Biology subjects

Lopez, L.

Publications and source records attributed to Lopez, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Folic acid polyglutamylation triggers MAP2K5 signaling to induce adipocyte lipid catabolism

Adipocyte signaling adaptively responds to macronutrients, but how essential micronutrients impact lipid homeostasis remains poorly understood. Here, we demonstrate that folate polyglutamylation, the sequential conjugation of glutamate residues to folate, serves as a dynamic biochemical process regulating metabolic signaling. Using our folate metabolomics platform, we show that polyglutamylated folic acid accumulates in healthy adipose tissue, but is depleted in obesity across mice and humans, independent of circulating folate levels. Genetic ablation of the polyglutamylation enzyme folylpolyglutamate synthase (Fpgs) in adipocytes suppresses lipid catabolism to induce cell-autonomous lipid accumulation, operating independently of canonical adipogenesis or downstream one-carbon flux. Target-engagement proteomics identifies monoglutamylated folic acid as a Map2k5-interacting molecule that inhibits Map2k5 activity, whereas Fpgs-mediated folic acid polyglutamylation acts as a chemical switch that disrupts this interaction to promote lipolysis. In vivo, whole-body inhibition of Map2k5 or adipose-targeted genetic depletion of Fpgs increases body fat mass in the absence of dietary obesogenic triggers. Furthermore, single-cell and single-nuclear transcriptomic analyses establish the Fpgs-Map2k5 pathway as a core transcriptional signature of mouse and human adipose tissues. These findings uncover a non-canonical signaling role for folate that regulates adipocyte lipid homeostasis.

biochemistry↗

bioRxiv2026

Fetal sex shapes placental inflammatory responses to extracellular mitochondrial DNA

Aberrant changes in circulating cell-free mitochondrial DNA (ccf-mtDNA) across gestation are associated with adverse pregnancy outcomes. Given the inflammatory properties of ccf-mtDNA via pattern recognition receptors such as Toll-like receptor 9 (TLR9), we hypothesized that extracellular mtDNA induces placental inflammation via TLR9 signaling and that this response differs by fetal sex. Pregnant Sprague-Dawley rats were treated intravenously with purified mtDNA (300 g/kg), nuclear DNA (nDNA), saline, and/or the TLR9 antagonist ODN2088 across five studies. Placental responses were evaluated 4 h (Studies 1-3) and 24 h (Study 4) post-treatment; pregnancy and neonatal outcomes were assessed at delivery (Study 5). Exposure to mtDNA, but not nDNA, increased placental il1{beta}, tnf, and il10 mRNA (p < 0.05), establishing response specificity. mtDNA-induced placental inflammation was fetal sex-dependent: mtDNA increased il6 and il1{beta} mRNA in male placentas (p [≤] 0.0004) but not female placentas, whereas ifn{gamma} was selectively induced in female placentas (p = 0.0004). TLR9 and MyD88 abundance increased in female but not male placentas, and TLR9 antagonism modified selected inflammatory responses with sex-specific patterns. The 4 h inflammatory transcriptional signature resolved by 24 h, whereas mtDNA exposure was associated with a sex-specific shift in antioxidant enzyme expression persisting to 24 h. Despite no effects on gestational length or neonatal biometrics, mtDNA exposure was associated with a higher estimated stillbirth count per litter (IRR = 4.23, 95% CI [0.89, 20.1], p = 0.069). These findings establish extracellular mtDNA as an acute, sex-differentiated placental inflammatory stimulus with partial TLR9 dependence and a potential impact on fetal viability. New & NoteworthyThis study demonstrates that acute exposure to extracellular mtDNA induces placental inflammatory responses in vivo. This response is specific to mtDNA, fetal-sex dependent, and partially mediated by TLR9, with male and female placentas engaging distinct inflammatory signals within hours of exposure. The biological effects extend beyond the initial inflammatory window, with mtDNA exposure producing lasting, sex-specific changes in antioxidant enzyme expression. mtDNA-exposed dams had higher expected stillbirth counts, suggesting extracellular mtDNA may affect fetal viability.

