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Osman, M.

Publications and source records attributed to Osman, M..

14 recordsLinked to original sources
bioRxiv2026

Removing an S-layer enables endolysin-derived probes to detect Paenibacillus thiaminolyticus in mixed bacterial populations

The emerging neonatal bacterial pathogen Paenibacillus thiaminolyticus causes sepsis and postinfectious hydrocephalus, yet few tools are available to study or specifically detect it. We developed fluorescent probes based on cell wall-binding domains (CBDs) from bacteriophage-derived cell-wall hydrolases. CBDs can target structurally conserved cell-wall glycans, making them attractive affinity reagents for bacterial detection. None of the 11 probes we designed labeled intact cells under standard conditions, and we identified a surface layer (S-layer) that prevented access to their cell-wall targets. Brief acidic treatment (pH 2.0) released abundant high-molecular-mass proteins from the cell surface and enabled labeling by five distinct CBD probes, each containing a single C-terminal S-layer homology domain. Mass spectrometry identified the main released protein as an ortholog of the P. alvei SpaA S-layer protein, which we designate SlsA. Across 26 surveyed P. thiaminolyticus genomes, we identified four distinct SlsA variants with 58-79% pairwise amino acid identity, encoded within a conserved cluster homologous to the P. alvei S-layer-associated locus. After either the acidic treatment or a quick flame fixation, the lead probe mGL-BDPt9 labeled six P. thiaminolyticus strains, including three Ugandan clinical isolates, as well as a P. dendritiformis clinical isolate from a US infant, and three additional Paenibacillus species. mGL-BDPt9 also distinguished P. thiaminolyticus from five gram-positive sepsis pathogens in pairwise mixtures and detected it in a five-species suspension. Together, these findings establish the presence of an S-layer in P. thiaminolyticus and provide a rapid fluorescent labeling strategy for multiple Paenibacillus pathogens associated with neonatal paenibacilliosis.

microbiology↗
bioRxiv2026

Transcriptomic signature of Human Cardiac Fibroblast in Hypertrophic Obstructive Cardiomyopathy

