Biology subjects

Bonnet, S.

Publications and source records attributed to Bonnet, S..

At least 19 recordsLinked to original sources

bioRxiv2026

XPO1 controls VDR localization and activity in triple-negative breast cancer cells

The association of cytoplasmic localization of VDR in TNBC tumors and disease aggressivity prompted investigation of its regulation by XPO1. In TNBC cell lines, the XPO1 inhibitors selinexor and eltanexor increased nuclear VDR localization. Their effects were particularly strong when combined with vitamin D treatment. Similarly, XPO1 knockdown increased nuclear VDR levels, both alone and in combination with vitamin D. These results identify XPO1 as an important regulator of VDR subcellular distribution. XPO1 inhibition also enhanced vitamin D-dependent VDR transcriptional activity. Indeed, selinexor, eltanexor, and XPO1 silencing increased vitamin D-dependent CYP24A1 reporter activity and the expression of genes such as CYP24A1 or CDH1. RNA sequencing showed that XPO1 modulation markedly reshaped the vitamin D transcriptional response. The affected genes were mainly involved in metabolism, cell-cycle regulation, protein localization, and cellular organization. Functional analyses demonstrated that cytoplasmic VDR promoted TNBC cell proliferation. Conversely, nuclear VDR was required for the antiproliferative effects of vitamin D. Accordingly, XPO1 inhibition or depletion potentiated vitamin D-mediated growth suppression. This finding suggested functional cooperation between XPO1-dependent export and VDR activity. Finally, high VDR expression was associated with poor disease-free or overall survival only in tumors with high XPO1 expression. Overall, XPO1 negatively regulates VDR nuclear localization and vitamin D responsiveness in TNBC. Targeting XPO1 may therefore enhance the therapeutic potential of vitamin D-based strategies in TNBC.

cell biology↗

bioRxiv2026

Perceptual integration of multisensory haptic, visual, and auditory feedback for roughness discrimination in augmented reality

Understanding how our different senses interact to shape our perception is essential to design realistic and immersive virtual and augmented reality (VR/AR) experiences. The present study investigated how roughness perception can be modulated through haptic, visual, and auditory cues in AR using a vibrotactile wristband. Participants compared virtual textures varying in vibration frequency/amplitude, visual grain size, and friction sound. Results revealed strong linear relationships between stimulus parameters and perceived roughness, with haptic frequency and visual cues driving the highest discrimination performance. Adding non-informative sensory feedback reduced perceptual sensitivity, acting as noise. Individual differences emerged: participants who rated haptic as the easiest modality showed greater sensitivity to haptic variations, while visual-reliant participants performed better with visual cues. We conclude that roughness in AR can be systematically manipulated, but is vulnerable to perceptual interference from irrelevant inputs, where our work provides actionable insights for implementing optimized and adaptive AR/VR interfaces.

neuroscience↗

bioRxiv2026

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

bioinformatics↗

bioRxiv2026

Pulmonary Arterial Hypertension Induces a Metabolic and Inflammatory Hepatopathy

Right ventricular failure (RVF) is a robust predictor of mortality in pulmonary arterial hypertension (PAH); however, the mechanisms linking RVF to end-organ dysfunction remain unclear. Hepatic impairments portend poor outcomes in PAH, but the cell-specific effects of PAH on the human liver are unknown. Here, we performed single nucleus RNA sequencing on autopsy-derived liver tissue from five PAH patients and four non-PAH controls and compared these findings to non-alcoholic steatohepatitis (NASH) and Fontan-associated liver disease (FALD). PAH hepatocytes were characterized by a pro-proliferative, Warburg-like metabolic phenotype. PAH endothelial cells (ECs) also adopted a Warburg-like profile. Although EC PI3K-Akt activation was present in PAH and FALD ECs, only PAH ECs demonstrated impaired adhesion/barrier signaling. In PAH hepatic stellate cells (HSCs), PI3K-Akt signaling was enriched, while NASH and FALD HSCs co-activated PI3K-Akt and TGF-{beta}. Activated HSC abundances were increased in PAH livers and associated with heightened central vein fibrosis. PAH and NASH macrophages showed elevated complement signaling but reduced JAK-STAT activity. PAH livers exhibited dysregulated vasoactive gene expression, increased interleukin-6 expression in HSCs, and suppressed hepatocyte ketone metabolism. Correlational analysis demonstrated that HSC HIF-1 activation was associated with PAH severity. In total, these findings define the metabolic and inflammatory hepatopathy of PAH.

biochemistry↗

bioRxiv2025

Exploring the Role of Hypusine Signaling in Vascular Smooth Muscle Cells for Mitigating Restenosis in Coronary Artery Disease.

