Biology subjects

Saleh, L.

Publications and source records attributed to Saleh, L..

9 recordsLinked to original sources

bioRxiv2026

Schwann cell dysfunction contributes to diabetic wound pathology which is partially ameliorated by oncostatin M treatment

Chronic diabetic wounds represent a major clinical burden and are strongly associated with peripheral neuropathy, yet the contribution of nerve-associated Schwann cells to impaired healing remains poorly defined. Here, we investigated Schwann cell dynamics in cutaneous wound repair using the db/db model of type 2 diabetes. Full-thickness excisional wounds in db/db mice exhibited delayed closure, reduced dermal and epidermal thickness, and diminished cellular proliferation compared to non-diabetic controls. Diabetic wounds also demonstrated impaired re-innervation and a marked reduction in both total (S100{beta}+) and dedifferentiated (p75NTR+) Schwann cells, including decreased Schwann cell proliferation. These findings indicate that diabetes disrupts the injury-induced Schwann cell response that is essential for normal repair. Transcriptomic analyses revealed that injury-activated Schwann cells upregulate multiple trophic factors, including oncostatin M (OSM), while single-cell RNA sequencing demonstrated broad expression of OSM receptors (Osmr and Il6st) across wound-resident keratinocytes, fibroblasts, and vascular-associated cells, suggesting widespread responsiveness to OSM signalling during repair. Therapeutic administration of OSM to diabetic wounds significantly accelerated closure, reduced wound width and area, and increased dermal and epidermal thickness. Mechanistically, OSM enhanced epidermal proliferation, angiogenesis, and cutaneous axon regeneration. Collectively, these data identify Schwann cell dysfunction as a contributor to impaired diabetic wound healing and demonstrate that augmenting a Schwann cell-derived paracrine signal can partially rescue key reparative processes. Our findings support a regulatory role for Schwann cells in coordinating epithelial, vascular, and neural repair responses and highlight OSM signalling as a potential therapeutic strategy for chronic diabetic wounds.

cell biology↗

bioRxiv2025

Discovery of T-dioxygenases in bacteriophages and identification of a subclass that is dependent on a regulator protein for oxidation

5-Methylpyrimidine dioxygenases (5mYOXs) are iron (II)/2-oxoglutarate-dependent enzymes that catalyze the oxidation of DNA 5-methylpyrimidines. Key members include mammalian ten-eleven translocation (TET) dioxygenases and J-base binding proteins (JBP) from trypanosomes, which oxidize 5-methylcytosine (5mC) and thymine (T) on DNA, respectively, and are essential in gene regulation. Using sequence similarity networks and genome mining, we highlight functional predictions within the 5mYOX superfamily and identify thousands of bacteriophage-derived sequences, often found in operons encoding DNA modification machinery and binding proteins. Through high-throughput in vivo functional assays, we confirm that T oxidation occurs in bacterial viruses, establishing the presence of T dioxygenases outside of eukaryotes. We provide the first evidence for a 5mYOX subclass that is inactive unless co-expressed with a regulator protein, and through structural modeling, show that this regulator bears homology to the bacterial partition protein B (ParB). We propose a model of interaction between ParB and 5mYOX that includes complex formation, with 5mYOX binding DNA and ParB utilizing CTP, as in bacteria, to form an optimal structural configuration for productive oxidation and possibly migration on the DNA. We show these enzymes retain key catalytic residues found in TET/JBP enzymes and employ AlphaFold2-guided mutagenesis to identify clade-specific features critical for T oxidation, including a variable insertion important for ParB-independent activity and a conserved C-terminal extension essential for T oxidation in ParB-dependent homologs. These findings uncover modular determinants, regulatory mechanisms, and the evolutionary diversity of T-dioxygenases, expanding the functional landscape of the 5mYOX superfamily. SignificanceThis study demonstrates that enzymatic oxidation of thymidine (T) by 5-methylpyrimidine dioxygenases (5mYOXs) occurs in nature outside eukaryotes. Through bioinformatics and in vivo screening, we elucidate minimal T-dioxygenases that share conserved catalytic properties with eukaryotic 5mYOXs, yet possess unique domains, lineage-specific inserts, and/or regulators essential for activity. We uncovered two distinct, bacteriophage-encoded T-dioxygenase subclasses: one requiring a partition protein B (ParB)-like regulator for oxidation and another independent of it. This regulator is predicted to structurally resemble bacterial segregation ParB, which utilizes CTP binding and hydrolysis to migrate along DNA, suggesting novel mechanisms for T oxidation in phages. Our identification of subclass-specific features provides a foundation for further investigation of substrate selectivity, oxidation regulation, and 5mYOX divergence across domains of life.

biochemistry↗

bioRxiv2025

Remote sensing of endogenous pigmentation by inducible synthetic circuits in grasses

