rho} enables direct cross-comparison of all datasets on a unified scale, effectively minimizing instrument-related biases. Using this approach, we demonstrate that apparent instrument dependent trends are largely removed when evaluated through {rho}, revealing consistent protocol driven effects across laboratories. Statistical modeling identified key variables influencing {rho}, including sample input amount, reduction and alkylation, and the use of n-dodecyl-{beta}-D-maltoside (DDM). While DDM was associated with improved {rho}, reduction and alkylation and additional handling steps led to reduced performance, particularly at low input levels. We further highlight practical considerations for the application of ratio based normalization, including the occurrence of values exceeding theoretical bounds, which reflect deviations from underlying assumptions and require appropriate filtering. Overall, this work establishes a generalizable analytical strategy for disentangling confounding factors in multicentric datasets and provides practical guidelines for optimizing high sensitivity proteomics (HSP) workflows. The proposed framework is broadly applicable to other analytical fields where cross laboratory comparability is required.

bioinformatics↗

bioRxiv2026

ST8SIA4-mediated polysialylation is critical for CCR2-driven monocyte egress from the bone marrow

Polysialylation is a rare post-translational protein modification essential for brain development and synaptic plasticity, where it fine-tunes cell-cell and cell-matrix interactions to direct neuronal migration, neurite outgrowth and synaptogenesis. Although polysialic acid is also expressed on circulating leukocytes, its functions in the immune system remain largely unexplored. Guided by analysis of publicly available human genomic data showing that naturally occurring variants of ST8SIA4, which encodes one of the two enzymes that mediate polysialylation, associate with reduced circulating monocyte counts, we investigated the in vivo role of this enzyme in monocyte biology. Using St8sia4-deficient mice, we show that ST8SIA4-dependent polysialylation is essential for CCR2-mediated egress of inflammatory monocytes from the bone marrow at steady state and during Mycobacterium tuberculosis infection. We confirm NCAM1 as the principal polysialylated protein in inflammatory monocytes and demonstrate that Ncam1-deficient mice phenocopy the monocyte defects observed in St8sia4-deficient animals. Mechanistically, loss of ST8SIA4-dependent polysialylation impairs engagement and internalization of the CCR2 ligands CCL2 and CCL7, accompanied by disrupted CCR2 surface organization and extensive cytoskeletal remodeling. Together, these findings identify polysialylation as a previously unrecognized regulator of CCR2 function and monocyte mobilization, with broad implications for immune surveillance and inflammatory responses. Highlights- Human ST8SIA4 variants are associated with reduced blood monocyte and lymphocyte counts and increased risk of SLE. - St8sia4-/- mice exhibit monocytopenia with impaired CCR2-mediated egress of inflammatory monocytes from the bone marrow both at steady state and during Mycobacterium tuberculosis infection. - ST8SIA4 polysialylates NCAM1 (CD56) in inflammatory monocytes, and Ncam1-/- - mice phenocopy the monocytopenia observed in St8sia4-/- mice. - Loss of ST8SIA4 and polysialylation impairs CCR2-mediated binding and endocytosis of CCL2 and CCL7 by monocytes. - Polysialic acid itself does not function as a co-receptor for these chemokines, revealing a new paradigm for its role in immune cell trafficking. - Proper CCR2 surface distribution and function, as well as cytoskeletal organization in inflammatory monocytes, depend on ST8SIA4-mediated polysialylation.

immunology↗

bioRxiv2025

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they acquire differ substantially, thus requiring tailored analysis algorithms. Hence, many dedicated bioinformatics workflows are developed. These are in constant evolution, and the community lacks a centralized platform for comparing their performance. Here, we propose ProteoBench, a single platform that brings together software developers and software users to provide an ever-evolving comparison of state-of-the-art proteomics data processing tools. ProteoBench is an open-source resource that enables the community to evaluate data analysis workflows, develop benchmarking modules dedicated to specific comparisons, and discuss the best methods to compare software tools. The platform ensures that the benchmark evolves alongside advances in proteomics data analysis workflows. ProteoBench guides researchers towards the best-suited tool and parameters for their specific project and data according to their needs, and developers can test their newly developed tools or workflows privately, before adding them as public references. This community-driven effort will increase transparency and reproducibility between MS data analysis workflows, as well as facilitate the development and publication of software workflows in the field.