BackgroundPost-surgical restenosis in patients with coronary artery disease (CAD) is a pathological vascular remodeling process characterized by neointimal hyperplasia, mainly driven by vascular smooth muscle cells (VSMCs) phenotypic switching toward synthetic and proliferative state. This study identifies novel signaling pathway promoting pro-proliferative phenotype of VSMC and contributing to the neointimal hyperplasia development. MethodsThe expression of hypusine signaling components was evaluated in human primary culture of coronary artery smooth muscle cells (CoASMCs) isolated from controls and patients with CAD, using comparative proteomic analysis and western blotting, as well as in three preclinical animal models of restenosis; rat carotid injury, mice carotid ligation and canine coronary artery bypass graft. CAD-CoASMCs proliferation was assessed by western blot and immunofluorescence with pharmacological (GC7) and molecular (shRNA) inhibitors of deoxyhypusine synthase (DHPS). The contribution of hypusine signaling to neointimal hyperplasia was investigated using both pharmacological and smooth muscle cell-specific knockout mice approaches. Additionally, human saphenous vein and human coronary artery tissue cultures were employed to explore the translational potential of targeting hypusine signaling to prevent neointimal hyperplasia. ResultsAll components of the hypusine pathway (eukaryote translational initiation factor 5A (eIF5A), deoxyhypusine hydroxylase (DOHH) and DHPS) were significantly overexpressed in CAD-CoASMCs and in preclinical animal models of restenosis. Pharmacological and molecular inhibition of DHPS reduced eIF5A hypusination, VSMC proliferation and expression of extracellular matrix proteins. Proteomic and KEGG analyses demonstrated disruption of cell cycle and DNA replication pathways, including a downregulation of threonine tyrosine kinase (TTK). Our findings suggest that TTK acts as a downstream effector of hypusine signaling, partly mediating to the proliferative effects observed in CAD-CoASMCs. In vivo, pharmacological and genetic inhibition of DHPS significantly reduced neointimal hyperplasia without adverse effects. Finally, ex vivo human tissue culture confirmed that GC7 mitigates growth factor-induced vascular remodeling. ConclusionsHypusine signaling is a critical regulator of VSMC proliferation for neointimal hyperplasia. Inhibiting DHPS reduces vascular remodeling, making it a promising target for preventing restenosis after coronary interventions. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIHypusine signaling is markedly upregulated in coronary artery smooth muscle cells (CoASMCs) from patients with coronary artery disease (CAD) and in multiple preclinical models of restenosis. C_LIO_LIProteomic profiling identifies DHPS, the rate-limiting enzyme for eIF5A hypusination, as a key driver of vascular smooth muscle cell (VSMC) pro-proliferative phenotype and extracellular matrix production. C_LIO_LIPharmacological (GC7) and genetic inhibition of DHPS effectively suppress eIF5A hypusination, attenuate the synthetic and proliferative CAD-CoASMCs phenotype, and significantly reduce neointimal hyperplasia in rodent models of vascular injury. C_LIO_LIEx vivo human tissue demonstrates that DHPS inhibition prevents neointimal hyperplasia, providing strong translational evidence. C_LI What Are the Clinical Implications?O_LIThese findings establish hypusine signaling as a previously unrecognized regulator of pathological VSMC activation in CAD and restenosis. C_LIO_LIDHPS inhibition emerges as a promising therapeutic strategy to prevent neointimal hyperplasia following coronary interventions such as angioplasty, stenting, or bypass grafting. C_LIO_LICollectively, our data support the clinical development of selective DHPS inhibitors as a novel class of therapeutics to improve long-term outcomes after coronary revascularization and potentially other occlusive vascular diseases. C_LI

pathology↗

bioRxiv2025

17β-Estradiol Promotes Right Ventricle Angiogenesis via Estrogen Receptor α and Apelin Signaling

