Biology subjects

Martin, J.

Publications and source records attributed to Martin, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A unique Cysteine-type protein domain regulates cuticular extracellular matrix assembly in nematodes

Apical extracellular matrices (aECMs) act as barriers against pathogens and shape tissue organization throughout animals. In nematodes, the cuticle is the aECM performing this function, representing a defining feature of this largest animal phylum. Morphological and molecular evidence supports that worm cuticles extend from the head into the mouth, the latter contributing to the large diversity of nematode feeding structures. However, the biochemical understanding of the compositions of nematode cuticles and head structures is largely limited to collagens. Here, we characterized a recently identified mucin-type protein DPY-6 as a constituent of the cuticle and mouth in the model organisms Pristionchus pacificus and Caenorhabditis elegans. Utilizing bioinformatic tools, we discover a unique cysteine-consisting motif at the N-terminus of DPY-6 with the amino acid sequence CxCxCxC. We demonstrate through in vitro biophysical experiments that this cysteine motif facilitates the intermolecular dimerization of DPY-6 proteins. In vivo studies in both species reveal that this motif is involved in the proper localization of the protein in the cuticle, but functions synergistically with other protein domains in a species-specific manner. Given that dpy-6 transcriptomic expression precedes other cuticle components, we speculate that DPY-6 acts as scaffold molecule for nematode cuticular aECM formation.

biochemistry↗

bioRxiv2026

Canavalia ensiformis intercrop to reduce weeds and stalk borer damage in sugarcane

The aim of this study was to assess the efficiency of two intercrop species, Canavalia ensiformis and Desmodium intortum, to reduce weed growth, herbicide use and damage by the stalk borer Chilo sacchariphagus in sugarcane cropping system in Reunion. We compared six inter-row management techniques: four treatments combined the two intercrops Canavalia ensiformis or Desmodium intortum sown either early (between 0 and 2.1 months after sugarcane emergence) or late (between 1.3 and 3.7 months after sugarcane emergence), a treatment where no weeding was carried out on the inter-row, and a treatment with chemical weeding of the inter-row (CcWp). In all treatments, the sugarcane row was weeded chemically and manually. The six treatments were compared in a multilocal randomized block design with three localities, during one or two crop cycles depending on the locality. Desmodium intortum produced poor ground coverage in half of the trial x crop cycles and was therefore found unsuitable for use as an intercrop of sugarcane in our conditions. On the opposite, Canavalia ensiformis quickly covered the inter-rows, regardless of the sowing date. The Canavalia ensiformis intercrops allowed a reduction of herbicide consumption by 63% when sown early and by 28% when sown late, compared to the CcWp control treatment. Both Canavalia ensiformis intercrops caused a reduction of weed coverage on the inter-row similar or better than the chemical control. However, the early sown Canavalia ensiformis intercrop caused a 18.6 t.ha-1 yield loss compared the chemical control. No yield loss was detected with the late sown intercrop. A significant reduction of stalk damage by a 0.8-fold factor was observed in the early sown Canavalia ensiformis treatment.

ecology↗

bioRxiv2026

Single-Cell RNA Sequencing Reveals Impaired Regulatory T Cell Function and a Pro-inflammatory Th17 Profile in Systemic Sclerosis

ObjectiveThis resource deeply characterizes the CD4+ T cell subpopulations populations in SSc patients, with a novel single-cell RNA sequencing (scRNA-seq) approach, offering unprecedented insights into the cellular and molecular underpinnings of the disease. MethodsWe performed scRNA-seq to analyze over 80,000 CD4+ T cells from 8 SSc patients and 8 healthy controls, integrating abundance, transcriptional, and TCR repertoire analysis, to define CD4+ T cell subtype-specific signatures associated with SSc. ResultsSSc CD4+ T cells displayed a global interferon-driven activation signature and significantly reduced TNF signaling. Key transcriptomic alterations included the downregulation of SOX4 and CD83, alongside an expansion of Th2 and proinflammatory, steroid-resistant Th17 cells. Furthermore, Tregs exhibited a destabilized state characterized by high FCRL3 and reduced FOXP3 expression. Finally, TCR repertoire analysis identified increased clonal expansion specifically within the central memory (Tcm) compartment. ConclusionTogether, this data revealed SSc-associated cell population states in CD4+ T cells with unique transcriptomic signatures and provided a publicly accessible interactive platform to facilitate exploration of this dataset by the research community.

