Biology subjects

Ali, M.

Publications and source records attributed to Ali, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Intra-uterine position modulates lifelong hippocampal neurogenesis and anxiety-related behavior

Individual differences in vulnerability to disease are a defining feature of biology and are especially prominent in mood disorders, where susceptibility to stress varies markedly across individuals. Strikingly, such individuality also emerges in inbred mice despite genetic homogeneity and controlled environments, suggesting that early non-genomic factors can durably shape behavioral trajectories. Yet the developmental origin of this variability remains largely unknown. Here, we identify the intra-uterine position (IUP) as a potent source of inter-individual variability in emotional behavior by showing that it influences prenatal steroid exposure, hippocampal development, adult neurogenesis, and anxiety-like traits in inbred mice. At embryonic day 18.5, embryos adjacent to one or two male siblings (i.e. 1M/2M) exhibited altered brain steroid profiles, coinciding with increased proliferation of neural stem and progenitor cells in the dentate gyrus, as compared to 0M mice. Single-nucleus RNA sequencing further revealed that IUP leaves a transcriptional imprint on hippocampal development, with 1M/2M neural stem cells showing reduced stemness and activation of a neurogenic transcription program. In adulthood, 1M/2M mice presented reduced hippocampal and dentate gyrus volumes, diminished radial-glia-like cell counts, lower cell proliferation, and impaired dendritic maturation of immature neurons. Behaviorally, both juvenile (PND22) and young adult (8-week) 1M/2M mice displayed increased trait anxiety, and 1M/2M males exhibited heightened stress reactivity. In vitro, testosterone, but not progesterone, directly enhanced proliferation of adult rat hippocampal stem/progenitor cells, whereas corticosterone reduced it. In vivo, administration of the androgen receptor agonist dihydrotestosterone (DHT) to pregnant dams recapitulated IUP effects by increasing embryonic dentate gyrus (DG) proliferation in female embryos, whereas antagonism reduced progenitor proliferation in male embryos. Together, these results indicate that IUP has long-lasting effects on hippocampal development and anxiety and may underlie natural variations in trait anxiety.

neuroscience↗

bioRxiv2026

Overcoming Daraxonrasib Resistance: Allele-Specific Mechanisms Guide Salvage Therapy in Pancreatic Cancer

Clinical-grade RAS inhibitors raise an unresolved question as to whether KRAS-alleles impose constraints on adaptive resistance that can be exploited therapeutically. Using daraxonrasib (RMC-6236), a multi-selective RAS(ON) inhibitor, we compared resistance mechanisms between KRASG12D and KRASG12R, alleles with fundamentally different RAS network dynamics. Daraxonrasib inhibited KRASMUT primarily through steric occlusion of effector binding, while engaging RASWT only modestly ([~]20%). KRASG12R is marked by its inability to transactivate RASWT, and it was observed that daraxonrasib resistant KRASG12R PDAC cells utilize EGFR/RASWT-GTP signaling as the dominant adaptive route. In contrast, KRASG12D resistance arose through retained KRASG12D-GTP signaling, with a decrease of cyclophilin A (CypA) protein, the binding partner required for daraxonrasib activity. The shift from KRASG12R dependence to the EGFR/RASWT conferred sensitivity to trametinib. We confirmed this clinically: a KRASG12R PDAC patient who progressed after 10 months on daraxonrasib showed intratumoral EGFR/RASWT activation, and rapid 3D-bioprinted patient-derived toroid modeling predicted sensitivity to trametinib-based combination therapy. Given the aggressive disease trajectory and lack of response to the two immediately preceding lines of therapy, sixth-line trametinib-based combination therapy achieved approximately 5 months of disease control. This patient ultimately achieved 40 months of overall survival, far exceeding the 8-12 month median for metastatic PDAC. Collectively, these data establish a framework in which allele-specific RAS network topology dictates the adaptive resistance landscape, enabling rational selection of targeted therapies with meaningful clinical benefit in metastatic PDAC. STATEMENT OF SIGNIFICANCEDaraxonrasib resistance mechanisms have allele-specific routes: CypA becomes downregulated in KRASG12D and reliance on EGFR/RASWT in KRASG12R. Rapid patient-derived toroids identified sixth-line targeted therapy strategies with an overall survival of 40 months.

