Biology subjects

Kadri, S.

Publications and source records attributed to Kadri, S..

9 recordsLinked to original sources

bioRxiv2026

Aggregated Low-Density Lipoprotein (agLDL) Triggers Inflammatory Responses in Macrophages through Toll-Like Receptor 4 (TLR4)

Atherosclerosis is a chronic inflammatory disease primarily initiated by the sub-endothelial retention and modification of low-density lipoproteins (LDL), such as oxidation and aggregation. While oxidized LDL (oxLDL) exists in atherosclerotic lesions, aggregated lipoproteins are also prominent. Aggregated LDL (agLDL), for instance, is viewed as a passive substrate for macrophages to uptake and form foam cells. Recent studies show that agLDL, through toll-like receptor 4 (TLR4), induces formation of lysosomal synapses, which drive agLDL degradation by macrophages, a process described as "digestive exophagy". As TLR4 is one of the pattern-recognition receptors for inflammatory responses in macrophages, we postulated that agLDL could initiate macrophage inflammation along with lipoprotein degradation/internalization, thereby contributing to a low degree of chronic inflammation in atherosclerosis. Here, we demonstrate that agLDL directly activates the canonical NF-{kappa}B signaling pathway and triggers a pro-inflammatory transcriptional program through TLR4, which closely resembles classical lipopolysaccharide (LPS)-mediated TLR4 activation. In addition, agLDL also activates TLR4 to generate inflammatory macrophages that recruit immune cells, a key process in the development of atherosclerotic lesions. Our findings therefore support a novel dual functionality of agLDL: a lipid donor and an inflammatory agonist. This establishes the agLDL-TLR4-NF-{kappa}B axis as a direct link between LDL aggregation in the intima and the initiation of sterile vascular inflammation. It also strengthens the understanding of the role of digestive exophagy with new mechanistic details.

cell biology↗

bioRxiv2025

Single cell decomposition of multicellular aging programs associated with impaired lung regeneration

Aging impairs the regenerative capacity of mammalian organs and is a major risk factor for organ fibrosis. Mechanisms underlying persistent fibrosis after lung injury in old individuals remain unclear. We used longitudinal single-cell RNA-seq after lung injury and dissected aging effects computationally and experimentally at baseline and during repair. In old mice, sustained fibroblast activation in the resolution phase of fibrosis was associated with prolonged epithelial senescence and persistent epithelial-mesenchymal crosstalk. Single-cell interpretable tensor decomposition analysis revealed that aging most strongly affected T/B-lymphocytes and macrophages. Notably, we identified a Granzyme K-high CD8+ T cell state that was unique to aged mice, co-localized with epithelial progenitors, and its co-culture or Gzmk treatments in lung organoids impaired progenitor function by inducing stem cell senescence. In summary, our study highlights the effects of immune aging on epithelial progenitor function and provides a time-resolved high resolution map of lung regeneration in the context of aging.

cell biology↗

bioRxiv2025

Optimization of Genome-wide CRISPR Screens using dual-guide RNA Infection with Cas9 Electroporation (DICE)

Single-guide RNA lentiviral infection with Cas9 protein electroporation (SLICE) enables CRISPR screening in primary cell types that require transient Cas9 expression yet is limited by scalability and robustness. Here, we introduce dual-guide RNA infection with Cas9 electroporation (DICE), which expresses two guides from the same lentiviral construct that target the same gene. In genome-wide screens, DICE outperformed SLICE in defining essential genes and modulators of PD-L1 expression in IFN gamma activated THP1 cells. Collectively, these data demonstrate that DICE can be utilized for reduced-scale CRISPR screens in cell types with transient Cas9 protein expression without sacrificing screening quality.