genetics↗

bioRxiv2026

Cognition does not automatically influence perception: Evidence from neural encoding of colours belonging to different categories

The firmest evidence in favour of models that posit early high-level influences of cognition on perception comes from electroencephalography (EEG). Enhanced early, pre-attentive processing of light and dark blue feature changes compared to light and dark green changes was reported in Greek speakers, who have two basic terms for blue (ghalazio/ble). In the present three-experiment study, we systematically re-evaluate this evidence and test an alternative model that the early difference waves in the human EEG instead mainly reflect contrast adaptation phenomena. We use the same classical oddball paradigm presenting alternating standards and deviants that systematically differ in colour and/or luminance and chromatic contrast. We then calculate the visual mismatch negativity (vMMN), a putative index of pre-attentive feature change processing and predictive coding derived from EEG data, by subtracting the activity elicited by standards from that elicited by task-irrelevant deviants. Our experiments demonstrate the following: 1) vMMN is driven by contrast adaptation, being observable only in the presence of contrast differences between the stimuli and not reliably observed for categorically different hues equated in contrast; 2) there is no reliable difference between green- and blue-related difference waves in speakers (Russian) with two basic blue colour categories, the difference waves, again, being driven by contrast rather than their categorical content. Our findings are highly significant for the debate concerning the interface between perception and cognition, as the absence of early categorical effects speaks against models that predict Whorfian-type pre-attentive cognitive influences on perception. Significance statementThe Whorfian hypothesis posits that basic language categories alter ones perception of the world in a fundamental manner. Some of the most compelling evidence in favour of this hypothesis came from electrophysiological responses that indicated early differences between speakers of languages with different number of basic colour categories. The brain response taken as an indicator of these differences was considered to be a robust marker of early, pre-attentive processing and predictive coding. In the current multi-experiment study, we present evidence that early electrophysiological differences to colour reflect signatures of hue, saturation and luminance contrast and adaptation to this contrast, rather than of linguistic categories. This means that evidence in favour of early, pre-attentive categorical colour perception has been significantly eroded.

neuroscience↗

bioRxiv2025

Thiol Scarcity in Cerebrospinal Fluid Renders Leptomeningeal Acute Lymphoblastic Leukaemia Therapeutically Vulnerable to Ferroptosis