physiology↗

bioRxiv2026

Focal radiotherapy improves CAR T cell therapy targeting prostate cancer

Chimeric antigen receptor (CAR) T cell therapy has limited efficacy against solid tumors such as prostate cancer due to the immunosuppressive tumor microenvironment (TME). Combining CAR T cells with existing therapies that remodel the TME and promote endogenous immune responses, such as radiation therapy and chemotherapies, may strengthen antitumor responses. Here, we assessed the potency of combining focal radiotherapy (RT), cyclophosphamide (Cy) preconditioning, and prostate stem cell antigen (PSCA)-CAR T cells against syngeneic prostate cancer models. Focal RT alone increased T cell and dendritic cell infiltration and activation in the irradiated tumor. Furthermore, the combination of all three therapies was critical for enhanced antitumor responses and survival across multiple subcutaneous, bone-metastatic, and multifocal disease models. This combination, in the irradiated TME and tumor-draining lymph nodes (tdLN), led to greater antigen presentation by myeloid cells and endogenous T cell activation and cytotoxicity. Our study demonstrates the potency of combining focal RT with PSCA-CAR T cells, significantly improving therapeutic responses in the irradiated tumor and contributing to a more robust systemic immune response against metastatic burden in prostate cancer.

Cancer Biology↗

bioRxiv2026

Acute exposure to cell-free mitochondrial DNA induces pregnancy-specific aortic endothelial dysfunction and organ-selective inflammation in rats

Pregnancy complications such as preeclampsia are associated with circulating cell-free mitochondrial DNA (mtDNA), a damage-associated molecular pattern capable of activating Toll-like receptor 9 (TLR9). We hypothesized that acute mtDNA exposure induces maternal inflammation and endothelial dysfunction during pregnancy via TLR9 activation. Non-pregnant and pregnant rats (gestational days 14-15) were treated intravenously with saline or purified mtDNA and euthanized 4 h after treatment. mtDNA increased cytokine mRNA expression in lung and liver of non-pregnant and pregnant rats, with magnitude varying by pregnancy status and organ. Aortas from pregnant, but not non-pregnant, rats exhibited reduced acetylcholine (ACh)-induced relaxation following mtDNA treatment (Emax, saline: 90.1 {+/-} 3.9 % vs. mtDNA: 62.1 {+/-} 20.7 % KClmax, p<0.05), while uterine artery function was preserved, indicating vascular bed-specific effects. Ex vivo incubation of aortic rings with mtDNA {+/-} white blood cells did not replicate in vivo findings, implicating systemic rather than direct vascular mechanisms. Nuclear DNA did not affect ACh-induced relaxation (p>0.05), confirming that the vascular effects were mtDNA-specific. Pharmacological antagonism of TLR9 with ODN2088 partially attenuated mtDNA-induced maternal endothelial dysfunction. Although overt vascular ROS increases were not detected, aortas from pregnant rats had reduced sod-1 expression (p<0.05) and increased eNOS protein abundance (p<0.05). Acute mtDNA exposure during pregnancy induces maternal organ inflammation and impairs endothelium-dependent vasodilation, with partial TLR9 involvement. In conclusion, aortic transcriptional changes in antioxidant pathways and increased eNOS abundance were also observed, though their functional significance remains to be determined. New & NoteworthyTo our knowledge, this is the first study to demonstrate that acute exposure to circulating mtDNA induces pregnancy-specific maternal endothelial dysfunction and organ-selective inflammatory responses. Our findings reveal pregnancy- and vascular-bed specific responses of the maternal vasculature to mitochondrial danger signals, with partial TLR9 involvement. Aortic transcriptional changes in antioxidant pathways and increased nitric oxide synthase abundance were identified as molecular correlates of this dysfunction.