BackgroundHypertrophic Cardiomyopathy (HCM) is a cardiac disorder characterized by an increased interstitial fibrosis and Extracellular Matrix (ECM) remodeling. Cardiac fibroblasts (CFs) have a crucial role in ECM remodeling as well as influencing contractility. There is accumulating evidence that the phenotype of CFs is disease-specific. Here, we investigate the transcriptome signature of CFs in Hypertrophic obstructive Cardiomyopathy (HOCM) patients and its functional significance. MethodsPrimary CFs were isolated from myectomy specimens of 12 clinically phenotyped HOCM patients and 3 controls. RNA libraries were prepared from cell isolates for whole transcriptome sequencing. Differential expression analysis was conducted using the Tuxedo pipeline. Pathway and Gene Ontology (GO) enrichment were performed using Protein-protein interaction network analysis and functional clustering were performed using Cytoscape StringApp. Expression of candidate genes and proteins was validated using quantitative PCR, Immunocytochemistry, immunohistochemistry, cytokines/chemokines profiling and western blotting, in patient-derived CFs extracts, CFs-conditioned media, and myocardial tissue sections. ResultsWhole transcriptome analysis identified 265 significant differentially expressed genes (DEGs) in HOCM fibroblasts compared to controls. The most significant GO terms identified were associated with ECM organization and inflammatory response. The most significant GO terms identified were associated with ECM organization and inflammatory response, with circos plot analysis further highlighting pathway-specific gene overlap within inflammatory and structural signaling clusters. The DEGs encompassed gene families such as collagens, proteases, fibulins, inflammatory cytokines, integrins and signaling receptors and kinases. MYC was upregulated alongside chemokine ligands and receptors, highlighting a MYC-linked chemokine signaling axis within the inflammatory HOCM-CFs phenotype. The protein expression of selected extracellular Matrix organization and inflammatory response genes confirmed the transcriptome results. ConclusionTranscriptomic profiling of patient-derived HOCM-CFs identified genes and pathways associated with inflammatory signaling, ECM remodeling, and altered cell-cell/matrix communication. These findings show that advanced HOCM-CFs acquire an inflammatory-remodeling phenotype, with ECM genes other than collagens. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIHypertrophic cardiomyopathy is characterized by myocardial hypertrophy, interstitial fibrosis, extracellular matrix remodelling, and inflammatory signalling. C_LIO_LIMost human HCM transcriptomic studies have been performed using whole myocardial tissue, which limits resolution of fibroblast-specific disease programmes. C_LI What New Information Does This Article Contribute?O_LIPatient-derived cardiac fibroblasts from patients with advanced hypertrophic obstructive cardiomyopathy exhibit a distinct transcriptomic signature enriched for inflammatory signalling, extracellular matrix organization, chemokine activity, and altered cell-matrix communication. C_LIO_LIThe HOCM-CF signature is not characterized by uniform collagen gene induction, but by selective ECM remodelling involving fibulins, proteases, integrins, matricellular genes, and downregulation of selected collagen-associated matrix components. C_LIO_LIComparison with bulk myocardial RNA-sequencing and publicly available human cardiomyopathy data supports the biological relevance of the fibroblast-derived signature while highlighting the limited sensitivity of bulk tissue transcriptomics for resolving fibroblast-specific programmes. C_LI What Is the Significance?This study identifies a disease-associated inflammatory and ECM-remodelling state in patient-derived HOCM cardiac fibroblasts. The findings extend the role of cardiac fibroblasts in HOCM beyond classical collagen deposition and suggest that fibroblast-mediated matrix remodelling, cytokine/chemokine signalling, and altered cell-matrix communication may contribute to myocardial remodelling in advanced obstructive disease. These data support the value of fibroblast-focused profiling for uncovering disease-relevant mechanisms that may be masked in whole myocardial tissue analyses and provide candidate pathways for future mechanistic and therapeutic studies.

cell biology↗
bioRxiv2026

A PERK/FOXO1 AXIS LINKS DNA DAMAGE TO FIBROBLAST SURVIVAL IN DIFFUSE CUTANEOUS SYSTEMIC SCLEROSIS

ObjectiveDiffuse cutaneous systemic sclerosis (dcSSc) is a life-limiting fibrotic disease. We and others have shown that dcSSc fibroblasts accumulate numerous somatic mutations associated with senescence-like features; however, the mechanism(s) enabling their survival remain unclear. MethodsSkin biopsies were obtained from lesional tissues from dcSSc (n=10), dcSSc treated with autologous hematopoietic stem cell transplantation (ASCT, n=8) or 7 age/sex-matched healthy controls. Primary dermal fibroblasts were generated from biopsies. Spatial RNA sequencing, immunoblotting, confocal microscopy, and functional assays were used to mechanistically delineate signaling pathways linking DNA-damage with fibroblast survival. ResultsdcSSc fibroblasts demonstrated increased pH2AX DNA double-strand-break foci yet remained apoptosis resistant. These cells displayed features of metabolic-stress remodeling, including mitochondrial hyperpolarization, increased reactive oxygen species production, and enhanced mitochondrial biogenesis. Spatial transcriptomics and subsequent biochemical analyses identified activation of a PERK/ATF4/FOXO1 axis, characterized by PERK phosphorylation, selective ATF4 translation, FOXO1 nuclear translocation, and induction of downstream antioxidant and metabolic programs. In contrast, fibroblasts from post-ASCT patients exhibited normalization of DNA-damage markers and mitochondrial parameters without ATF4/FOXO1 activation. Pharmacologic inhibition of either PERK or FOXO1 selectively restored mitochondrial-dependent apoptosis in dcSSc fibroblasts, demonstrating that this axis is required for their survival following extensive genomic injury. ConclusiondcSSc fibroblasts persist despite substantial genomic injury by engaging a PERK/ATF4/FOXO1 metabolic-adaptation program that suppresses mitochondrial-dependent apoptosis. This survival axis is not present after ASCT. Targeting PERK or FOXO1 restores apoptosis selectively in dcSSc fibroblasts, highlighting its potential use as a therapeutic target for eliminating pathogenic senescence-like fibroblasts in dcSSc. HighlightsO_LIBoth ex-vivo skin and in-vitro primary dermal fibroblasts derived from dcSSc patients have a higher frequency of intrinsic DNA damage signals and senescence-associated features; yet they evade mitochondrial-dependent apoptosis. C_LIO_LIPathogenic dcSSc fibroblasts rewire their metabolism, characterized by mitochondrial hyperpolarization and elevated ROS. C_LIO_LISpatial transcriptomics and functional analyses reveal a PERK/ATF4/FOXO1 stress-adaptation axis that drives fibroblast survival in dcSSc. C_LIO_LIThis maladaptive survival program characterized by increased genotoxic stress, and mitochondrial remodelling is absent in post-ASCT fibroblasts. C_LIO_LITargeting PERK or FOXO1 selectively sensitizes dcSSc fibroblasts to apoptosis revealing a potential promising therapeutic strategy in dcSSc. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/706443v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1b3f791org.highwire.dtl.DTLVardef@42548aorg.highwire.dtl.DTLVardef@bc4ce1org.highwire.dtl.DTLVardef@5b4d48_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗
bioRxiv2025