Plant synthetic biology holds great promise for engineering plants to meet future demands. Genetic circuits are being designed, built, and tested in plants to demonstrate proof of concept. However, developing these components in monocots, which the world relies on for grain, lags behind dicot models, such as Arabidopsis thaliana and Nicotiana benthamiana. Here, we show the successful adaptation of a ligand-inducible sensor to activate an endogenous anthocyanin pathway in the C4 monocot model Setaria viridis. We identify two transcription factors sufficient to induce endogenous anthocyanin production in S. viridis protoplasts and whole plants in a constitutive or ligand-inducible manner. We also test multiple ligands to overcome physical barriers to ligand uptake, identifying triamcinolone acetonide (TA) as a highly potent inducer of this system. Using hyperspectral imaging and a discriminative target characterization method in a near-remote configuration, we can non-destructively detect anthocyanin production in leaves in response to ligands. This work demonstrates the use of inducible expression systems in monocots to manipulate endogenous pathways, stimulating plants to overproduce secondary metabolites with value to human health. Applying inducible pigmentation coupled with sensitive detection algorithms could enable crop plants to report on the status of field contamination or detect undesirable chemicals impacting agriculture, ushering in an era of agriculture-based sensor systems. SummaryO_ST_ABSSynbio tools for C4 grass modelC_ST_ABS[bullet] Advantage of synthetic switches as tools for biopharming and functional genomics [bullet]Our workflow to optimize the gene circuits from a transient system to a stable transgenic [bullet]Testing and taming golden gate elements in monocot system, S. viridis

plant biology↗

bioRxiv2023

Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans

Enzymatic modification of DNA nucleobases can coordinate gene expression, protection from nucleases, or mutagenesis. We recently discovered a new clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX, e.g., TET) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for additional post-replicative enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX-dependent glycosyltransferase (GT) enzymes that catalyze linkage of diverse glycans directly onto 5hmC reactive nucleobase substrates. Using targeted bioinformatic mining of the phage metavirome databases, we discovered thousands of new biosynthetic gene clusters (BGCs) containing enzymes with predicted roles in cytosine sugar hypermodification. We developed a pathway reassembly platform for high-throughput functional screening of GT-containing BGCs, relying on the endogenous E. coli metabolome as a substrate pool. We successfully reconstituted a subset of phage BGCs and isolated novel and highly diverse sugar modifications appended to 5hmC, including mono-, di-, or tri-saccharide moieties comprised of hexose, N-acetylhexosamine or heptose sugars. Structural predictions and sugar product analyses suggest that phage GTs are related to host lipopolysaccharide, teichoic acid, and other small molecule biosynthesis enzymes and have been repurposed for DNA substrates. An expanded metagenomic search revealed hypermodification BGCs within gene neighborhoods containing phage structural proteins and putative genome defense systems. These findings enrich our knowledge of secondary modifications on DNA and the origins of corresponding sugar writer enzymes. Post-replicative cytosine hypermodification by virus-encoded GTs is discussed in the context of genome defense, DNA partitioning and virion assembly, and host-pathogen co-evolution.

microbiology↗

bioRxiv2022

T cell subsets in chronic hepatitis C patients genotype 4 who achieved SVR following DAAs Therapy

BackgroundT cells are the primary effector cells that mediate viral clearance in spontaneous recovery from HCV infection and T cell dysfunction is a hallmark of progression to chronic HCV infection. Material and methodsThis study included 49 well charcterised HCV genotype 4-infected patients at Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt, who were enrolled to receive direct acting antiviral therapy for hepatitis C. Immuno-phenotyping was performed to assess the expression of multiple T cell lineage, activation and inhibitory receptors. This was done before treatment, during treatment, at end of treatment and one year after treatment. 50 patients were also enrolled as control. ResultsOur data showed, significant increase in the percentages of CD8+ cells as compared to control group. The percentages of PD-1 expression on the CD8+ T-cell population were signifecntly elevated in patients before treatment (p<0.001). Significant increase in Treg (CD4+CD25hFoxP3+) subsets was noticed in comparison with control pateints. The expression of the inhibitory and activated markers in CD8+ T-cells was markedly reduced but more obvios in exhausted cytotoxic T cells compared to baseline finding (p<0.001). exhausted (PD1+CD8+) T-cells from HCV+ individuals reduced markedly after 4 weeks of DAA therapy (by 3 folds, p <0.001). Intereatingly it started to increase gradually again at the end of treatment and after 1 year but the increase doesnt reach levels noticed in healthy control subjects. ConclusionUnderstanding the mechanisms of immune dysfunction and barriers to immune restoration after HCV cure will aid in better understanding of the remaining negative long-term health outcomes for HCV patients and the possibility of HCC development.

immunology↗

bioRxiv2022

The human placenta dictates the phenotype of decidual macrophages.