physiology↗

bioRxiv2026

IL12-engineered human PSMA-CAR T cells for the treatment of advanced prostate cancer

Adoptive cell therapies used to treat advanced prostate cancer are being developed to target several tumor-associated antigens, including prostate-specific membrane antigen (PSMA). Chimeric antigen receptor (CAR) T cell therapy using the single chain variable fragment (scFv) derived from the humanized murine mAb clone, J591, as the antigen-binding domain has shown promising anti-tumor activity. However, it has also been associated with macrophage activation syndrome and other unwanted toxicities, highlighting the need for more specific and human-derived antigen-binders with optimized construct designs for improved safety and efficacy. Here, we optimize a human scFv-based PSMA-targeted CAR (hPSMA-CAR) with highly selective PSMA targeting. We further introduce a membrane-bound IL-12 (mbIL12) molecule, which enhances potency with increased T cell expansion, IFNy production and anti-tumor cell activity in vitro. Using two clinically-relevant bone-metastatic prostate cancer models, we show that mbIL12-engineered hPSMA-CAR T cells drive potent in vivo anti-tumor responses. In summary, we have developed a promising therapeutic that has potential to promote safe and effective treatment of advanced PSMA+ prostate cancer.

bioengineering↗

bioRxiv2026

A MET-Targeted Variable New Antigen Receptor Theranostic for Non-Small Cell Lung Cancer

The MET receptor tyrosine kinase is mutated or amplified in [~]6% of non-small cell lung cancer (NSCLC) and overexpressed in [~]80% of all NSCLC cases. A theranostic agent that can both see and treat MET-altered NSCLC has never been described before in the literature. Here, we report a shark-derived single-domain variable new antigen receptor (VNAR) for MET with theranostic applications. Following the immunization of a juvenile nurse shark (Ginglymostoma cirratum) with the extracellular domain of human MET, we identified a VNAR clone that specifically engaged MET with high affinity. Engineering the lead VNAR into a bivalent human Fc, vMET1-Fc, yielded a construct that selectively targeted and was internalized by MET-positive cells without affecting cell viability or downstream MET signaling. When radiolabeled with the positron emitting isotope Zr-89, [89Zr]Zr-vMET1-Fc enabled longitudinal PET/CT imaging. High tumor uptake with low background was observed in MET-positive NSCLC xenografts administered [89Zr]Zr-vMET1-Fc. As a targeted beta-particle radiotherapy, [{superscript 1}Lu]Lu-vMET1-Fc resulted in marked tumor-growth delay and exhibited a favorable toxicity profile, collectively improving progression-free survival in NSCLC mouse models. Non-human primate PET/CT imaging studies with ([Zr]Zr-vMET1-Fc in healthy rhesus macaques confirmed favorable biodistribution and dosimetry, predictable clearance, and minimal off-target uptake. Additional blood chemistry analysis found no significant immune response or cytotoxicity. Together, these findings establish vMET1-Fc as a theranostic agent for imaging and treating MET-altered NSCLC. Statement of SignificanceA shark-derived antibody selectively targeting MET shows preclinical efficacy as a theranostic agent for MET-altered cancer.

cancer biology↗

bioRxiv2025

Persistent trade-offs balance competition and colonization across centuries

Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature--or are eroded as lineages adapt through compensatory changes--remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins--phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare--while the tailocins production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient -- historical genomes spanning two centuries show that the trade-off has been maintained for at least 10-10 generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome. SignificanceWhen a microbe colonizes a host, it must both establish infection and outcompete other organisms. Short-term experiments show that gains in competitive ability can reduce colonization, creating trade-offs, but whether microbes resolve these conflicts over long evolutionary timescales is unknown. We show that a trade-off between competitive killing and host colonization has been stably maintained for centuries in natural Pseudomonas populations infecting Arabidopsis thaliana. Tailocins--phage-derived weapons--provide strong competitive advantages, yet their production reduces colonization success, explaining why the most broadly lethal variants remain rare. Genomic surveys and historical genomes spanning two centuries reveal that the polymorphisms underlying this trade-off have persisted across 10-10 generations. Understanding such long-lived constraints can inform antimicrobial strategies that exploit evolutionary trade-offs.