APOBEC3A-Induced DNA Damage Drives Polymerase Theta Dependency and Synthetic Lethality in Cancer

APOBEC3 cytidine deaminases drive cancer evolution. There is an unmet need to target cancer cells with APOBEC3 activity. Here, we identify error-prone theta-mediated end joining (TMEJ) as the main pathway for repairing APOBEC3-induced double-strand breaks (DSBs). Using fluorescent DSB repair reporters and a novel biochemical assay, we demonstrate that APOBEC3A competes with replication protein A (RPA) for single-stranded DNA overhangs, exposing microhomologous sequences to shift DSB repair towards error-prone TMEJ. Genomic analysis of clinical tumor samples confirmed the co-occurrence and proximity between APOBEC3-induced mutational footprints, microhomology-mediated deletions (MMDs), and TMEJ-associated chromosomal instability signatures. Crucially, inhibition of DNA polymerase theta (Pol{theta}) synergizes with APOBEC3A-induced DSBs to induce synthetic lethality in vitro and in vivo. Collectively, our findings identify TMEJ as the preferred mechanism for repairing APOBEC3A-induced DSBs and establish Pol{theta} inhibition as a novel promising strategy to eliminate cancer cells with APOBEC3A activity.

cancer biology↗
bioRxiv2025

Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

CD8+ T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8+CD103+ T cells with a tissue-resident memory T (TRM) cell phenotype have been favourably correlated with patient prognoses1-6, the tumour microenvironment also contains dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features, leading to conflation of these two populations. Here, we deconvolute TRM and TEX cells within the intratumoural CD8+CD103+ T cell pool across human cancers, ascribing markers and gene signatures that distinguish these CD8+ populations and enable their functional distinction. We found that while TRM cells exhibit superior functionality and are associated with long-term survival post-tumour resection, they are not associated with responsiveness to immune checkpoint blockade. Deconvolution of the two populations showed that tumour-associated TEX and TRM cells are clonally distinct, with the latter comprising both tumour-independent bystanders and tumour-specific cells segregated from their cognate antigen. Intratumoural TRM cells can be forced towards an exhausted fate when chronic antigen stimulation occurs, arguing that the presence or absence of continuous antigen exposure within the microenvironment is the key distinction between respective tumour-associated TEX and TRM populations. These results suggest unique roles for TRM and TEX cells in tumour control, underscoring the need for distinct strategies to harness these T cell populations in novel cancer therapies.