cancer biology↗

bioRxiv2026

New genes play a prominent role in evolution of new sperm classes of Drosophila

The widespread and regulated production of infertile parasperm assisting fertilization of eusperm provides a compelling model for elucidating the mechanisms of cellular innovation and altruism. Here we identify two specific parasperm lineages in Drosophila pseudoobscura that are segregated in development from the eusperm lineage by their single-cell transcriptomes. Most X-linked genes, except for species-specific new genes, show testis-specific repressive epigenetic modifications and become downregulated upon meiotic entry, supporting meiotic X chromosome inactivation. Between sperm classes, nearly half of the known meiotic arrest genes and their downstream targets are differentially transcribed, with over 200 genes displaying a gradient of transcription levels correlated with that of tail lengths. New genes are overrepresented throughout the hierarchical regulatory network of sperm divergence and over 60% of them exhibit a new cell-level expression compared to their parental copies. These results together indicate that new genes play a prominent role in the emergence of low-cost parasperm that shield the eusperm until fertilization.

evolutionary biology↗

bioRxiv2026

A non-enzymatic role for METTL3 as an Androgen Receptor co-regulator that promotes prostate cancer proliferation.

Metastatic prostate cancer (PCa) continues to be a major cause of death in males, despite advances in treatment. Most treatment focuses on targeting the Androgen Receptor (AR), the main oncogene responsible for driving most prostate tumors. Despite these therapies targeting AR, the majority of patients still succumb to AR-driven disease. Therefore, there is a critical need for understanding how AR functions to promote prostate cancer growth and identify alternative therapeutic targets in AR-driven PCa. One avenue garnering attention is targeting epigenetic regulators that promote AR-activity; however, the importance of epitranscriptomic regulators, like those that modify mRNAs, is not well understood. Here, we identify a new role for the key catalytic subunit of the RNA N6-methyladenosine (m6A) transferase complex, METTL3, as an AR-coregulator. METTL3 is overexpressed in prostate tumors compared to normal tissue, and METTL3 protein is elevated in AR-expressing cell lines. Depletion of METTL3 significantly reduces proliferation of cancer cells and has no effect on the growth of non-transformed prostate epithelial cells, despite decreasing global m6A levels on mRNA. The catalytic activity of METTL3 is dispensable for the growth of both non-transformed and PCa cell lines, as pharmacologic inhibition of METTL3 does not inhibit proliferation, despite the reduction of global m6A on mRNA. Overexpression of both wild-type and catalytically inactive METTL3 mutants enhances cell viability and rescues cells in which METTL3 is knocked down. Finally, we report on direct interaction between AR and METTL3, their co-localization on chromatin, and reduced AR-cistromic occupancy within cells with METTL3 knockdown. Together, these findings identify a non-enzymatic role for METTL3 in supporting AR-driven transcriptional programs and PCa proliferation.

cancer biology↗

bioRxiv2026

Segmentation and classification of retinal pigment granules in fluorescence lifetime imaging microscopy (FLIM) data

Alterations of fluorescence properties in retinal pigment epithelium (RPE) cells caused by diseases such as age-related macular degeneration (AMD) highlight the need for detailed analysis of the fluorescent RPE granules at the individual level. Precise segmentation and classification of these granules remain challenging due to their limited visual separability. In this study, we present Classi4RPE, a computational algorithm designed to accurately segment RPE granules and classify them into three categories -- lipofuscin (L), melanolipofuscin (ML), and melanin (M) -- based on fluorescence lifetime imaging data, which provide distinctive contrast. The method is implemented in a custom Python framework and employs seeded watershed segmentation to isolate individual granules. Lipofuscin granules are identified as hyperfluorescent structures with longer lifetimes, while granules with shorter lifetimes are further analyzed based on their spatial lifetime distribution from the center to edge, enabling discrimination of ML from other melanin-rich granules. Our approach achieves high performance, with mean sensitivities of 0.99 for L granules and 0.90 for ML granules, and corresponding specificities of 0.93 and 0.98, respectively, compared to manually annotated ground truth. These results demonstrate the potential of Classi4RPE to surpass human visual limitations and provide a robust tool for quantitative RPE analysis.