evolutionary biology↗

bioRxiv2025

CXCR6⁺ CD127- Tr1 Cells Balance Immunity and Persistence in Plasmodium falciparum Infection

Plasmodium falciparum (Pf) induces the clonal expansion of antigen-specific type 1 regulatory T (Tr1) cells with a capacity for long-term memory. Tr1 cells comprise nearly 90% of the Pf blood stage antigen-specific CD4+ T cell pool in children. Though, whether Tr1 cells contribute to protection from malaria remains undetermined. To address this critical gap in knowledge, we first performed scRNAseq on gated cell populations to validate CXCR6+ CD127- as new phenotypic markers to enrich for bona-fide Tr1 cells. Importantly, these Tr1 cells potently suppressed the proliferation of other CD4+ T cells in vitro via IL-10 secretion. Among children living in malaria-endemic Uganda, CXCR6+ CD127- Tr1 cells were the dominant responding subset to Pf-infected red blood cell stimulation in vitro. They also rapidly expanded following malaria and expressed IL-10 and IFNg during infection in vivo. Tr1 abundance correlated with plasma concentrations of granzyme A, IFNg, IL-10, and LAG3, suggesting that these cells act systemically. Higher CXCR6+ CD127- Tr1 cell frequencies correlated with a lower probability of symptoms given parasitemia but were also associated with delayed parasite clearance among untreated, asymptomatic children. These data suggest that Tr1 cells help mediate clinical immunity to malaria but may also facilitate parasite persistence through mechanisms of immune regulation.

immunology↗

bioRxiv2025

Climatic Influence on COVID-19: Investigating the Role of Temperature and Humidity in the Spread of the Omicron Variant

Understanding how climate modulates infectious disease dynamics is critical for anticipating epidemic patterns. This study examines the association between climatological variables--specifically temperature and relative humidity--and the incidence of the SARS-CoV-2 Omicron variant (B.1.1.529) during its global wave (2021-2022). Using global epidemiological and climate data, we applied Scale-Dependent Correlation (SDC) analysis to detect transient, scale-specific associations across regions and periods. We identified consistent negative correlations between incidence and both temperature and humidity, especially in mid-latitudes during colder months. These findings were compared with predictions from stochastic population-based compartmental models incorporating climate-dependent transmission parameters. Among the tested formulations, the temperature-based model achieved the best fit to observed case trajectories. Our results highlight a robust climatological influence on Omicron transmission dynamics and underscore the importance of integrating climate indicators into epidemic modeling and preparedness strategies.

systems biology↗

bioRxiv2025

Mitochondrial DNA damage in substantia nigra parscompacta astrocytes exacerbates dopaminergic neuron lossin a 6-hydroxydopamine mouse model of parkinsonism