immunology↗
bioRxiv2025

Polysialylation is a general feature of immune activation

Sialic acids are critical regulators of immune responses and the sialic acid-Siglec axis has receive much attention recently for it role as a new immune checkpoint. While 2,3- and 2,6-linked sialosides have been well studied, much less is known about the 2,8-linked polysialic acid (polySia), especially in the adaptive immune system. We demonstrate here that polySia is actually found in all major classes of circulating immune cells, including B and T cells, where it is strongly associated with prior antigen exposure. Cell surface expression of polySia could be observed within 24 h of activation of naive T cells but did not correlate with expression of the immune-specific polysialyltransferase ST8Sia4. Finally, we assessed the effects of smoking on polySia levels, and noted substantial increased levels of polySia, particularly on effector T cells and preferentially in males. Significance StatementThe immune system is central to human health and holds the key to treating many chronic diseases. We show for the first time that the immunomodulatory glycan polysialic acid is widespread in the human immune system and associated with immune cell activation. Moreover, sex-dependent increases in polysialic acid could be observed on key populations of immune effector cells in smokers. This study offers insight into how glycans might contribute to sex differences in development and progression of chronic diseases.

immunology↗
bioRxiv2023

UVB modifies skin immune-stroma cross-talk and promotes effector T cell recruitment during cryptic Leishmania donovani infection

Many parasites of significant public health importance assume skin residency without causing overt pathlogy. How immune and stromal cells respond to such "cryptic" infections and how exposure to UVB alters such responses in poorly understood. We combined scRNA-seq, spatial transcriptomics and inferential network analysis to address these questions in a model of cryptic skin infection by Leishmania donovani. In infected C57BL/6 mice, p-selectin and CXCL12 interactions dominate intercellular communication between leucocytes, fibroblast and endothelial cells, but effector T cell function remains muted. Following UVB exposure, increased numbers of IFN{gamma}+ CD4+ Th1 cells and NK cells enter the skin, communicating with stromal cells via CCL5-CCR5 and LFA-1-ICAM1/2. However, spatial mapping indicated that Th1 cells and macrophages occupied distinct niches after UVB exposure, likely limiting effector function. Our data provide the first holistic view of the immune landscape during cryptic L. donovani infection and demonstrate how UVB exposure fundamentally reshapes this response. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/526940v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1238cbaorg.highwire.dtl.DTLVardef@ec350eorg.highwire.dtl.DTLVardef@18f412corg.highwire.dtl.DTLVardef@1ffd468_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗
bioRxiv2021

A Transparent Ultrasound Array for Real-time Optical, Ultrasound and Photoacoustic Imaging

Objective and Impact StatementSimultaneous imaging of ultrasound and optical contrasts can help map structural, functional and molecular biomarkers inside living subjects with high spatial resolution. There is a need to develop a platform to facilitate this multimodal imaging capability to improve diagnostic sensitivity and specificity. IntroductionCurrently, combining ultrasound, photoacoustic and optical imaging modalities is challenging because con-ventional ultrasound transducer arrays are optically opaque. As a result, complex geometries are used to co-align both optical and ultrasound waves in the same field of view. MethodsOne elegant solution is to make the ultrasound transducer transparent to light. Here, we demonstrate a novel transparent ultrasound transducer (TUT) liner array fabricated using a transparent lithium niobate piezoelectric material for real-time multimodal imaging. ResultsThe TUT array consisted of 64 elements and centered at [~] 6 MHz frequency. We demonstrate a quad-mode ultrasound, Doppler ultrasound, photoacoustic and fluorescence imaging in real-time using the TUT array directly coupled to the tissue mimicking phantoms. ConclusionThe TUT array successfully showed a multimodal imaging capability, and has potential applications in diagnosing cancer, neuro and vascular diseases, including image-guided endoscopy and wearable imaging.

bioengineering↗
bioRxiv2021

Interferon-γ-producing CD4+ T cells drive monocyte activation in the bone marrow during experimental Leishmania donovani infection.

