Biology subjects

Ammar, A.

Publications and source records attributed to Ammar, A..

5 recordsLinked to original sources

bioRxiv2026

Neutrophil remodeling is associated with human meibomian gland dysfunction and enables IFN-γ- and PAD4-dependent gland obstruction in mice

Meibomian gland dysfunction (MGD), a disorder of the eyelid's modified sebaceous glands, is the leading cause of dry eye disease and ocular surface morbidity, yet the immune mechanisms driving gland obstruction remain poorly defined. In a cross-sectional study of 66 patients with ocular surface inflammation, we used meibography and spectral flow cytometry of tear washes to identify a disease-associated, remodeled neutrophil state whose abundance is associated with gland atrophy. Using single-cell transcriptomics in a murine model of immune-mediated MGD, we revealed a disease-associated neutrophil state that exhibited ocular surface-enrichment, CD14 and ICAM-1 expression, and elevated IFN-{gamma} response and inflammatory signatures. Spatial transcriptomics localized IFN-{gamma} signaling and neutrophil migration signatures to the periglandular compartment. The remodeled neutrophils exhibited PAD4-dependent histone citrullination, with Padi4 deletion reducing NET-associated obstructive plugging, thus identifying PAD4-dependent NETotic activity as their disease-producing output. Inhibition of IFN-{gamma} signaling phenocopied Padi4 deficiency, yet combined disruption of these pathways provided no additive protection, indicating that IFN-{gamma} and PAD4 function as separable required inputs. Remodeled neutrophils accumulated under both conditions, uncoupling disease severity from cell abundance alone. Our findings support immune-mediated obstructive MGD as a mechanistic endotype driven by the IFN-{gamma}- and PAD4-dependent effector output of a remodeled neutrophil state.

immunology↗

bioRxiv2026

User-friendly transcriptomic data analysis with ArrayAnalysis

Transcriptomic profiling has become a cornerstone of modern biomedical research. To make transcriptomic analyses accessible to a broader scientific community, specifically including researchers with limited bioinformatics expertise, we introduced ArrayAnalysis in 2013 as a user-friendly web-based application for microarray data analysis. We now present a major update (https://arrayanalysis.org), introducing a strongly interactive platform that facilitates the dedicated exploration and analysis of both microarray and RNA-seq data, and allows for the generation of publication-ready outputs. Users can perform key analysis steps, including data pre-processing and quality control, differential expression analysis, and gene set analysis, via a sequential, interactive workflow. At each step, the application provides interactive visualizations accompanied by information pages to support interpretation. Users can dynamically adjust figure layouts and colour palettes and export figures as vector graphics and high-resolution raster images. For non-expert users, ArrayAnalysis offers step-by-step guidance to support correct usage and facilitate learning, while for experienced bioinformaticians, it provides a streamlined and flexible workflow ideal for large-scale analyses requiring efficient and consistent processing. ArrayAnalysis is available both as a web application and for local deployment as a desktop application, Docker image, or R package, making it suitable for diverse computational environments, user groups, and analytical purposes. Together, ArrayAnalysis empowers a broad community of biomedical researchers to unlock the full potential of transcriptomic data. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/738193v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1072123org.highwire.dtl.DTLVardef@11095e0org.highwire.dtl.DTLVardef@1dfaee7org.highwire.dtl.DTLVardef@53d31e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Persistence of tobacco-mutated alveolar progenitor cells after smoking cessation mirrors long term risk of lung adenocarcinoma

Tobacco smoke shapes mutations, selection and clonal expansion in lung epithelial cells. Smoking cessation leads to divergent epidemiology in the two most common lung cancers: squamous cell carcinoma risk declines sharply, while adenocarcinoma risk is preserved. To investigate this discrepancy, we analysed 806 genomes of alveolar type II (AT2) cells and found persistently elevated mutation burdens after cessation. In contrast, in the proximal airway, rare basal stem cells with near-normal mutation burden expand after cessation, protecting against squamous cell carcinoma. Targeted single-molecule DNA sequencing of AT2 cells revealed positive selection for TP53 and cell cycle and MAPK genes, supporting continued cancer risk. A multistage carcinogenesis model emphasised the importance of a small population of hypermutated cells in the alveoli and reproduced the divergent epidemiological trajectories following cessation due to distinct regenerative dynamics. Our findings suggest that differences in mutational burden and clonal regeneration explain post-cessation trends in lung cancer subtypes. One sentence summaryCancer risk reflects not only cumulative exposure to toxins, but the capacity of tissues to erase genomic damage through regeneration from protected cells with clonal advantage.