The leptomeninges present a challenging tumour microenvironment with cells receiving low levels of nutrients and oxygen from cerebrospinal fluid (CSF), however these metabolic constraints are yet to be exploited therapeutically. Central nervous system (CNS) relapse in acute lymphoblastic leukaemia (ALL) remains a formidable clinical challenge because the leptomeningeal niche restricts drug penetration and immune surveillance. Current CNS-directed treatments rely on neurotoxic intrathecal chemotherapy, underscoring the urgent need for novel targeted strategies. Here, we uncover a profound niche-specific metabolic vulnerability in CNS-resident ALL cells, characterised by an obligate reliance on LRP8-mediated selenium uptake to sustain selenocysteine biosynthesis and GPX4 activity under profound glutathione limitation. We show that scarcity of thiols and cystine in CSF creates an inherently pro-ferroptotic microenvironment. Interference with selenocysteine biosynthesis under these conditions induces synthetic lethality in both in vitro and in vivo CNS-ALL models. This vulnerability is exploitable both by genetic targeting of the selenocysteine biosynthesis pathway and, notably, through repurposing the FDA-approved agent Auranofin, which disrupts selenium utilisation, induces lipid peroxidation, and demonstrates CNS-specific anti-leukaemic eaicacy with excellent tolerability in vivo. These findings identify a novel mechanistically grounded approach, leveraging features of the unique leptomeningeal microenvironment to selectively kill invading cells, with potential implications for all leptomeningeal-tropic malignancies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/693383v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@2303dforg.highwire.dtl.DTLVardef@d357ceorg.highwire.dtl.DTLVardef@129cb26org.highwire.dtl.DTLVardef@d83183_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO The leptomeningeal tumour microenvironment is intrinsically pro-ferroptotic due to low concentrations of free thiols and cystine in cerebrospinal fluid. ALL cells in this niche exhibit disrupted glutathione metabolism and a novel dependency on LRP8-mediated SELENOP uptake to sustain GPX4 levels and thus protect themselves from spontaneous ferroptotic cell death. Perturbation of selenocysteine biosynthesis via genetic inhibition SEPHS2 or LRP8 leads to synthetic lethality in leukaemic cells exposed to CSF in vitro and in vivo - an effect phenocopied by use of Auranofin. C_FIG

cancer biology↗

bioRxiv2025

pylifemap: Mapping Data onto the Tree of Life

O_LIThe need to visualize data associated with NCBI Taxonomy Identifiers is growing in various biological fields ranging from comparative genomics to metagenomics and metabarcoding, and even for outreach. C_LIO_LINo tool today allows visualization of such data while still keeping the full vision of the whole taxonomy, possibly causing a biased view of the data at hand. C_LIO_LIHere we introduce pylifemap, a Python package that allows users to map their own data directly on the interactive taxonomic tree proposed by Lifemap. Through a simple syntax, layers (points, lines, icons, heatmaps, etc.) depicting any type of data are superimposed on the Lifemap basemap, producing an interactive map to inspect biological datasets. The produced visualizations can easily be shared with others through notebooks or standalone HTML files, or exported as static images. C_LIO_LIWe illustrate the utility of pylifemap in the exploration of two contrasting datasets: the IUCN Red List of Threatened Species and the output of a large-scale environmental metagenomics experiment. C_LI Data/Code for peer reviewpylifemap is available at PyPI and easily installable with pip or uv. The development version can be found at https://lifemap-tol.github.io/pylifemap/ along with extensive documentation and examples.

evolutionary biology↗

bioRxiv2025

Identification and characterization of host-modulating effectors encoded by the Cluster F1 mycobacteriophage NormanBulbieJr

NormanBulbieJr (NBJ) is a temperate siphovirus isolated on the host Mycobacterium smegmatis mc2155 that encodes 102 gene products, 60 of which have no known function (NKF). Based on gene content, NBJ is classified as a Cluster F, Subcluster F1 phage and shares 70% of its encoded gene phamilies with Girr, another F1 mycobacteriophage that was recently analyzed in a genome-wide overexpression screen and found to encode 29 diverse gene products capable of inhibiting growth of M. smegmatis. Similar functional screens in other mycobacteriophages have uncovered a growing repertoire of diverse, phage-encoded bacterial growth inhibitors, providing prime candidates for dissecting novel bacterial-phage interactions. An arrayed overexpression library encoding all 102 genes was constructed and systematically screened using a plate-based cytotoxicity assay, identifying 29 genes that inhibit mycobacterial growth. Because mycobacteriophage genomes are also known to encode systems involved in phage-phage competition, we conducted additional phage defense assays for a subset of NBJ genes in our library. This analysis confirmed homotypic immunity by the predicted immunity repressor and identified gp45 as a second defense factor that protects against Cluster F phages and promotes NBJ lysogen stability. Additional mechanistic analyses indicate that gp45 functions in a secretion-dependent manner, acting after phage adsorption to reduce productive infection and early phage transcript accumulation. Escape mutant and bacterial two-hybrid analyses implicate Cluster F tape measure proteins as the likely target of gp45, consistent with disruption of an early step in phage genome delivery. Finally, we extended our analysis to explore the essentiality of all identified host-modulating genes in the NBJ life cycle, using CRISPR-enhanced recombineering to generate phage deletion mutants, revealing two host modulators that are critical for lytic growth. Conducted as part of the SEA-GENES undergraduate research consortium, this study adds to a growing functional genomics resource and provides new insights into the complex interactions between phage gene products and the mycobacterial host cell.