Right ventricular (RV) failure is the major cause of mortality in pulmonary hypertension (PH). Adaptive angiogenesis and RV endothelial cell (RVEC) function are major modifiers of RV adaptation in PH, but the underlying mechanisms and their regulators remain incompletely understood. RV adaptation in PH is sexually dimorphic, and 17{beta}-estradiol (E2) exerts protective effects on RV cardiomyocytes. Whether E2 modifies angiogenesis and RVEC function in RV failure remains unknown. We hypothesized that E2 and estrogen receptor (ER) promote RV angiogenesis and RVEC homeostasis in PH and aimed to identify underlying mechanisms. We assessed E2s angiogenic effects using cultured human cardiac microvascular endothelial cells (hCMVECs), RVECs from PH patients with RV failure, and RVECs from sugen/hypoxia (SuHx) and monocrotaline (MCT) rat models. In vivo, we evaluated RV capillary density in PH rats treated with E2 or ER-selective agonist. Apelin signaling was evaluated via apelin receptor blockade. E2 enhanced angiogenesis in male hCMVECs and RV capillary density in female SuHx-PH rats. E2 reversed angiogenic alterations in RVECs from SuHx-PH rats via apelin receptor signaling. In RVECs from PH patients with RV failure, E2 stimulated vascular network formation. In rat and human PH-RVECs, ER was necessary and sufficient to mediate E2-induced angiogenesis. Activation of ER with ER-specific agonist restored RV capillary density in vivo. ER-mediated angiogenesis required apelin signaling. These data indicate that E2 promotes RV angiogenesis via ER and apelin signaling and identify a novel ER-apelin axis in RVECs as a potential therapeutic target to restore RV vascular integrity in PH.

cell biology↗

bioRxiv2025

Physical determinants of perceived vibration intensity: Insights from haptic feedback given at the wrist

Understanding how mechanical vibrations applied to the skin translate into touch sensations is key to advancing tactile interfaces, from non-invasive neuroprosthetics to effective haptic tools. We investigate how modulating vibration waveform, frequency, and amplitude of a wrist-worn vibrotactile device influence perceived touch intensity, while simultaneously measuring accelerations at the actuator and skin surface. Thirty participants provided free-magnitude estimates of perceived intensity, showing that perceived intensity is significantly influenced by all parameters, while being strongly correlated with actuator and skin accelerations. Modulating the waveform shape showed that square waves are consistently rated as more intense. Vibration frequency exerted a non-linear influence, with perceived intensity peaking ~150 Hz and secondary acceleration and perceptual peaks were found at low frequencies for square and sawtooth waveforms. Thus, the skin faithfully preserves the mechanical signature of vibrations, which are clearly differentiated perceptually. These findings demonstrate that precise tactile characterization, both physically and perceptually, is essential, where device vibrations delivered to the skin determine what is perceived to a very high degree. As vibrations are relatively easy to control and apply, this opens up opportunities to convey a multitude of sensations, from brief taps to pressure, as well as more complex percepts like roughness and texture.

neuroscience↗

bioRxiv2025

Impaired Lung BCAA Metabolism Promotes Ferroptosis and Resultant Pulmonary Arterial Hypertension-Associated Hepatopathy

BackgroundDysregulated branched chain amino acid (BCAA) homeostasis occurs in pulmonary arterial hypertension (PAH) as BCAA metabolites accumulate and cause metabolic alterations in pulmonary artery smooth muscle cells (PASMC). In other cells, altered BCAA metabolism promotes ferroptosis, a PAH-inducing metabolic pathway. However, the interplay between BCAAs, lung ferroptosis, and PAH is unexplored, as is the impact of PAH severity on liver molecular regulation, a key unknown as recent clinical data highlight the importance of the lung-right heart-liver axis in PAH outcomes. MethodsHuman metabolomic and transcriptomic studies examined BCAA metabolism and ferroptosis pathways. The relationship between BCAAs and ferroptotic-phenotypes in PASMCs was evaluated. Multi-omics and physiological analyses evaluated how modulation of BCAA catabolism impacted preclinical PAH multi-organ physiology. Confocal microscopy and proteomic analyses assessed hepatic alterations in human PAH. ResultsMetabolomic analyses identified alterations in BCAA metabolites across multiple physiological gradients in patients with pulmonary vascular disease. RNA sequencing demonstrated deficits in the BCAA catabolic and ferroptosis pathways in PAH lungs and smooth muscle cells. In vitro, excess BCAAs induced mitochondrial fragmentation, reactive oxygen species generation, and lipid peroxidation in PASMC. Moreover, BCAAs promoted PASMC death, which ferrostatin-1, a ferroptosis antagonist, rescued. BT2, a small-molecule inducer of BCAA catabolism, reduced PAH severity, improved RV function, and enhanced maximal exercise capacity in monocrotaline rats. BT2 blunted pro-ferroptotic changes in lung metabolites and proteins, and combatted peri-vascular complement deposition. In the liver, BT2 blocked mechanical shear stress phenotypes including hepatocyte nuclear expansion and restructured mitochondrial protein regulation and the metabolomic signature. Additionally, a low BCAA diet modestly combatted preclinical PAH severity. Finally, human PAH livers exhibited increased hepatocyte nuclear size and derangements in liver metabolic regulation. ConclusionsImpaired BCAA metabolism promotes PAH via ferroptosis. PAH severity is associated with hepatic pathological shear stress phenotypes and metabolic alterations, which are combatted by a BCAA-targeted therapy. Graphical Abstract/Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/672819v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1649980org.highwire.dtl.DTLVardef@199c40aorg.highwire.dtl.DTLVardef@1586fdorg.highwire.dtl.DTLVardef@15166c1_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