bioinformatics↗

bioRxiv2026

Wobble Vaccines: Cross-Strain Protection Through Epitope Hierarchy Manipulation

Vaccination remains the most successful preventative measure against viral infection, but methods to stably deter rapidly-evolving pathogens have remained elusive. Vaccines capable of incorporating and anticipating viral evolution could address current challenges in seasonal vaccination efforts against SARS-CoV-2 and influenza where economic and disease burdens remain high despite decades of combined study. Rare epitope suppression (RES) is an underutilized concept within vaccine design, where humoral epitope targeting can be molded using complex antigen pools. Based in mRNA vaccine technology, wobble vaccines represent the novel application of RES to human pathogens designed to anticipate and resist viral evolution. To establish this platform, public SARS-CoV-2 sequencing data was compiled from the first two years of the COVID-19 pandemic to identify high-diversity sites across the receptor binding domain (RBD) of the spike protein. Wobble RBD (WobbRBD) libraries reflecting that entropy were synthesized and incorporated into established self-amplifying (SA) vaccine constructs. Animals immunized with these complex antigen pools showed no obvious adverse effects. By three days-post vaccination, WobbRBD stimulated robust primary immune activation with distinctive characteristics compared to traditional single-strain vaccine modalities. By day 14, germinal centers, class switching, and antibody-secreting cells were induced, creating potent SARS-CoV-2 spike-binding IgG antibodies. Despite similar overall activation profiles, WobbRBD generated significantly increased breadth against SARS-CoV-2 variant spikes in comparison to single-strain controls - even against future-emerging strains. Taken together, wobble vaccines represent a novel method for anticipating and preventing viral escape with promising applications in SARS-CoV-2, influenza, HIV, and beyond.

immunology↗

bioRxiv2026

Plasma proteomics identifies an IL-6–associated SAA axis linked to muscle wasting in patients with cancer cachexia

Nearly half of patients with advanced lung cancer develop cachexia, a debilitating syndrome that worsens prognosis. We conducted longitudinal clinical and plasma proteomic profiling of 67 patients with non-small cell lung cancer, with and without cachexia, during first-line treatment. Patients with cachexia at diagnosis exhibited elevated risk of hospitalization and treatment-delaying toxicity. At diagnosis, 128 plasma proteins were upregulated and 67 downregulated in cachectic relative to non-cachectic patients. Longitudinal assessments of body composition, physical performance, metabolism, clinical outcomes, and nutritional risk revealed distinct fat and muscle wasting phenotype trajectories. 71 proteins were associated with fat loss, 92 with muscle loss, and 177 with concurrent muscle and weight loss. We identified and functionally validated 8 plasma proteins linked to muscle loss and adverse clinical outcomes. In a separate cohort of 147 patients with advanced pancreatic cancer receiving the interleukin-6 (IL-6) inhibitor tocilizumab, pharmacological suppression of serum amyloid A (SAA) levels following IL-6 inhibition suggests a systemic IL-6-SAA axis. These results collectively highlight SAA1 and SAA2 as IL-6-driven, cachexia-associated factors that reduce human myotube width. These findings uncover new potential therapeutic targets for cachexia.

Systems Biology↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2026

Characterization Standard for In-situ Cryo-electron Tomography

Standardized biological specimens are essential for optimizing cryoEM workflows and benchmarking instrument performance. While apoferritin fulfills this role for single-particle analysis, no equivalent exists for cryo-electron tomography. Ribosomes are frequently used but require large datasets due to C1 symmetry and structural heterogeneity, limiting rapid optimization and standardized comparison of workflows. Here, we present PP7 virus-like particles (VLPs) overexpressed in E. coli as a scalable in situ benchmark. VLPs have high orders of symmetry enabling rapid, high-resolution validation of tomographic pipelines from minimal datasets, while their distinct structural features across low to high resolutions provide a practical resolution metric.