microbiology↗

bioRxiv2025

Identification of AB8939, a novel synthetic microtubule destabilizer and ALDH inhibitor that overcomes multidrug resistance in tumor cells as a drug candidate for the treatment of refractory acute myeloid leukemia

We identified AB8939, a novel small synthetic molecule that exhibits strong and broad antiproliferative activity against a panel of various cancer cell types with IC50 values in the nanomolar range. In vitro investigations showed that AB8939 is a novel microtubule-targeting agent that interacts with the colchicine-binding site of tubulin. AB8939 disrupts the microtubule network, leading to mitotic arrest in G2/M phase and subsequent apoptosis. Importantly, AB8939 overcomes drug resistance mechanisms, including overexpression of efflux transporters such as P-glycoprotein (P-gp) and aberrant expression of {beta}3-tubulin. AB8939 displays high cytotoxicity against blasts from AML patients, including blasts resistant to cytarabine (Ara-C). In vivo, AB8939 shows strong antitumor activity in MOLM-14, an Ara-C-resistant AML model, as evidenced by tumor growth inhibition and substantial increase in mouse survival. Further experiments performed on an AML PDX TG-AML-36 model demonstrated that AB8939 efficiently kills leukemic stem cells (CD34+/CD38-). Reverse proteomic experiments revealed that AB8939 inhibits ALDH1 and ALDH2, enzymes often overexpressed in tumors and tumor stem cells, thereby favoring tumor progression and relapse. AB8939 is a novel dual-targeting drug that acts on both tubulin and ALDH enzymes, with potential activity against various cancer types, especially refractory AML with complex karyotypes such as those displaying MECOM rearrangement and AML with mutations associated with poor prognosis, such as ASXL1 and TP53.

cell biology↗

bioRxiv2025

Loss of CD44 re-educates pancreatic cancer-associated fibroblasts modulating their fibrotic and immunosuppressive functions

Pancreatic tumors are characterized by a prominent stroma that makes up to 90% of the tumor. Due to the significant upregulation of CD44, a family of transmembrane glycoproteins, in pancreatic cancer-associated fibroblasts (CAFs), we investigated its role in myofibroblastic and inflammatory CAF subsets. Conditional deletion of Cd44 in CAFs in Cd44fl/fl;Pdgfr{beta}CreERT2 mice, significantly decreased the tumor volume. In human CAFs CRIPSR/Cas9-edited to delete CD44, the morphology of the fibroblasts changed drastically: CAFs lost their elongated phenotype and adopted a round shape, reflecting their inactivation. This was accompanied by a significant downregulation of activation markers, unresponsiveness to exogenous stimuli and reduced contractile activity. CD44 absence not only downregulated extracellular matrix proteins in CAFs, thus influencing fibrosis, but also changed the immunomodulatory cytokine secretion. Finally, this inactivation of CAFs upon CD44 deletion influenced their immunosuppressive effect on dendritic cells (DCs) and on cytotoxic T cells (CTLs), resulting in decreased expression of immunosuppressive cytokines in DCs and enhanced tumor-cell-killing by CTLs.