A critical contribution of cardiac myofibroblasts in right ventricular failure and the role of UCP2 SNPs in the predisposition to RV decompensation in pulmonary arterial hypertension

The mechanism of transition from compensated (cRV) to decompensated right ventricle (dRV) in pulmonary arterial hypertension (PAH) is unknown. We explored the role of RV cardiac myofibroblasts (cMFB) on this transition utilizing a rat model and 3 cohorts of 81 patients which included clinical data, RV tissues and blood. We hypothesized that the loss of UCP2, critical for mitochondrial calcium (mCa++) regulation and cardiac fibroblasts (cFB) differentiation, is associated with dRV in rats and humans; and that a loss-of-function UCP2 SNP (rs659366) may predict dRV in human PAH. We separated rat cRV from dRV based on catheterization and echocardiographic criteria and found a significant increase in cMFB in dRV. In isolated hearts, RV contractility was lower in dRV but not in isolated cardiomyocyte (CM), pointing to a non-CM cause. Mitochondrial respiration was lower in dRV cMFB than in control and cRV cFB. mCa++ was progressively decreased from normal to cRV to dRV c(M)FB, and the same was true for c(M)FB (but not CM) UCP2 levels. Human PAH, but not secondary pulmonary hypertension, dRVs had more cMFB and less UCP2 than control and cRVs. Decreased UCP2 (protein and mRNA) levels and the presence of heterozygous/homozygous UCP2 SNP were associated with worse RV performance (TAPSE, cardiac index), even among patients with similar mean pulmonary arterial pressure. Our data point to a change of cell identity (cFB to cMFB) in the RV as a driver of RV decompensation. UCP2 SNPs are promising biomarkers for early cRV transition to dRV in PAH.

molecular biology↗

bioRxiv2024

Pharmacological Inhibition of Epac1 Protects against Pulmonary Fibrosis by Blocking FoxO3a Neddylation

BackgroundIdiopathic Pulmonary fibrosis (IPF) is characterized by progressive scarring and fibrosis within the lungs. There is currently no cure for IPF; therefore, there is an urgent need to identify novel therapeutic targets that can prevent the progression of IPF. Compelling evidence indicates that the second messenger, cyclic adenosine monophosphate (cAMP), inhibits lung fibroblast proliferation and differentiation through the classical PKA pathway. However, the contribution of the exchange protein directly activated by cAMP 1 (Epac1) to IPF pathophysiological processes is yet to be investigated. ObjectiveTo determine the role of the cAMP-binding protein Epac1 in the progression of IPF. MethodsWe used lung samples from IPF patients or healthy controls, mouse lung samples, or lung fibroblast isolated from a preclinical mouse model of PF induced by bleomycin intratracheal injection. The effect of bleomycin (BLM) treatment was determined in Epac1 knock-out mice or wild-type littermates. Epac1 expression was modulated in vitro by using lentiviral vectors or adenoviruses. The therapeutic potential of the Epac1-selective pharmacological inhibitor, AM-001, was tested in vivo and in vitro, using a bleomycin mouse model of PF and an ex vivo precision-cut lung slices (PCLs) model of human lung fibrosis. ResultsEpac1 expression was increased in the lung tissue of IPF patients, in IPF-diseased fibroblasts and in BLM-challenged mice. Furthermore, Epac1 genetic or pharmacological inhibition with AM-001 decreased normal and IPF fibroblast proliferation and the expression of profibrotic markers, SMA, TGF-{beta}/SMAD2/3, and interleukin-6 (IL-6)/STAT3 signaling pathways. Consistently, blocking Epac1 protected against BLM-induced lung injury and fibrosis, suggesting a therapeutic effect of Epac1 inhibition on PF pathogenesis and progression. Global gene expression profiling revealed a decrease in the key components of the profibrotic gene signature and neddylation pathway in Epac1-deficient lung fibroblasts and IPF human-derived PLCs. Mechanistically, the protective effect of Epac1 inhibition against PF development involves the inhibition of FoxO3a neddylation and its subsequent degradation by NEDD8, and in part, by limiting the proliferative capacity of lung-infiltrating monocytes. ConclusionsWe demonstrated that Epac1 is an important regulator of the pathological state of fibroblasts in PF and that small molecules targeting Epac1 can serve as novel therapeutic drugs against PF.