cell biology↗

bioRxiv2026

Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer

ABSTRACTUlcerative colitis is a chronic inflammatory bowel disease that can progress from dysplasia to cancer. Inflammatory responses are critical drivers in this process, typically triggered by epithelial lesions and the ensuing infiltration of microbiota into the interstitial layer. Here, we focus on the pro-inflammatory state of the interstitial fibroblasts, which promotes immune infiltration and augments disease progression. The study aims to provide a mechanistic link how fibroblasts of the colitis-associated microenvironment integrate inflammatory signals, microbial infiltration and cellular memory. To this end, we investigated a large number of primary colon fibroblasts obtained from normal, colitis and colon cancer samples using a range of in vitro approaches and an in vivo co-inoculation cancer model. mRNA sequencing analysis identified that the disease-associated fibroblasts are exhibit a cellular inflammatory status, which involves the injury-induced senescence pathway. Using CXCL8, a potent chemokine upregulated in colitis and cancer colon fibroblasts, as a paradigm, this inflammatory status is triggered by the activation of the NF{kappa}B signaling via immune-derived cytokines (TNF, IL-1{beta}), bacterial signals (LPS) and the microbiome itself using mycoplasma as a paradigm. Finally, iPSC reprogramming studies indicate that fibroblasts from ulcerative colitis retain an epigenetic memory that sustains elevated CXCL8 expression. Together, our findings demonstrate that the senescence associated secretory phenotype of colon fibroblasts is a robust indicator for inflammation-driven colon tumorigenesis.

cancer biology↗

bioRxiv2026

Biodegradable Architected Stents for Endoscopic Internal Drainage

Postoperative gastric leak after bariatric surgery is a serious complication associated with prolonged treatment, repeated interventions, and substantial morbidity. Endoscopic internal drainage using double pigtail stents is widely adopted. However, current stents, originally designed for biliary use and often based on simple cylindrical geometries, are not optimized for post-bariatric gastric leak anatomy, mechanical support, or fluid drainage. Here, we present BRIDGE (Biodegradable aRchitected Internal DrainaGE), a stent concept integrating triply periodic minimal surface (TPMS) architectures to control mechanical compliance, kink resistance, and drainage performance. Using computational modeling, mechanical testing, and benchtop flow studies, we evaluate TPMS designs and identify volume fraction as a key parameter balancing flexibility, structural integrity, and hydraulic performance. TPMS-integrated designs tolerated a 7.1-fold smaller bend radius than a commercial stent without kinking and achieved up to a 2-fold increase in drainage. We also developed a stereolithography-printable biodegradable resin and fabricated a prototype lattice-integrated stent. TeaserA biodegradable, 3D-printed stent with an architected lattice design improves flexibility, kink resistance, and abscess drainage while eliminating the need for device removal.

bioengineering↗

bioRxiv2026

Reversible hypervascularization drives cognitive decline and blood-brain barrier damage during aging

Cerebrovascular dysfunction emerges early in neurodegeneration, yet how vascular structure, blood-brain barrier (BBB) failure, and cognition are linked remains undefined. Using VesselPro, a whole-brain pipeline integrating perfusion-resolved 3D imaging with spatial proteomics, we mapped vascular aging across the mouse lifespan. We identify two discrete trajectories: a hypovascular state and a previously unrecognized hyper-vascular, BBB-compromised state, defined relative to a young-adult vascular baseline. The hyper-vascular trajectory, concentrated in the cortex and hippocampus, was associated with marked spatial memory impairment and pervasive BBB leakage. Spatial proteomics revealed a coordinated program involving angiogenic activation, endothelial stress, cytoskeletal remodeling, and inflammatory signaling. Cross-species comparison with human proteomic biomarkers from the UK Biobank showed strong alignment between the mouse hypervascular signature and vascular dementia risk, but minimal concordance with Alzheimers disease, defining a vascular-specific dementia endotype. Transient Tie2 activation with AKB-9778 attenuated this trajectory, improving vessel organization, BBB integrity, and memory performance. Our findings show that endothelial instability is a key mechanistic driver of this heterogeneous vascular aging state. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/720441v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@39494aorg.highwire.dtl.DTLVardef@faa4acorg.highwire.dtl.DTLVardef@1511dd5org.highwire.dtl.DTLVardef@7db29b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVesselPro: we developed a pipeline for capturing perfused blood vessels in the brain: unexpected bifurcation in vascular aging: traditional hypovascular state and a novel, hypervascular, BBB-compromised state. C_LIO_LIHypervascular pathology: Linked the hypervascular profile in the cortex and hippocampus to spatial memory impairment, pervasive BBB leakage, and angiogenic inflammatory signaling. C_LIO_LIClinical endotype: Cross-species analysis via the UK Biobank confirms this hypervascular signature aligns with vascular dementia risk rather than Alzheimers disease. C_LIO_LIPharmacological stabilization: Demonstrated that Tie2 signaling activation (AKB-9778) improves the vessel organization, BBB integrity, and memory performance. C_LI