During human pregnancy, placenta-derived extravillous trophoblasts (EVT) invade the decidua and communicate with maternal immune cells. The decidua can be distinguished into basalis (decB) and parietalis (decP), the latter being unaffected by placentation. By defining a novel gating strategy, we report accumulation of myeloid cells in decB. We identified a decidua basalis-associated macrophage (decBAM) population with a differential transcriptome and secretome when compared to decidua parietalis-associated macrophages (decPAMs). decBAMs are CD11chi and efficient inducers of Tregs, proliferate in situ and secrete high levels of CXCL1, CXCL5, M-CSF, and IL-10. In contrast, decPAMs exert a dendritic cell-like, motile phenotype characterized by induced expression of HLA class II molecules, enhanced phagocytosis, and the ability to activate T cells. Strikingly, EVT-conditioned media are able to convert decPAMs into a decBAM phenotype. Cumulatively, these findings assign distinct macrophage phenotypes to decidual areas depending on placentation and further highlight a critical role for EVTs in the induction of pregnancy-tolerant macrophage polarization. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/486171v3_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@130f55dorg.highwire.dtl.DTLVardef@13cad47org.highwire.dtl.DTLVardef@942b9forg.highwire.dtl.DTLVardef@1bbe575_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsIn this study, we identified so far unrecognized, placenta-induced immune responses at the maternal-fetal interface. Altogether, we imply that placenta-derived trophoblasts induce a pregnancy-tolerant phenotype by suppressing antigen-presenting cell-like functions in maternal tissue macrophages.

immunology↗

bioRxiv2019

EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA

Bisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. However, bisulfite treatment damages DNA resulting in fragmentation, loss of DNA and biased sequencing data. To overcome this, we developed Enzymatic Methyl-seq (EM-seq), an enzymatic based approach that uses as little as 100 pg of DNA. EM-seq outperformed bisulfite converted libraries in all metrics examined including coverage, duplication, sensitivity and nucleotide composition. EM-seq libraries displayed even GC distribution, improved correlation across input amounts as well as increased representation of genomic features. These data indicate that EM-seq is more accurate and reliable than whole genome bisulfite sequencing (WGBS).

genomics↗

bioRxiv2019

Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution.

The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite treated DNA we applied a new enzymatic deamination approach, termed EM-seq (Enzymatic Methyl-seq) to long-range sequencing technologies. Our methodology, named LR-EM-seq (Long Range Enzymatic Methyl-seq) preserves the integrity of DNA allowing long-range methylation profiling of 5-mC and 5-hmC over several kilobases of genomic DNA. When applied to known differentially methylated regions (DMR), LR-EM-seq achieves phasing of over 5 kb resulting in broader and better defined DMRs compared to previously reported. This result demonstrated the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long range epigenetic analysis at single molecule and single nucleotide resolution.

genomics↗

bioRxiv2017

Zwitterionic hydrogels modulate the foreign body response in a modulus-dependent manner

Reducing the foreign body response (FBR) to implanted biomaterials will enhance their in vivo performance in tissue engineering. Poly(ethylene glycol) (PEG) hydrogels are increasingly popular for this application due to their low cost and ease of use. PEG hydrogels can elicit chronic inflammation upon implantation, but recent evidence has suggested that extremely hydrophilic, zwitterionic hydrogels can reduce the FBR to particles and gels. To expand on this approach, we synthesized hydrogels of co-monomers PEG and the zwitterion phosphorylcholine (PC) to quantify the combinatorial effects of modulus and hydrophilicity on the FBR. Surprisingly, hydrogels with the highest amount of zwitterionic co-monomer elicited the highest FBR we observed. Lowering the hydrogel modulus (165 kPa to 3 kPa), or PC content (20 wt% to 0 wt%), mitigated this effect. A high density of macrophages was found at the surface of implants associated with a high FBR, and mass spectrometry analysis of the proteins adsorbed to these gels implicated extracellular matrix, immune response, and cell adhesion protein categories as drivers of macrophage recruitment to these hydrogels. Overall, we show that modulus regulates macrophage adhesion to zwitterionic-PEG hydrogels, and demonstrate that chemical modifications to hydrogels should be studied in parallel with their physical properties to optimize implant design.\n\nHighlightsO_LIModulus and zwitterion content independently modulate the foreign body response to soft hydrogels\nC_LIO_LISoft PEG hydrogels synthesized with the zwitterionic PC co-monomer are pro-inflammatory as modulus is increased\nC_LIO_LIThe chemical and physical properties of hydrogels influence the foreign body response via macrophage recruitment and protein adsorption\nC_LI

bioengineering↗