cancer biology↗

bioRxiv2025

Dynamic neutrophil lipidome remodeling during induction of NETosis

Neutrophil Extracellular Trap formation (NETosis) affects a wide variety of clinically relevant human diseases. Although lipid remodeling is essential for neutrophil function and membrane rupture during NETosis, the neutrophil lipidome and its dynamics have not been characterized. Thus, we establish the first quantitative lipidome of human neutrophils comprising 1,039 species across nine orders of magnitude and map its remodeling during NETosis. NET formation caused profound alterations in the phosphatidylinositol, phosphatidic acid, diacylglycerol and lysoglycerophospholipid levels. Calcium- and reactive oxygen species-dependent NETosis pathways displayed distinct lipidomic trajectories, yet converged on the significance of phospholipid lipase networks. Pharmacological inhibition of this networks altered lipid composition and markedly impaired NETosis, while diacylglycerol (DG) treatment revoked the effect. Altogether our findings reveal lipid remodeling as a fundamental determinant of NETosis and identify interconnected and dependent phospholipid lipase networks with downstream DG-dependent signaling as a potential therapeutic target in NET-associated diseases.

molecular biology↗

bioRxiv2025

A Structure-Aware Generative Framework for Exploring Protein Sequence and Function Space

The rapid expansion of protein sequence databases has far outpaced experimental structure determination, leaving many unannotated sequences, particularly the more remote homologs with low sequence identity. Because protein folds are more conserved and functionally informative than sequences alone, structural information offers a powerful lens for analysis. Here, we introduce a generative, structure-aware framework that integrates geometric encoding and coevolutionary constraints to map, cluster, and design protein sequences. Our approach employs the 3D interaction (3Di) alphabet to convert local residue geometries into compact, 20-state discrete representations. Using ProstT5, we enable bidirectional translation between amino acid sequences and 3Di representations, facilitating sensitive homology detection and structure-guided sequence generation. We then augment the latent generative landscape methodology by combining 3Di-based alignments with direct coupling analysis (DCA) and variational autoencoders (VAE), imbuing tasks such as clustering, annotation, and design with structural information. This integrative framework enhances the detection of coevolutionary signals and enables rational sampling of structural variants, even without functional labels. We demonstrate the utility of our method across diverse protein families, including globins, kinases, and malate dehydrogenases, achieving improved contact prediction, homology inference, and sequence generation. Together, our approach offers a quantitative, generative view of protein structure space, advancing protein evolution and design studies. Significance StatementProtein sequence databases are growing far faster than our ability to experimentally determine structures, leaving much of protein space poorly annotated, especially for distant homologs. Because protein structure is more conserved and informative than sequence alone, new approaches are needed to exploit structural signals at scale. We present a generative framework that integrates compact structural representations with evolutionary constraints to map, cluster, and design protein sequences. By combining geometric encoding with coevolutionary modeling, our approach enables sensitive homology detection, improved inference of structural contacts, and rational exploration of sequence space without requiring functional labels. This work provides a quantitative bridge between protein sequence and structure, advancing our ability to interpret protein evolution and guide protein design.

biophysics↗

bioRxiv2025

Preliminary insights into salivary proteomic versus targeted biomarker profiles associated with acute physical fatigue

Introduction: Physical fatigue is a key determinant of operational readiness in tactical athletes. Hormonal, immune, and enzymatic biomarkers have been proposed for fatigue assessment, but reliability can be affected by external factors. Therefore, this study aimed to compare targeted stress-related biomarkers, proteins identified via untargeted salivary proteomics, and a combined panel of both for classifying acute physical fatigue. Methods: Ten recreationally active adults (6M, 4F) completed a fatiguing protocol within a 3-day sample collection window. Saliva samples were analyzed for targeted biomarkers via commercial immunoassays and proteins via untargeted liquid chromatography-mass spectrometry. Targeted, protein, and combined panels were identified using nested leave-one-subject-out cross-validation with FDR correction and stability selection, then classified via ridge-penalized logistic regression. Models were extended across the full protocol to evaluate classification of fatigue onset, rest, and recovery states. Results: A candidate identified protein (C1S) achieved slightly higher classification accuracy (80%) relative to a panel of targeted biomarkers (IgA and UA 70%), with superior sensitivity but similar specificity. In comparison, the combined panel, spanning immune (IgA), oxidative/metabolic (UA), complement (C1S), and cellular stress-related (ANG) outperformed both single-platform models with 90% accuracy, sensitivity, and specificity. Conclusions: Improved classification accuracy observed with the inclusion of candidate salivary proteins provide preliminary support for non-invasive proteomic monitoring of fatigue in tactical settings, and in particular the combination of complementary targeted and proteomic panels to capture a more complete physiological signature of acute fatigue. Future studies should validate these findings in larger, more diverse populations and assess applicability for chronic fatigue monitoring.