genomics↗

bioRxiv2022

Optimization of genomewide CRISPR screens using AsCas12a and multi-guide arrays

Genomewide loss-of-function (LOF) screening using CRISPR (clustered regularly interspaced short palindromic repeats) has facilitated the discovery of novel gene functions across diverse physiological and pathophysiological systems. A challenge with conventional genomewide CRISPR/Cas9 libraries is the unwieldy size (60,000 to 120,000 constructs), which is resource intensive and prohibitive in some experimental contexts. One solution to streamlining CRISPR screening is by multiplexing two or more guides per gene on a single construct, which enables functional redundancy to compensate for suboptimal gene knockout by individual guides. In this regard, AsCas12a (Cpf1) and its derivatives, e.g., enhanced AsCas12a (enAsCas12a), have enabled multiplexed guide arrays to be specifically and efficiently processed for genome editing. Prior studies have established that multiplexed CRISPR/Cas12a libraries perform comparably to the larger equivalent CRISPR/Cas9 libraries, yet the most efficient CRISPR/Cas12a library design remains unresolved. Here, we demonstrate that CRISPR/Cas12a genomewide LOF screening performed optimally with three guides arrayed per gene construct and could be adapted to robotic cell culture without noticeable differences in screen performance. Thus, the conclusions from this study provide novel insight to streamlining genomewide LOF screening using CRISPR/Cas12a and robotic cell culture.

genetics↗

bioRxiv2021

PTEN differentially regulates endocytosis, migration, and proliferation in the enteric protozoan parasite Entamoeba histolytica

PTEN is a lipid phosphatase that is highly conserved and involved in a broad range of biological processes including cytoskeletal reorganization, endocytosis, signal transduction, and cell migration in all eukaryotes. Although regulation of phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P3] signaling via PTEN has been well established in model organisms and mammals, it remains elusive in the parasitic protist E. histolytica, which heavily relies on PtdIns phosphate(s)-dependent membrane traffic, migration, and phago- and trogocytosis for its pathogenesis. In this study, we characterized the major PTEN from E. histolytica, EhPTEN1, which shows the highest expression at the transcript level in the trophozoite stage among 6 possible PTENs, to understand the significance of PtdIns(3,4,5)P3 signaling in this parasite. Live imaging of GFP-EhPTEN1 expressing amebic trophozoites showed localization mainly in the cytosol with a higher concentration at pseudopods and the extending edge of the phago- and trogocytic cups. Furthermore, quantitative analysis of phago- and trogocytosis using a confocal image cytometer showed that overexpression of EhPTEN1 caused reduction in trogo- and phagocytosis while transcriptional gene silencing of EhPTEN1 gene caused opposite phenotypes. These data suggest that EhPTEN1 has an inhibitory role in these biological processes. Conversely, EhPTEN1 acts as a positive regulator for fluid-phase and receptor-mediated endocytosis in E. histolytica trophozoites. Moreover, we showed that EhPTEN1 was required for optimal growth and migration of this parasite. Finally, the phosphatase activity of EhPTEN1 towards PtdIns(3,4,5)P3 was demonstrated, suggesting that the biological roles of EhPTEN1 are likely linked to its catalytic function. Taken together, these results indicate that EhPTEN1 differentially regulates multiple cellular activities essential for proliferation and pathogenesis of the organism, via PtdIns(3,4,5)P3 signaling. Elucidation of biological roles of PTEN and PtdIns(3,4,5)P3 signaling at the molecular levels promotes our understanding of the pathogenesis of this parasite and potentially leads to the design of novel therapeutics against amebiasis. Author summaryEntamoeba histolytica is an intestinal protozoan parasite that causes amoebic dysentery and liver abscesses in humans. It has been well understood how the amoebas ability to ingests and destroy human cells and invade tissues contributes to disease symptoms such as bloody diarrhea. The underlying mechanisms for such activities, called pathogenicity, include trafficking (transport) and secretion of cytolytic proteins, migration (ameboid movement), and ingestion and destruction of human cells, heavily rely on the signal transduction system via metabolism (synthesis and decomposition) of phosphoinositides (phosphatidylinositols containing 0-5 phosphates), and downstream regulation of cytoskeleton (dynamic network of interlinking protein filaments, such as actin, in the cytoplasm). In this study, we characterized one enzyme called EhPTEN1, which degrades and inactivate PtdIns(3,4,5)P3. We have shown that EhPTEN1 is involved in migration, internalization of soluble and solid materials (endocytosis, trogo-, and phagocytosis). EhPTEN1 apparently regulates cell migration, endocytosis, trogo-, phagocytosis, and proliferation in a complex fashion. Our findings help in the elucidation of the physiological significance of PTEN and cellular events regulated via phosphoinositides in this enteric parasite and other pathogenic parasites, and potentially lead to the development of new control measures against parasitic diseases.