physiology↗

bioRxiv2024

Exploring Integrin α5β1 as a Potential Therapeutic Target for Pulmonary Arterial Hypertension: Insights from Comprehensive Multicenter Preclinical Studies

Pulmonary arterial hypertension (PAH) is characterized by obliterative vascular remodeling of the small pulmonary arteries (PA) and progressive increase in pulmonary vascular resistance (PVR) leading to right ventricular (RV) failure. Although several drugs are approved for the treatment of PAH, mortality remains high. Accumulating evidence supports a pathological function of integrins in vessel remodeling, which are gaining renewed interest as drug targets. However, their role in PAH remains largely unexplored. We found that the arginine-glycine-aspartate (RGD)-binding integrin 5{beta}1 is upregulated in PA endothelial cells (PAEC) and PA smooth muscle cells (PASMC) from PAH patients and remodeled PAs from animal models. Blockade of the integrin 5{beta}1 or depletion of the 5 subunit resulted in mitotic defects and inhibition of the pro-proliferative and apoptosis-resistant phenotype of PAH cells. Using a novel small molecule integrin inhibitor and neutralizing antibodies, we demonstrated that 5{beta}1 integrin blockade attenuates pulmonary vascular remodeling and improves hemodynamics and RV function in multiple preclinical models. Our results provide converging evidence to consider 5{beta}1 integrin inhibition as a promising therapy for pulmonary hypertension. One sentence summaryThe 5{beta}1 integrin plays a crucial role in pulmonary vascular remodeling.

pathology↗

bioRxiv2024

RV-specific Targeting of Snai1 Rescues Pulmonary Hypertension-induced Right Ventricular Failure by Inhibiting EndMT and Fibrosis via LOXL2 Mediated Mechanism