Parkinsons disease (PD) is the fastest growing neurological disorder with no known cure. Our ability to develop disease-modifying treatments that slow down the loss of substantia nigra pars compacta (SNc) dopaminergic (DA) neurons is hindered by a dearth of knowledge on roles for non-neuronal elements such as astrocytes during PD pathogenesis. More specifically, the extent to which mitochondrial DNA (mtDNA) damage in SNc astrocytes contributes to SNc DA neuron loss during PD remains unknown. To address this knowledge gap, we utilized an adeno-associated virus (AAV) called Mito-PstI that expresses the restriction enzyme PstI as an approach to damage mtDNA in SNc astrocytes and assess the effect of astrocytic mtDNA damage on SNc DA neuron function and viability in mice. Mito-PstI-induced mtDNA damage in SNc astrocytes disrupted mitochondrial morphology, caused increased wrapping of SNc astrocytic processes around SNc DA neurons, and abnormally increased dopamine release by SNc DA neuron axonal terminals within the dorsolateral striatum (DLS). In addition, mice injected with Mito-PstI in the SNc showed increased spontaneous and apomorphine-induced rotations contralateral to the side with SNc Mito-PstI injections. In further experiments, we used a parkinsonian mouse model with low dose 6-hydroxydopamine (6-OHDA) injection into the DLS to show that Mito-PstI expression in SNc astrocytes caused a worsening of 6-OHDA-induced spontaneous contralateral rotational behavior, and exacerbated SNc DA neuron loss. These results suggest that mitochondria in SNc astrocytes are not only critical for the function of SNc DA neurons, but are also a new target for developing disease-modifying strategies against PD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/673287v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@b4a98aorg.highwire.dtl.DTLVardef@e6e2fcorg.highwire.dtl.DTLVardef@402b93org.highwire.dtl.DTLVardef@ecdfd2_HPS_FORMAT_FIGEXP M_FIG C_FIG Main PointsO_LIMito-PstI expression in mouse SNc astrocytes increases dopamine release C_LIO_LIMito-PstI expression in SNc astrocytes worsens contralateral rotational behavior in mice C_LIO_LIMito-PstI expression in SNc astrocytes increases DA neuron loss in 6-OHDA mice C_LI

neuroscience↗

bioRxiv2025

Gestational Chronic Intermittent Hypoxia Triggers Maternal Inflammation and Disrupts Placental Stress Responses

Gestational hypoxia is associated with placental cellular responses, including oxidative stress and inflammation. Circulating cell-free mitochondrial DNA (ccf-mtDNA) is a marker of cell stress, that can be transported within extracellular vehicles (EVs), eliciting proinflammatory responses. We hypothesized that systemic exposure to chronic intermittent hypoxia (CIH) during late pregnancy would increase maternal inflammation, alter circulating EV characteristics, and disrupt placental stress responses. Pregnant rats were exposed to CIH (n=8) or normoxia (n=9) during gestational days 15-20 (term 22-23 days). On GD20, ccf-mtDNA and EV-associated mtDNA (EV-mtDNA) were quantified with qRT-qPCR, while maternal circulating cytokines were quantified using a MILLIPLEX(R) cytokine array. Systemic oxidative stress was measured by plasma advanced oxidation protein products (AOPP). Placental stress responses were evaluated by examining the balance between proinflammatory and antioxidant gene expression and the activation of proteins involved in apoptotic and autophagic processes. CIH exposure increased placental weights (p=0.015) and reduced placental efficiency (p=0.0006) without affecting fetal biometrics (p>0.05). Absolute ccf-mtDNA and EV-mtDNA content were unchanged (p>0.05), but EV concentrations were reduced (p=0.011) in response to CIH, suggesting an increase in EV-mtDNA per EV. Maternal interleukin-18 (IL-18) concentrations increased in the CIH group (p=0.047). Placental mRNA expression of catalase (p=0.048) and sod2 (p=0.038) were upregulated, while autophagy-related proteins Beclin-1 (p=0.006) and p62 (p=0.023) were also increased in response to CIH, with no changes in LC3A/B expression (p>0.05). Gestational CIH disrupts maternal EV and inflammatory profiles, reduces placental efficiency, and modulates placental antioxidant and autophagic mechanisms, without impairing fetal growth in rats.

physiology↗

bioRxiv2025

A low protein diet drives short- and long-term improvements in metabolic health in a mouse model of sleeve gastrectomy