physiology↗

bioRxiv2025

Human chronic inflammation is orchestrated by spatially restricted inflammation-activated Dendritic cells

Dendritic cells (DCs) form coordinated networks that orchestrate inflammatory responses across tissues. Upon activation, conventional dendritic cells (DCs) undergo changes in their transcriptome, phenotype, and function, depending on the tissue microenvironment. The role of DC activation during human chronic inflammation has yet to be explored. To address this, we aimed to investigate activated DCs across a range of chronically inflamed human tissues, with a focus on cervical lymph nodes (LNs). We performed scRNAseq and flow cytometry on healthy, acutely, chronically inflamed, and cancer-associated human cervical (LNs) and identified a novel inflammation-associated DC (iaDC) cell state, found only within chronically inflamed LNs. iaDCs were defined by a unique cytokine expression profile (CXCL9, CXCL10, IL1B) and could be phenotypically distinguished from other activated DCs by their elevated expression of CD1C, CD206, CD319, and CD274. Functionally, we found that IFN{gamma} signaling induces DC2s to enter the iaDC cell state and that this process can be abrogated by inhibition of JAK-STAT signaling. Using spatial transcriptomics, we observed LN iaDC residing within a specific chronic inflammatory niche, which was enriched for inflammatory monocytes, NK cells, and effector memory CD4+ and CD8+ T cells. Extrapolating our findings to other chronic inflammation-associated diseases, we similarly observed the emergence of iaDCs within the intestines of treatment-resistant Crohns Disease patients, synovial membranes and lymph nodes of rheumatoid arthritis patients and lungs of sarcoidosis patients. Similarly to the lymph node, iaDCs were found to reside in conserved chronic inflammation-associated spatial niches within the small intestine of affected individuals and displayed equivalent transcriptional characteristics and surrounding cellular neighborhoods. Collectively, these data highlight a previously unexplored role of iaDCs in human chronic inflammatory diseases and propose a conserved spatially restricted iaDC-populated chronic inflammatory niche associated with resistance to therapy. These findings highlight novel avenues to shape inflammatory trajectories by targeting iaDCs and their spatial niches, for example, by inhibiting JAK-STAT signaling.

immunology↗

bioRxiv2025

Could instructor talk drive CURE effectiveness? A comparative study of instructor talk in introductory lab courses

Course-based undergraduate research experiences (CUREs) are thought to enhance students motivation to continue in college, in science, and in research. Yet, how CUREs enhance student motivation is largely undefined. Theories of instructor immediacy, self-efficacy, and task values suggest that CURE instructors may talk in ways that influence students motivational beliefs. We characterized the non-content related talk of instructors teaching 48 introductory biology lab courses, half CUREs and half non-CUREs. We identified 14 types of instructor talk that fit these theoretical perspectives: fostering students closeness with their instructor (i.e., immediacy talk), building students confidence in their scientific abilities (i.e., self-efficacy talk), and promoting students sense of worth in their work (i.e., task value talk). Course type had a medium effect on talk type, with CURE instructors utilizing more immediacy, self-efficacy, and task values talk than non-CURE instructors but also showing more variation in these types of talk. Our results suggest that motivation-related instructor talk is more prevalent in CUREs than non-CUREs, but wide variation in CURE instructor talk indicates additional investigation is needed before non-content talk can be considered a mechanism for the motivational influences of CUREs. HIGHLIGHTThis study compares non-content instructor talk in CURE and non-CURE lab courses using immediacy, self-efficacy, and task value theories. CURE instructors use more talk than non-CURE instructors, but variation in CURE instructor talk leaves open the question of whether talk is a causal factor in the motivational influence of CURE instruction.