BackgroundPulmonary hypertension (PH)-induced right ventricular (RV) failure (PH-RVF) is a significant prognostic determinant of mortality and is characterized by RV hypertrophy, endothelial-to-mesenchymal transition (EndMT), fibroblast-to-myofibroblast transition (FMT), fibrosis, and extracellular matrix (ECM)-remodeling. Despite the importance of RV function in PH, the mechanistic details of PH-RVF, especially the regulatory control of RV EndMT, FMT, and fibrosis, remain unclear. The action of transcription factor Snai1 is shown to be mediated through LOXL2 recruitment, and their co-translocation to the nucleus, during EndMT progression. We hypothesize that RV EndMT and fibrosis in PH-RVF are governed by the TGF{beta}1-Snai1-LOXL2 axis. Furthermore, targeting Snai1 could serve as a novel therapeutic strategy for PH-RVF. MethodsAdult male Sprague Dawley rats (250-300g) received either a single subcutaneous injection of Monocrotaline (MCT, 60mg/kg, n=9; followed for 30-days) or Sugen (SU5416 20mg/kg, n=9; 10% O2 hypoxia for 3-weeks followed by normoxia for 2-weeks) or PBS (CTRL, n=9). We performed secondary bioinformatics analysis on the RV bulk RNA-Seq data from MCT, SuHx, and PAB rats and human PH-PVF. We validated EndMT and FMT and their association with Snai1 and LOXL2 in the RVs of MCT and SuHx rat models and human PH-RVF using immunofluorescence, qPCR, and Western blots. For in vivo Snai1 knockdown (Snai1-KD), MCT-rats either received Snai1-siRNA (n=7; 5nM/injection every 3-4 days; 4-injections) or scramble (SCRM-KD; n=7) through tail vein from day 14-30 after MCT. Echocardiography and catheterization were performed terminally. Bulk RNASeq and differential expression analysis were performed on Snai1- and SCRM-KD rat RVs. In vitro Snai1-KD was performed on human coronary artery endothelial cells (HCAECs) and human cardiac fibroblasts (HCFs) under hypoxia+TGF{beta}1 for 72-hrs. ResultsPH-RVF had increased RVSP and Fulton index and decreased RV fractional area change (RVFAC %). RV RNASeq demonstrated EndMT as the common top-upregulated pathway between rat (MCT, SuHx, and PAB) and human PH-RVF. Immunofluorescence using EndMT- and FMT-specific markers demonstrated increased EndMT and FMT in RV of MCT and SuHx rats and PH-RVF patients. Further, RV expression of TGF{beta}1, Snai1, and LOXL2 was increased in MCT and SuHx. Nuclear co-localization and increased immunoreactivity, transcript, and protein levels of Snai1 and LOXL2 were observed in MCT and SuHx rats and human RVs. MCT rats treated with Snai1-siRNA demonstrated decreased Snai1 expression, RVSP, Fulton index, and increased RVFAC. Snai1-KD resulted in decreased RV-EndMT, FMT, and fibrosis via a LOXL2-dependent manner. Further, Snai1-KD inhibited hypoxia+TGF{beta}1-induced EndMT in HCAECs and FMT in HCFs in vitro by decreasing perinuclear/nuclear Snai1+LOXL2 expression and co-localization. ConclusionsRV-specific targeting of Snai1 rescues PH-RVF by inhibiting EndMT and Fibrosis via a LOXL2-mediated mechanism.

physiology↗

bioRxiv2024

The SUMOylation inhibitor TAK-981 (Subasumstat) triggers IFN-I-dependent activation of Natural Killer cells against Acute Myeloid Leukemias.

Natural Killer (NK) cells play a pivotal role in mounting an anti-cancer immune response. Patients with diminished NK cells number and activity face less favorable prognosis. Promising therapeutic strategies include the adoptive transfer of NK cells or the reactivation of patients own NK cells. TAK-981, a first-in-class inhibitor of SUMOylation undergoing phase I/II clinical trials for cancer, is emerging as an immunomodulatory drug. Here, we demonstrate that TAK-981 activates NK cells from healthy donors and patients with Acute Myeloid Leukemia (AML), a cancer with very poor prognosis. TAK-981 heightens their degranulation capacity, secretion of inflammatory cytokines (IFN-{gamma}, TNF-, FasL), and cytotoxicity against AML cells. In vivo, TAK-981 also enhances the anti-leukemic activity of ex-vivo expanded human NK cells. At the molecular level, TAK-981 first induces IFNB1 gene in NK cells, leading to the secretion of type I Interferon (IFN-I), which binds to the Interferon receptor IFNAR. This induces Interferon-Stimulated Genes (ISG) and activates NK cells in vitro and in vivo. Finally, TAK-981 stimulates IFN-I secretion by monocytes, which contributes to the activation of NK cells in trans. Altogether, targeting SUMOylation could be a promising strategy to reactivate AML patients NK cells and enhance the efficiency of NK cells-based therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/580882v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1a5fd47org.highwire.dtl.DTLVardef@974336org.highwire.dtl.DTLVardef@bdb99dorg.highwire.dtl.DTLVardef@1e4fe15_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Endothelial fatty acid-binding proteins contribute to the pathogenesis of pulmonary hypertension