microbiology↗

bioRxiv2021

Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression

Classification and characterization of neuronal types are critical for understanding their function and dysfunction. Neuronal classification schemes typically rely on measurements of electrophysiological, morphological, and molecular features, but aligning such datasets has been challenging. Here, we present a unified classification of mouse retinal ganglion cells (RGCs), the sole retinal output neurons. We used visually-evoked responses to classify 1859 mouse RGCs into 42 types. We also obtained morphological or transcriptomic data from subsets and used these measurements to align the functional classification to publicly available morphological and transcriptomic data sets. We created an online database that allows users to browse or download the data and to classify RGCs from their light responses using a machine learning algorithm. This work provides a resource for studies of RGCs, their upstream circuits in the retina, and their projections in the brain, and establishes a framework for future efforts in neuronal classification and open data distribution.

neuroscience↗

bioRxiv2020

The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen Plasmodium falciparum

RNA as an effector of biological functions often adopts secondary and tertiary structural folds. Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis, combining high-throughput nuclease mapping of RNA structures by duplex RNA-seq, immunoaffinity purification and RNA analysis, collectively measured differentially base-paired RNA regions during the parasite development. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, ~71% of the genes with secondary structures are found to be protein coding mRNAs. Mapping pattern of these base-paired RNAs corresponded to all parts of protein-coding mRNAs, including 5 UTR, CDS and 3 UTR. In addition to histone family genes which are known to form secondary structures in their mRNAs, transcripts from genes which are important for transcriptional and post-transcriptional control, such as unique plant-like transcription factor family, ApiAP2, DNA/RNA binding protein family, Alba, ribosomal proteins and eukaryotic initiation factors involved in translational control and the ones important for RBC invasion and cytoadherence also show strong accumulation of duplex RNA reads in various asexual stages. Intriguingly, our study determined a positive relationship between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.

molecular biology↗

bioRxiv2020

Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean)

The brown mussel Perna perna is a marine bivalve that is widely distributed and consumed along the east coast of Algeria. Due to its filter-feeding capacity, this mollusk can accumulate large quantities of pathogenic microorganisms from the surrounding waters, thus acting as bio-indicator of coastal environments. The objective of this study is to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected from four different sites in the Gulf of Annaba through physicochemical, biochemical and molecular analysis. The obtained results revealed that the levels of fecal indicator bacteria (FIB) were alarmingly high at Sidi Salem and Rezgui Rachid when compared with the two other sites (p < 0.05) and largely exceeded the permissible limits. Besides, P. perna collected from all sites were several fold more contaminated by these germs than seawater samples, notably, during the warm season of the study period. Biochemical and molecular analysis showed that isolated bacteria from both environmental compartments were mostly potentially pathogenic species such as E. coli, Salmonella, Staphylococcus, Klebsiella, Pseudomonas and Proteus. These principal findings demonstrate the strong involvement of anthropogenic activities on the microbiological quality of the Gulf and highlight the role of P. perna as an effective bio-indicator of the bacteriological quality of coastal waters.

ecology↗

bioRxiv2019

Different energetic diets affect the maintenance of Apis mellifera L. colonies during off-season

The aim of this study wasto evaluate the best energetic foodforuse in the maintenance of honey bee colonies during the off-season. To do this, 20Apis mellifera beehives were used(with five beehives per treatment): CTL,control (without feeding); SJ,sugarcane juice; SS,sugar syrup; and IS,inverted sugar. We evaluated the food consumption, population development, and physiological state (expression of vitellogenin and hexamerin 70agenes)of eachcolony.The results showed that the supplementation of colonieswith sugar syrup resulted in an intermediateconsumption and thebetter development of the colony.In addition, this diet ensured that the colonies were in a good physiological state,as beesfed this diet presentedthe highest relative expression levels of vitellogenin and hexamerin 70ameasuredamong all thediets tested.Therefore, sugar syrup was concluded to be the best artificial energetic food for use in thesupplementation of honey bee colonies during the off-season.

genetics↗