scientific communication and education↗

bioRxiv2025

Genome-wide DNA methylation study reveals specific signatures in the affected arterial tissue of giant cell arteritis patients

ObjectivesGiant cell arteritis (GCA) is a large-vessel vasculitis, potentially causing complications such as blindness and strokes. This study aims to gain insights into the pathogenesis of GCA by identifying specific DNA methylation signatures in the arterial tissue of patients with this vasculitis. MethodsDNA methylation profiling was analyzed in 79 temporal artery biopsy samples (69 patients with GCA and 10 controls) by performing an epigenome-wide association study (EWAS). Differential analysis was performed to identify differentially methylated positions (DMPs) and regions (DMRs). Lastly, we compared our findings with previous transcriptomics and epigenomics studies on GCA-affected arteries. ResultsEWAS identified 3,644 DMPs (FDR < 0.05, |{Delta}{beta}| > 0.3), indicating a profound alteration within GCA-affected arterial tissue. These DMPs were annotated to 1,517 potentially dysregulated genes. 282 additional genes were identified by annotation of significant DMRs. Pathway enrichment analysis revealed a significant alteration of inflammatory mechanisms, such as interleukins 2 and 7, as well as pathways related to vascular remodeling. Omics study comparison revealed 37 genes consistently affected across datasets, many of them linked to immune signaling and T cell regulation. Notably, markers of exhausted T cells, including SLAMF6 and HAVCR2, were present among them. ConclusionsOur study identified GCA-specific DNA methylation signatures in arterial tissue, revealing disrupted inflammatory and vascular pathways, and suggesting the involvement of exhausted T cells in this condition. These findings offer new insights into GCA pathogenesis and provide new potential targets for the treatment of this debilitating disease. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABS{square} Affected arteries by giant cell arteritis (GCA) exhibit unique epigenetic signatures, reflecting significant disruptions in gene regulation. However, small sample sizes have constrained the clinical translation and broader interpretation of these findings, leaving key gaps in understanding GCA pathogenesis and identifying therapeutic targets. What this study adds{square} This study provides the largest-to-date epigenome-wide DNA methylation profiling in GCA-affected arteries, uncovering thousands of epigenetic changes and revealing profound disruptions in inflammatory and vascular pathways, including IL-2, IL-7, and CXCR4 signaling. {square}We compiled 37 genes consistently affected across different omics datasets in GCA-affected arteries, providing a robust list of candidates for further research into GCA pathogenesis and treatment. {square}Our findings provide evidence of T cell exhaustion in GCA-affected arteries, supported by consistent changes in key markers such as SLAMF6 and HAVCR2 (TIM-3), suggesting a novel mechanism of immune dysregulation in GCA. How this study might affect research, practice or policy{square} This study nominates exhausted T cells, the NLRP3 inflammasome, and CXCR4 signaling as novel contributors in GCA pathogenesis, suggesting new therapeutic targets for further research in the treatment of this disease.

immunology↗

bioRxiv2025

NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART.