Despite the largely beneficial impact of bariatric surgery on obesity and metabolic disease, continued post-surgical obesity and weight recurrence is common and may be impacted by diet. While guidelines recommend a high-protein diet based on the theory that this will preserve lean mass, emerging evidence suggests that both humans and mice are metabolically healthier on low protein diets. We assessed the effect of varying dietary protein levels on post-surgical weight loss and weight regain in a mouse model of one type of bariatric surgery, sleeve gastrectomy. We found that a low protein diet optimally drives post-surgical weight loss, boosting energy expenditure and improving blood glucose regulation. Using a multi-omics approach, we identified clusters of differentially expressed genes and metabolites that correlated with these phenotypes and found that diet heavily influences the livers molecular response to sleeve gastrectomy. These results suggest that current post-surgical high protein guidelines may limit both the short-and long-term benefits of surgery, and a low protein diet may improve patient outcomes.

physiology↗

bioRxiv2025

Solid tumor CAR T cells engineered with fusion proteins targeting PDL1 for localized IL-12 delivery

CAR T cell efficacy in solid tumors is limited due in part to the immunosuppressive TME. To improve anti-tumor responses, we hypothesized that enabling CAR T cells to secrete bifunctional fusion proteins consisting of a cytokine modifier (e.g., TGF{beta}trap, IL15, or IL12) combined with an immune checkpoint inhibitor (e.g., PDL1) will provide tumor localized immunomodulation to improve CAR T cell functionality. To that end, we engineered CAR T cells to secrete TGF{beta}trap, IL15, or IL12 molecules fused to PDL1 scFv, and assessed in vitro functionality and in vivo safety and efficacy in prostate and ovarian cancer models. CAR T cells engineered with PDL1-IL12 were superior in safety and efficacy compared to CAR T cells alone and to those engineered with PDL1 fused with TGF{beta}trap or IL15. Further, PDL1-IL12 engineered CAR T cells improved T cell trafficking and tumor infiltration, localized IFN{gamma} production, TME modulation, and anti-tumor responses, with reduced systemic inflammation-associated toxicities. We believe our PDL1-IL12 engineering strategy presents an opportunity to improve CAR T cell clinical efficacy and safety across multiple solid tumor types.

bioengineering↗

bioRxiv2025

EGFR-Mediated Mechanotransduction in Aortic Valve Cells: A Key Pathway in Response to Wall Shear Stress

AimBlood flow-induced mechanical forces, particularly wall shear stress (WSS), play a fundamental role in aortic valve remodeling and maturation. Dysregulation of these processes contributes to age-related valve diseases, such as aortic stenosis and regurgitation. While epidermal growth factor receptor (EGFR) signaling has been implicated in valve development, its role in mechanotransduction remains unclear. This study aims to investigate how EGFR regulates WSS-induced signaling in valvular cells and explore its interaction with the mechanosensitive ion channel PIEZO1. Methods and ResultsTo investigate the role of EGFR in valvular cell mechanotransduction, we used conditional Egfrflox allele to selectively delete Egfr in valvular cells. Histological analysis revealed increased valve leaflet thickness and hyperproliferation of mesenchymal cells when Egfr was deleted both endothelial (Tie2-Cre lineage) and mesenchymal (Sm22-Cre lineage) cells. This was accompanied by a reduction in maturation-related genes (Egr1, Nos3, Tgf-{beta}) and extracellular matrix (ECM) components. We previously demonstrated that Egr1 expression is regulated by WSS in valvular endothelial cells, prompting further exploration of Egr1s role in valvular cells. In vitro, Egr1 overexpression and shRNA-mediated knockdown confirmed its role in regulating Nos3, Col1a1, and Tgf-{beta}, key mediators of valve remodeling. Using a pulsatile WSS-mimicking device, we found that WSS induces Erk1/2 phosphorylation and Egr1 expression in valvular cells, both of which were abolished by EGFR inhibition. However, direct EGFR activation via EGF failed to replicate WSS-induced Egr1 expression, suggesting the involvement of additional mechanosensitive pathways. Pharmacological studies further revealed that PIEZO1 inhibition impaired WSS-induced Egr1 expression, while PIEZO1 activation (via YODA) mimicked WSS effects on Erk1/2 phosphorylation and Egr1 expression. These findings suggest a functional interaction between EGFR and PIEZO1 in mechanotransduction, linking mechanical forces to key molecular pathways in valve remodeling. ConclusionOur findings establish EGFR as a critical mediator of WSS-induced mechanotransduction in valve remodeling, working in synergy with PIEZO1 to regulate flow-sensitive transcription factors such as Egr1. This study provides new insights into the molecular mechanisms governing valve maturation and highlights potential therapeutic targets for age-related valve pathologies linked to abnormal WSS responses. Translational PerspectiveOur study highlights the pivotal role of EGFR and the mechanosensitive ion channel PIEZO1 in aortic valve cell responses to wall shear stress (WSS), offering new insights into valve remodeling. The findings suggest that dysregulated EGFR signaling contributes to valve thickening and stenosis, key factors in age-related valvular heart disease. By identifying EGFR-PIEZO1 as a critical mechanotransduction pathway, our work provides a potential therapeutic target for early intervention in aortic valve disease. Modulating EGFR or PIEZO1 activity could help mitigate pathological valve remodeling, presenting novel strategies for treating or preventing degenerative valve disorders.