Ly6Chi inflammatory monocytes develop in the bone marrow and migrate to the site of infection during inflammation. Upon recruitment, Ly6Chi monocytes can differentiate into dendritic cells or macrophages. According to the tissue environment they can also acquire different functions. Several studies have described pre-activation of Ly6Chi monocytes in the bone marrow during parasitic infection, but whether this process occurs during experimental visceral leishmaniasis and, if so, the mechanisms contributing to their activation are yet to be established. In wild type C57BL/6 (B6) mice infected with Leishmania donovani, the number of bone marrow Ly6Chi monocytes increased over time. Ly6Chi monocytes displayed a highly activated phenotype from 28 days to 5 months post infection (p.i), with >90% expressing MHCII and >20% expressing iNOS. In comparison, in B6.Rag2-/- mice <10% of bone marrow monocytes were MHCII+ at day 28 p.i., an activation deficiency that was reversed by adoptive transfer of CD4+ T cells. Depletion of CD4+ T cells in B6 mice and the use of mixed bone marrow chimeras further indicated that monocyte activation was driven by IFN-{gamma} produced by CD4+ T cells. In B6.Il10-/- mice, L. donovani infection induced a faster but transient activation of bone marrow monocytes, which correlated with the magnitude of CD4+ T cell production of IFN-{gamma} and resolution of the infection. Under all of the above conditions, monocyte activation was associated with greater control of parasite load in the bone marrow. Through reinfection studies in B6.Il10-/- mice and drug (AmBisome) treatment of B6 mice, we also show the dependence of monocyte activation on parasite load. In summary, these data demonstrate that during L. donovani infection, Ly6Chi monocytes are primed in the bone marrow in a process driven by CD4+ T cells and whereby IFN-{gamma} promotes and IL-10 limits monocyte activation and that the presence of parasites/parasite antigen plays a crucial role in maintaining bone marrow monocyte activation.

immunology↗
bioRxiv2020

Rejection in early life is associated with high and long-lasting stress and higher incidence of infections in owl monkeys

1.BackgroundThe mothers of owl monkeys sometimes reject their new-borns. When this occurs in captive colonies, the rejected infants are manually raised by veterinarians, allowing them to survive. However, maternal rejection can induce chronic stress, which in turn is associated with infectious diseases. Rescued, rejected owl monkeys might experience high rates of stress and infections which go undetected. MethodologyTo test this hypothesis, we evaluated the connection between maternal rejection, stress and infections in owl monkeys (Aotus nancymaae) from the IVITA Center for Conservation and Reproduction of Primates (UNMSM, Peru). Specifically, we compared the stress rates and frequency of infection treatment in juveniles (19-24 months) rejected in the first month of life and controls. To assess stress, we compared cortisol levels in hair using a competitive ELISA and recorded behaviours using cameras. We analysed past medical treatments and medication to compare incidence of infection treatment in subjects. We then studied the correlation between the frequency of infection treatments and cortisol using a linear regression. ResultsRejected owl monkeys showed significantly higher cortisol levels (p=0.0123), a higher incidence of stereotypical behaviour and overeating (pacing p=0.0159; head twirling p=0.0476, eating p=0.0238) compared to controls. Rejected owl monkeys also received significantly more treatment for infections than controls per month lived (p=0.0009). Moreover, infection rates observed in this population were positively although weakly associated with concentration of cortisol in hair (R2=0.307, p=0.0075). ConclusionMaternal rejection in the first month of life is associated with high and long-lasting stress levels and infections in the IVITA owl monkey colony. IVITA owl monkeys will be a useful model for studying the long-term effects of early life stress at the population level.

neuroscience↗
bioRxiv2020

Erythroid precursors and progenitors suppress adaptive immunity and get invaded by SARS-CoV-2