Despite antiretroviral therapy (ART), people with HIV (PWH) on ART experience higher rates of morbidity and mortality vs. age-matched HIV negative controls, which may be driven by chronic inflammation due to persistent virus. We performed bulk RNA sequencing (RNA-seq) on peripheral CD4+ T cells, as well as quantified plasma immune marker levels from 154 PWH on ART to identify host immune signatures associated with immune recovery (CD4:CD8) and HIV persistence (cell-associated HIV DNA and RNA). Using a novel dimension reduction tool - Pairwise Controlled Manifold Approximation (PaCMAP), we defined three distinct participant transcriptomic clusters. We found that these three clusters were largely defined by differential expression of genes regulated by the transcription factor NF-{kappa}B. While clustering was not associated with HIV reservoir size, we observed an association with CD4:CD8 ratio, a marker of immune recovery and prognostic factor for mortality in PWH on ART. Furthermore, distinct patterns of plasma IL-1{beta}, TNF- and GCSF were also strongly associated with the clusters, suggesting that these immune markers play a key role in CD4+ T cell transcriptomic diversity and immune recovery in PWH on ART. These findings reveal novel subgroups of PWH on ART with distinct immunological characteristics, and define a transcriptional signature associated with clinically significant immune parameters for PWH. A deeper understanding of these subgroups could advance clinical strategies to treat HIV-associated immune dysfunction.

microbiology↗

bioRxiv2025

A single-cell transcriptome atlas of adult male and female human hookworm Ancylostoma ceylanicum

Hookworms infect over 500 million people globally and represent a major neglected tropical disease. The prevalence, high reinfection rate, limited drugs and emerging resistance underscore the need for new therapeutic or vaccine targets. To mitigate halted progress of discovering targets, we provide new molecular insights into sex-specific expression and cellular heterogeneity by generating the first single-cell atlas of male and female transcriptome for the human hookworm Ancylostoma ceylanicum. We systemically annotated 10 transcriptionally distinct cell types in female and 13 in male hookworm by comparing marker genes with tissue-specific knowledge. Non-reproductive tissues included pharynx, intestine, cephalic and pharyngeal glands, muscle and hypodermis, complemented with female reproductive tissues (ovary, uterus, eggs, seminal receptacle), and male reproductive tissues (testis, seminal vesicle, cement gland, sperm). Anatomical confocal microscopy and fluorescence in situ hybridization assisted in visualizing these tissues and confirming marker genes. Functional comparisons revealed previously undescribed tissue pathways and molecular markers, providing previously unrecognized insights into hookworm biology, and new targets. Overall, this study presents a detailed cell-type atlas for adult stages of this important yet neglected metazoan parasite. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/631133v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@ed5de0org.highwire.dtl.DTLVardef@1ae2bf6org.highwire.dtl.DTLVardef@1c835c6org.highwire.dtl.DTLVardef@1429bb4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Multiplex base editing of BCL11A regulatory elements to treat sickle cell disease

Sickle cell disease (SCD) is a genetic anemia caused by the production of an abnormal adult hemoglobin. The clinical severity is lessened by elevated fetal hemoglobin (HbF) production in adulthood. A promising therapy is the transplantation of autologous, hematopoietic stem/progenitor cells (HSPCs) treated with CRISPR/Cas9 to downregulate the HbF repressor BCL11A via generation of double strand breaks (DSBs) in the +58-kb erythroid-specific enhancer. Here, to further enhance HbF production without increasing the mutagenic load, we targeted both +58-kb and +55-kb BCL11A erythroid-specific enhancers using base editors. We systematically dissected DNA motifs recognized by the key transcriptional activators within these regions and identified the critical nucleotides required for activator binding. Multiplex base editing of these residues was efficient and safe and generated no or little DSBs and genomic rearrangements. We observed substantial HbF reactivation, exceeding the levels achieved using the CRISPR/Cas9 nuclease-based strategy, thus efficiently rescuing the sickling phenotype. Multiplex base editing was efficient in long-term repopulating HSPCs and resulted in potent HbF reactivation in vivo. In summary, these results show that multiplex base editing of BCL11A erythroid-specific enhancers is a safe and potent strategy for treating sickle cell disease.

molecular biology↗