developmental biology↗

bioRxiv2025

Remodelling of supernumerary leaflet primordia leads to bicuspid aortic valve (BAV) caused by loss of primary cilia

AimsBicuspid aortic valve (BAV), where two valve leaflets are found instead of the usual three, affects 1-2% of the general population and is associated with significant morbidity and mortality. Despite its frequency, the majority of cases remain unexplained. This is, at least in part, because there are two types of valve leaflet primordia: endocardial cushions and intercalated valve swellings (ICVS). Moreover, multiple progenitors make distinct contribution to the formation of these primordia. Genomic studies in mouse and human have suggested a correlation between BAV and malfunctional primary cilia. However, the precise requirement for cilia during early embryonic valvulogenesis remains unknown. Methods and resultsHere, we disrupted primary cilia by deleting the ciliary gene Ift88 in the main progenitor cells forming the aortic valve using specific Cre drivers: Wnt1-Cre for neural crest cells, Isl1-Cre for second heart field cells (SHF); Tie2-Cre for endocardial-derived cells and Tnnt2-Cre for direct-differentiating SHF in the ICVS. Loss of Ift88, and thus primary cilia, from neural crest cells and endocardium did not impact aortic valve formation. However, primary cilia are essential in SHF cells for aortic valve leaflet formation, with over half of Ift88f/f;Isl1-Cre mutants presenting with BAV. As the valve leaflets are forming, 50% of the Ift88f/f;Isl1-Cre mutants have two small leaflets in the position of the usual posterior leaflet, meaning that at this stage the aortic valve is quadricuspid, which then remodels to BAV by E15.5. Mechanistic studies demonstrate premature differentiation of SHF cells as the ICVS form, leading to the formation of a broadened ICVS that forms two posterior leaflet precursors. This abnormality in the formation of the ICVS is associated with disruption of Notch-Jag1 signalling pathway, with Jag1f/f;Isl1-Cre mutants presenting with a similar phenotype. ConclusionsThese data show that primary cilia, via the Notch-Jag1 signalling pathway, regulate differentiation of SHF cells in the aortic valve primordia. Additionally, we identify a mechanistic link between the developmental basis of quadricuspid and bicuspid arterial valve leaflets. Translational PerspectiveSeveral genomic studies in human and mouse have suggested that disruption of cilia-related genes may be a significant cause of CHD. Although there is limited data from animal models to suggest a link between cilia and bicuspid aortic valve (BAV), the mechanisms underpinning BAV formation during early valvulogenesis have not been described. Here, we established a potential mechanism underpinning BAV formation, highlighting a role for primary cilia in a subset of valve interstitial cells (VIC) derived from second heart field progenitors. Loss of cilia altered VIC differentiation and valvulogenesis. This study confirms that disruption of cilial formation and/or function can lead to arterial valve defects and could pave the way to finding therapies for patient benefit.