bioinformatics↗

bioRxiv2025

Drosophila melanogaster miPEP8 regulates cell size through its interaction with ref(2)P/p62

MiPEPs are microproteins encoded by primary transcripts of microRNAs (pri-miRNAs). Initially identified in plants, we recently characterized a miPEP in Drosophila melanogaster, named miPEP8, which is involved in the regulation of wing size. However, mechanisms at play are unknown. In the present study, we take advantage of the drosophila cell line Schneider 2 (S2) to further investigate miPEP8 function at the molecular level. Overexpressing miPEP8 in S2 cells induced a reduction of cell size as well as an increase of the proportion of cells in the G1 phase of the cell cycle and an increase of the autophagic flux. A proteomics analysis revealed that miPEP8 overexpression in S2 cells induces the upregulation of several proteins including the autophagosome cargo protein ref(2)P (the orthologue of the human p62/Sequestosome 1 protein). The interactome of miPEP8 was generated and revealed interactions between this miPEP8 and the mTORC1/autophagy pathway. Bioinformatics analysis identified a short linear motif (SLiM) on miPEP8 sequence. Mutation of this SLiM prevented the interaction between ref(2)P/p62 and miPEP8. Mutation of the SLiM also reverted the smaller cell size phenotype observed when overexpressing miPEP8 in S2 cells. Finally, the cell size phenotype was reversed when cells were treated with RNA interference targeting ref(2)P/p62, suggesting that this protein plays a role in regulating the cell size in Drosophila.

biochemistry↗

bioRxiv2021

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).

bioinformatics↗

bioRxiv2020

Irgm2 and Gate-16 cooperatively dampen targeting of caspase-11 to Gram-negative bacterial products

Inflammatory caspase-11 (rodent) and caspases-4 and -5 (human) detect gram-negative bacterial component LPS in the host cell cytosol, which promotes activation of the non-canonical inflammasome. Although non-canonical inflammasome-induced pyroptosis and IL-1 related cytokine release is of importance to mount an efficient immune response against various bacteria, its unrestrained activation drives sepsis. This suggests that cellular components might tightly control the threshold level of the non-canonical inflammasome in order to ensure efficient but not deleterious inflammatory response. Here we show that the IFN-inducible protein Irgm2 and the ATG8 family member Gate-16 cooperatively slow down non-canonical inflammasome activation both in macrophages and in vivo. Specifically, the Irgm2/Gate-16 axis dampens caspase-11 targeting to intracellular bacteria, which lower caspase-11-mediated pyroptosis and cytokine release. Specifically, deficiency in Irgm2 or Gate16 opens an alternative road for caspase-11 targeting to intracellular bacteria, independently of the classical pathway driven by the Guanylate Binding Proteins (GBPs). Thus, our findings provide new molecular effectors involved at fine-tuning the optimal non-canonical inflammasome response and add novel insights in the understanding of the immune pathways they control.

immunology↗

bioRxiv2019

Yellow adipocytes comprise a new adipocyte sub-type present in human bone marrow

During energy demanding conditions, white adipocytes store triglycerides and release fatty acids through lipolysis. In contrast, bone marrow adipocytes (BM-Ad) increase in size during caloric restriction, suggesting this fat depot exhibits precise metabolic specificity. We found subcutaneous adipocytes (SC-Ad) and BM-Ad share morphological features, but possess distinct lipid metabolism. BM-Ad show enrichment in cholesterol-oriented metabolism that correlates with increased free cholesterol content, while proteins involved in lipolysis were downregulated. A strong down-regulation in expression of monoacylglycerol (MG) lipase was observed leading to an accumulation of major MG species and accordingly the basal and induced lipolytic responses were absent in BM-Ad. These features are not recapitulated in vitro using differentiated bone marrow mesenchymal stem cells. Since our data demonstrate that BM-Ad comprise a distinct class of adipocytes, we propose renaming them yellow adipocytes.

physiology↗