neuroscience↗

bioRxiv2026

Minoxidil hydrochloride impedes NLRP3 inflammasome activation via upregulation of AMPK-mediated autophagy

NLRP3 inflammasome is a cytosolic multi-protein complex that plays a crucial role in the immune system, responding to various exogenous and endogenous stimuli by triggering protective inflammatory responses. However, aberrant NLRP3 inflammasome activation is implicated in numerous inflammatory diseases. Therefore, the NLRP3 inflammasome is an important pharmacological target for the treatment of multiple diseases. In this context, we screened various US-FDA-approved drugs for NLRP3 inflammasome inhibition. We found that among various drugs, minoxidil hydrochloride (MXL) effectively inhibits NLRP3 inflammasome, evidenced by reduced secretion of IL-1{beta} and IL-18 in J774A.1 cells treated with MXL. The IC50 values of MXL for inhibition of IL-1{beta} and IL-18 were calculated to be 1.2 and 1.06 {micro}M, respectively. MXL was found to prevent ASC oligomerization, thereby inhibiting the NLRP3 inflammasome and leading to CASP1 cleavage. Further investigation revealed that MXL also utilizes AMPK-mediated autophagy to modulate NLRP3 inflammasome activity. Using siAMPK and bafilomycin A1, an end-stage autophagy inhibitor, we elucidated crosstalk between the NLRP3 inflammasome and autophagic pathways, which was modulated by MXL. Furthermore, we demonstrated the efficacy of MXL in two different mouse models of inflammation, involving the NLRP3 inflammasome. MXL at doses of 10 and 20 mg/kg effectively inhibited the activation of NLRP3 inflammasome by monosodium urate in the air pouch model and by ATP in the peritoneal inflammation model, as evidenced by reduced secretion of 1{beta} and IL-18 in the lavage. Our study identifies MXL as a potent NLRP3 inflammasome inhibitor, warranting further investigation as a potential therapeutic agent for inflammatory diseases.

immunology↗

bioRxiv2026

Increased CSF volume, altered brain development and emotional reactivity after postnatal Zika virus infection in infant rhesus macaques

Although congenital Zika virus (ZIKV) syndrome is well-characterized, the neurodevelopmental consequences of postnatal infection are less understood. Here we used a rhesus macaque model to investigate the developmental consequences of ZIKV infection during infancy on the brain and behavior, building on our prior research. Male and female infant rhesus macaques infected with ZIKV at 1 month of age were compared to sex-, age-, and rearing-matched uninfected controls and infants treated with the TLR3 agonist PolyIC as a control for activation of the innate immune system. Longitudinal behavioral assessments revealed alterations in emotional regulation following ZIKV exposure, including poor state control scores obtained from the Infant Neurobehavioral Assessment Scale early after ZIKV infection and longer-term displays of increased hostility during an acute stressor. While attachment bonds to caregivers were preserved, ZIKV-infected infants showed sex-specific alterations in behavioral regulation during caregiver separation compared to controls. At 3 months of age, MRI scans revealed larger total cerebrospinal fluid (CSF) volume and reduced volumes in visual processing regions in ZIKV-infected infants compared to controls. Postnatal ZIKV exposure also resulted in sex-specific brain structural alterations with males exhibiting amygdala hypertrophy, whereas ZIKV-infected females had volumetric reductions in temporal-limbic and temporal-auditory cortices. These findings demonstrate that postnatal ZIKV infection disrupts the development of sensory, social and emotion-regulatory systems and CSF function, highlighting the critical need for long-term monitoring of exposed children. One-Sentence SummaryPostnatal Zika virus infection disrupts emotional regulation and alters brain development in infant rhesus macaques, revealing a critical window of neurodevelopmental vulnerability that extends beyond the fetal period.