developmental biology↗

bioRxiv2025

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

evolutionary biology↗

bioRxiv2024

Investigating Novel Streptomyces Bacteriophage Endolysins as Potential Antimicrobial Agents

BackgroundAs antibiotic resistance has become a major global threat; the World Health Organization (WHO) has urgently called for alternative strategies for control of bacterial infections. Endolysin, a phage-encoded protein, can degrade bacterial peptidoglycan (PG) and disrupt bacterial growth. According to the WHO, there are only three endolysin products currently in clinical phase development. In this study we explore novel endolysins from Streptomyces phages as only a few of them have been experimentally characterized. Using several bioinformatics tools, we identified nine different functional domain combinations from 250 Streptomyces phages putative endolysins. LazerLemon gp35 (CHAP; LL35lys), Nabi gp26 (amidase; Nb26lys), and Tribute gp42 (PGRP/amidase; Tb42lys) were selected for experimental studies. We hypothesized that (1) the proteins of interest will have the ability to degrade purified PG, and (2) the proteins will have potential antimicrobial activity against bacteria from families of importance in antibiotic resistance, such as ESKAPE safe relatives (Enterococcus raffinosus, Staphylococcus epidermidis, Klebsiella aerogenes, Acinetobacter baylyi, Pseudomonas putida, and Escherichia coli). ResultsLL35lys, Nb26lys, and Tb42lys exhibit PG-degrading activity on zymography and hydrolysis assay. The enzymes (100 {micro}g/mL) can reduce PG turbidity to 32-40%. The killing assay suggests that Tb42lys has a broader range (E. coli, P. putida, A. baylyi and K. aerogenes). While Nb26lys better attacks Gram-negative than Gram-positive bacteria, LL35lys can only reduce the growth of the Gram-positive ESKAPE strains but does so effectively with a low MIC90 of 2 {micro}g/mL. A higher concentration ([≥]300 {micro}g/mL) of Nb26lys is needed to inhibit P. putida and K. aerogenes. ConclusionFrom 250 putative endolysins, bioinformatic methods were used to select three putative endolysins for cloning and study: LL35lys, Nb26lys, and Tb42lys. All have shown PG-degrading activity, a critical function of endolysin. With a low MIC, LL35lys shows activity for the Gram-positive ESKAPE strains, while Nb26lys and Tb42lys are active against the Gram-negatives. Therefore, endolysins from Streptomyces phage have potential as possible antimicrobial agents against ESKAPE bacteria.

microbiology↗

bioRxiv2024

DCs targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors

Cross-presentation by type 1 cDCs (cDC1) is critical to induce and sustain antitumoral CD8 T cell responses to model antigens, in various tumor settings. However, the impact of cross-presenting cDC1 and the potential of DC-based therapies in tumors carrying varied levels of bona-fide neoantigens (neoAgs) remains unclear. Here we generated a non-small cell lung cancer model with distinct ranges of TMB and MHC-I neoepitopes to test immunogenicity and response to Flt3L+CD40 (DC-therapy). We found that cDC1 are required to broaden the pattern of CD8 responses to basal and acquired neoAgs and DC-therapy strongly inhibits the growth of TMBhigh tumors. In contrast, TMBlow tumors induce weaker responses that are not sufficient to block progression. scRNA transcriptional analysis, immune profiling and functional assays show that DC-therapy triggers the accumulation of lung cDC1 with increased immunostimulatory properties and CD8 T cells with enhanced cytotoxic functions and reduced exhaustion, most prominently in neoAgshigh tumors. We conclude that boosting cDC1 activity is critical to broaden the diversity of anti-tumoral CD8 T cell responses and to leverage neoAgs content for therapeutic advantage.

immunology↗