genomics↗

bioRxiv2025

The characteristic of epithelial-specific phenotypes and immunosuppressive microenvironment in the context of tumour budding in colorectal cancer

BackgroundTumour budding (TB), defined as a small cluster of up to four cells at the invasive front of the tumour, is a well-established independent and robust prognostic biomarker in colorectal cancer (CRC). This is strongly associated with adverse clinicopathological features and poor survival outcomes. Despite its clinical relevance, the precise underlying mechanism responsible for TB phenomenon remains unclear. MethodsMulti-omic approaches from bulk, regional GeoMx and Spatial Molecular Imager (SMI) RNA were used to identify the underlying mechanism of TB and its possible correlation with tumour microenvironment (TME) in CRC tissue. The results were validated using immunohistochemistry (IHC) and multiplex immunofluorescence (mIF) staining. ResultsPatients with high TB experience worse outcomes and associate with adverse clinical factors across two independent CRC cohorts. Bulk and regional RNA expression analyses reveal that tumours with high TB are significantly enriched for TNF- and TGF-{beta} signatures in both cohorts. Single cell CosMx SMI analysis confirmed TB cells exhibit higher expression of these signatures than adjacent invasive edge tumour cells. Elevated cyclinD1 expression was also observed within TB, and high cyclinD1 levels tend to experience poorer CRC prognosis. Furthermore, regional bulk RNA expression within the non-tumour (PanCK-) invasive edge areas demonstrated that tumours exhibiting high TB revealed the significantly differential expressions of immune-related genes (e.g. CD3, NKG7, IL6, CXCR6, CD47, IFNAR1 and VSIR). Single cell CosMx SMI analysis revealed that cancer-associated fibroblasts (CAFs) were physically the closest cells to TB cells. This spatial proximity was confirmed at the protein level using mIF, where the distance from TB to CD68+ macrophages predicted significantly poorer CRC outcomes. ConclusionThis multi-omic study confirms the prognostic significance of TB in CRC patients across two independent cohorts. Our findings highlight that TNF- and TGF-{beta} signalling play a crucial role in budding cells development by regulating cyclinD1. Furthermore, the transcriptomic analysis reveals an immunosuppressive niche characterised by reduced immune activity and close spatial interactions with CAFs and macrophages Ultimately, this study provides valuable insight into TBs underlying mechanism and its complex interactions within the TME. This could provide a foundation for developing targeted therapeutic strategies in CRC.

cancer biology↗

bioRxiv2024

Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches

In medicine, parasitic cysts or cysticerci (fluid-filled cysts, larval stage of tapeworms) are believed to be sterile (no bacteria), and therein, the treatment of cysticerci infestations of deep extra-intestinal tissues (e.g., brain) relies almost exclusively on the use of antiparasitic medications, and rarely antibiotics. To date, however, it is unclear why common post-treatment complications include abscessation. This study quantified the microbial composition of parasitic cyst contents in a higher-order rodent host, using multi-kingdom shotgun metagenomics, to improve our understanding of gut microbial translocation and adaptation strategies in wild environments. Analysis was conducted on DNA from two hepatic parasitic cysts (Hydatigera (Taeenia) taeniaeformis) in an adult vole mouse (Microtus arvalis), and from feces, liver, and peritoneal fluid of three other vole family members living in a vegetable garden in Ohio, USA. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, including Parabacteroides distasonis, Klebsiella variicola, Enterococcus faecium, and Lactobacillus acidophilus, inhabiting the cysts. Parabacteroides distasonis and other species were also present outside the cyst in the peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, but unexpectedly, it detected an insect-origin virus from the army moth (Pseudaletia/Mythimna unipuncta) known as Mythimna unipuncta granulovirus A (MyunGV-A) in both cysts, and in one fecal and one peritoneal sample from two different voles, indicating survival of the insect virus and adaption in voles. Metagenomics also revealed a significantly lower probability of fungal detection in the cysts compared to other samples (peritoneal fluid, p<0.05; and feces p<0.05), with single taxon detection in each cyst for Malassezia and Pseudophaeomoniella oleicola. The samples with a higher probability of fungi were the peritoneal fluid. In conclusion, commensal/pathobiont bacterial species can inhabit parasitic tapeworm cysts, which needs to be considered during therapeutic decisions of cysticerci or other chronic disease scenarios where immune privileged and spatially restricted ecosystems with limited nutrients and minimal presence of immune cells could facilitate microbial adaptation, such as within gut wall cavitating micropathologies in Crohns disease.

microbiology↗