neuroscience↗

bioRxiv2026

Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores

Antibody-antigen binding prediction remains a central challenge for AI-driven therapeutic discovery, particularly in discriminating cognate interactions from structurally plausible but incorrect pairings. We present a controlled, AI-method- and antibody-format-agnostic evaluation framework that measures binding specificity under realistic conditions. Using 106 experimentally determined single-chain antibody (nanobody)-antigen complexes and 11,342 shuffled non-cognate pairings, we benchmarked publicly-available state-of-the-art structure prediction methods (AlphaFold3, Boltz-2, Chai-1). Although the methods tested often generated geometrically plausible complexes, internal confidence metrics (ipTM) frequently failed to discriminate correct from incorrect pairings. Increased sampling improved structural refinement but not pairing discrimination, indicating that computational resources are better allocated across independent seeds and explicit negative controls. We conclude that internal confidence scores are not inherently calibrated to binding specificity and require validation against realistic decoys. To enable community benchmarking and method development, we release [~]1.8 million AI-generated complex structures and guidance for the benchmarks ahead.

bioinformatics↗

bioRxiv2026

Characterising recent antimalarial resistance in West Africa: Insights from amplicon sequencing of 17,384 Plasmodium falciparum infection samples

Plasmodium falciparum (P. falciparum) infection remains a significant public health threat in West Africa, where chemoprevention and first-line therapies are key interventions against malaria. However, the development and spread of resistance to commonly used antimalarials poses a growing threat to the efficacy of these strategies. This study characterises the recent landscape of antimalarial resistance in West Africa by analysing targeted amplicon sequences from 17,384 P. falciparum infection samples. Across countries, the prevalence of the pyrimethamine resistance-associated dhfr triple mutant allele (51I/59R/108N) exceeded 80%, while its combination with the sulphadoxine resistance-associated dhps 437G exceeded 60% of infections. Unlike the parasite genotypes in East Africa, the prevalence of the dhps 540E mutant was low (1.5%), whereas dhps 436A was common (43.8%). The chloroquine resistance marker crt 76T showed greatest geographic heterogeneity, ranging from low prevalence in Ghana (1.3%) to very common in The Gambia (64.9%). Non-synonymous mutants of kelch13 were uncommon, most with unknown relevance to artemisinin resistance and observed for the first time in Africa. However, mutants that are artemisinin resistance-associated elsewhere were detected in three infection samples from Ghana (574L, 561H, 469Y), and one in Cameroon (538V). This large-scale genomic surveillance of P. falciparum infections highlights the need for ongoing monitoring of drug resistance and for data integration throughout the region.

genomics↗

bioRxiv2026

Thrombo-inflammatory endothelial signatures in JAK2-mutated myeloproliferative neoplasms