SARS-CoV-2 infection is associated with lower blood oxygen levels even in patients without hypoxia requiring hospitalization. This discordance illustrates the need for a more unifying explanation as to whether SARS-CoV-2 directly or indirectly affects erythropoiesis. Here we show significantly enriched CD71+ erythroid precursors/progenitors in the blood circulation of COVID-19 patients that have distinctive immunosuppressive properties. A subpopulation of abundant erythroid cells, CD45+CD71+cells, co-express ACE2, TMPRSS2, CD147, CD26 and these can be infected with SARS-CoV-2. In turn, pre-treatment of erythroid cells with dexamethasone significantly diminished ACE2/TMPRSS2 expression and subsequently reduced their infectivity with SARS-CoV-2. Taken together, pathological abundance of erythroid cells might reflect stress erythropoiesis due to the invasion of erythroid progenitors by SARS-CoV-2. This may provide a novel insight into the impact of SARS-CoV-2 on erythropoiesis and hypoxia seen in COVID-19 patients.

immunology↗
bioRxiv2020

High speed, three-dimensional imaging reveals chemotactic behavior specific to human-infective Leishmania parasites

Cellular motility is an ancient eukaryotic trait, ubiquitous across phyla with roles in predator avoidance, resource access and competition. Flagellar-dependent motility is seen in a variety of parasitic protozoans and morphological changes in flagellar structure and function have been qualitatively described during differentiation. However, whether the dynamics of flagellar motion vary across lifecycle stages and whether such changes serve to facilitate human infection is not known. Here we used holographic video microscopy to study the pattern of motility in insect midgut forms of Leishmania (procyclic promastigotes; PCF) and differentiated human infective metacyclic promastigotes (META). We discovered that PCF swim in a slow, corkscrew motion around a gently curving axis while META display run and tumble behaviour in the absence of stimulus, reminiscent of bacterial behaviour. In addition, we demonstrate that META specifically respond to a macrophage-derived stimulus, modifying swimming direction and speed to target host immune cells. Thus, the motility strategy employed by Leishmania appears as a random search that is replaced with a ballistic swimming motion in the presence of an immunological stimulus. These findings shed unique insights into how flagellar motion adapts to the particular needs of the parasite at different times in its lifecycle and define a new pre-adaptation for infection of the human host.

biophysics↗
bioRxiv2019

An improved growth medium for enhanced inoculum production of the plant growth-promoting fungus Serendipita indica

The plant endophytic fungus Serendipita indica colonizes roots of a wide range of plant species and can enhance growth and stress resistance of these plants. Due to its ease of axenic cultivation and its broad host plant range including the model plant Arabidopsis thaliana and numerous crop plants, it is widely used as a model fungus to study beneficial fungus-root interactions. In addition, it was suggested to be utilized for commercial applications, e.g. to enhance yield in barley and other species. To produce inoculum, S. indica is mostly cultivated in a complex Hill-Kafer medium (CM medium), however, growth in this medium is slow, and yield of chlamydospores, which are often used for plant root inoculation, is relatively low. We tested and optimized a simple vegetable juice-based medium for an enhanced yield of fungal inoculum. The described vegetable juice (VJ) medium is based on commercially available vegetable juice and is easy to prepare. VJ medium was superior to the currently used CM medium with respect to biomass production in liquid medium and hyphal growth on agar plates. Using solid VJ medium supplemented with sucrose (VJS), a high amount of chlamydospores developed already after 8 days of cultivation, producing significantly more spores than on CM medium. Use of VJ medium is not restricted to S. indica, as it also supported growth of two pathogenic fungi often used in plant pathology experiments: the ascomycete Fusarium graminearum, the causal agent of Fusarium head blight disease on wheat and barley, and Verticillium longisporum, the causal agent of verticillium wilt. The described VJ medium is recommended for a streamlined and efficient production of inoculum for the plant endophytic fungus Serendipita indica and might prove superior for the propagation of other fungi for research purposes.

plant biology↗