BackgroundClassical myeloproliferative neoplasms (MPN)--essential thrombocythemia, polycythemia vera, and primary myelofibrosis--are characterized by clonal hematopoiesis, overproduction of mature blood cells, and a high burden of thromboembolic events. Although thrombosis is the leading cause of morbidity and mortality in MPN, the contribution of the vascular endothelium remains incompletely defined. We investigated patient-derived endothelial colony-forming cells (ECFCs) as a surrogate for vascular endothelium in individuals with JAK2 V617F-mutated MPN. MethodsECFCs were cultured from peripheral blood of patients with MPN and healthy controls, phenotyped for thrombo-inflammatory and adhesive markers, tested for JAK2 V617F, and profiled by bulk RNA sequencing. Functional assays assessed endothelial-dependent factor Xa generation. Transcriptomes were benchmarked against public HUVEC reference datasets processed through an identical quantification pipeline. ResultsECFCs were obtained more frequently and in greater numbers from patients with MPN than from controls, indicating enhanced endothelial regenerative or activation potential. MPN ECFCs exhibited increased von Willebrand factor and P-selectin expression and release, along with elevated endothelial cell-dependent factor Xa generation, consistent with a thrombo-inflammatory, procoagulant phenotype. JAK2 V617F was not detected in any ECFC colonies, supporting a non-clonal origin of these endothelial abnormalities. Transcriptomic analysis identified 289 differentially expressed genes in MPN versus control ECFCs, with pathway enrichment revealing coordinated dysregulation of blood coagulation, platelet activation, plasminogen regulation, vascular permeability, extracellular matrix organization, and angiogenesis. Benchmarking against HUVEC datasets confirmed strong endothelial identity of ECFC-derived cells, with MPN-associated changes reflecting endothelial activation rather than loss of endothelialness. ConclusionsECFCs from patients with JAK2-mutated MPN display functional and transcriptomic signatures of endothelial dysfunction in the absence of detectable driver mutations. These findings support a model in which a primed, thrombo-inflammatory endothelium cooperates with clonal hematopoiesis to promote the heightened thrombotic risk characteristic of MPN.

cell biology↗

bioRxiv2026

In silico transcriptomic analysis reveals shared molecular signatures and immune-associated pathways between Hashimotos thyroiditis and type 2 diabetes with exploratory drug repurposing

The management of Hashimotos thyroiditis (HT), one of the most prevalent autoimmune disorders worldwide, becomes more complex when it coexists with type 2 diabetes (T2D) compared with the management of either disease alone. This complexity may arise from overlapping genetic, metabolic, and immune dysregulation, as well as potential therapeutic conflicts. Although HT and T2D are known to co-occur and share immune and metabolic features, the molecular characteristics underlying these overlaps have not been systematically explored. This study aimed to identify shared gene expression signatures and associated biological pathways between HT and T2D using an in silico, hypothesis-generating approach, and to explore candidate compounds that may be relevant to both conditions. Independent transcriptomic datasets (GSE138198 for control/HT and GSE29231 for control/T2D) were analyzed, leading to the identification of 59 genes that were differentially expressed in both HT and T2D compared with control samples. Protein-protein interaction (PPI) network analysis prioritized five shared key genes (sKGs): CDC42, CD74, FOS, RAC2, and YWHAB. Functional enrichment analysis of these sKGs revealed overlapping biological processes, molecular functions, cellular components, and immune-related signaling pathways, as well as shared regulatory networks involving transcription factors (FOXC1 and HNF4A) and microRNAs (hsa-miR-221-3p and hsa-miR-29a-3p). Immune infiltration analysis demonstrated broadly similar patterns of immune dysregulation in both diseases, providing additional biological context for the observed shared molecular signatures. Finally, an exploratory in silico drug repurposing pipeline incorporating molecular docking, ADMET profiling, drug-likeness assessment, and molecular dynamics simulations prioritized three candidate compounds: gliquidone, oleanolic acid, and glipizide for further investigation. Overall, this study provides a hypothesis-generating framework highlighting shared molecular features between HT and T2D, which may inform future experimental validation and clinical research. Author SummaryIn this work, we wanted to better understand why Hashimotos thyroiditis, an autoimmune condition that affects the thyroid gland, is often seen in people who also have type 2 diabetes. Treating patients who live with both conditions can be difficult, and we were interested in finding out whether they share common biological causes. To do this, we examined genetic data from individuals with each disease and looked for patterns that appeared in both groups. We discovered several genes that seem to act in similar ways in the two conditions, particularly genes linked to immune system activity and associated pathways. This finding suggests that shared molecular signatures and immune-associated pathways may play a role in the development of both diseases. We also explored how these shared genetic features influence larger biological processes and immune responses. The similarities we found support the idea that the two diseases may be connected through related biological pathways. In addition, we used computer-based screening methods to identify existing drugs that might influence these shared pathways. While these results need further testing, we hope our findings help open new directions for research and eventually contribute to better care for patients affected by both conditions.

bioinformatics↗