Pulmonary arterial hypertension (PAH) is a devastating disease characterized by obliterative vascular remodeling and persistent increase of vascular resistance, leading to right heart failure and premature death. Understanding the cellular and molecular mechanisms will help develop novel therapeutic approaches for PAH patients. Single-cell RNA sequencing (scRNAseq) analysis found that both FABP4 and FABP5 were highly induced in endothelial cells (ECs) of Egln1Tie2Cre (CKO) mice, which was also observed in pulmonary arterial ECs (PAECs) from idiopathic PAH (IPAH) patients, and in whole lungs of pulmonary hypertension (PH) rats. Plasma levels of FABP4/5 were upregulated in IPAH patients and directly correlated with severity of hemodynamics and biochemical parameters using plasma proteome analysis. Genetic deletion of both Fabp4 and 5 in CKO mice (Egln1Tie2Cre/Fabp4-5-/-, TKO) caused a reduction of right ventricular systolic pressure (RVSP) and RV hypertrophy, attenuated pulmonary vascular remodeling and prevented the right heart failure assessed by echocardiography, hemodynamic and histological analysis. Employing bulk RNA-seq and scRNA-seq, and spatial transcriptomic analysis, we showed that Fabp4/5 deletion also inhibited EC glycolysis and distal arterial programming, reduced ROS and HIF-2 expression in PH lungs. Thus, PH causes aberrant expression of FABP4/5 in pulmonary ECs which leads to enhanced ECs glycolysis and distal arterial programming, contributing to the accumulation of arterial ECs and vascular remodeling and exacerbating the disease.

molecular biology↗

bioRxiv2023

Emergence of disease specific endothelial and stromal cell populations involved in arterial remodeling during development of pulmonary arterial hypertension

AbstractPulmonary arterial hypertension (PAH) is a severe and lethal pulmonary vascular disease characterized by arteriolar pruning and occlusive vascular remodeling leading to increased pulmonary vascular resistance and eventually right heart failure. While endothelial cell (EC) injury and apoptosis are known triggers for this disease, the mechanisms by which they lead to complex arterial remodeling remain obscure. We employed multiplexed single-cell RNA sequencing (scRNA-seq) at multiple timepoints during the onset and progression of disease in a model of severe PAH to identify mechanisms involved in the development of occlusive arterial lesions. There was significant loss of arterial volume as early as 1-week by microCT, preceding any evidence of occlusive arteriopathy, consistent with early arteriolar dropout. Maximal arterial pruning was seen by 5 to 8 weeks, with signs of progressive occlusive remodeling. Analysis of the scRNA-seq data resolved 44 lung cell populations, with widespread early transcriptomic changes at 1 week affecting endothelial, stromal and immune cell populations. Notably, this included emergence of a relatively dedifferentiated (dD) EC population that was enriched for Cd74 expression compared to general capillary (gCap) ECs which were primed to undergo endothelial-mesenchymal transition, as evidenced by RNA velocity analysis. However, at late timepoints (5 and 8 weeks), activated arterial ECs (aAECs) were the only cell population exhibiting persistent differential gene expression. This was characterized by a growth regulated state, including high expression of Tm4sf1, a gene implicated in cancer cell growth, which was also expressed by a smooth muscle (SM)-like pericyte cluster. Both these populations were localized to regions of arterial remodeling in the rat model and PAH patients, with aAECs contributing to intimal occlusive lesions and SM-like pericytes forming bands of medial muscularization. Together these findings implicate disease-specific vascular cells in PAH progression and suggest that TM4SF1 may be a novel therapeutic target for arterial remodeling.

molecular biology↗

bioRxiv2023

RIP140 regulates HES1 oscillatory expression and mitogenic activity in colon cancer cells

BackgroundThe transcription factor RIP140 (Receptor Interacting Protein of 140 kDa) regulates intestinal homeostasis and tumorigenesis through the Wnt signaling. In this study, we have investigated its effect on the Notch/HES1 signaling pathway. MethodsThe impact on HES1 expression and activity was evaluated in colorectal cancer (CRC) cell lines and in transgenic mice, invalidated or not for the Rip140 gene in the intestinal epithelium. A tumor microarray and transcriptomic data sets were used to investigate RIP140 and HES1 expression in relation with patient survival. Statistical comparisons were performed with Mann-Whitney or Kruskal-Wallis or Chi2 tests. ResultsIn CRC cells, RIP140 positively regulated HES1 gene expression at the transcriptional level via an RBPJ/NICD-mediated mechanism. In support of these in vitro data, RIP140 and HES1 expression significantly correlated in mouse intestine and in a cohort of CRC samples, analyzed by immunohistochemistry, thus supporting the positive regulation of HES1 gene expression by RIP140. Interestingly, when the Notch pathway is fully activated, RIP140 exerted a strong inhibition of HES1 gene transcription controlled by the level of HES1 itself. Moreover, RIP140 directly interacts with HES1 and reversed its mitogenic activity in human CRC cells. In line with this observation, HES1 levels were associated with a better patient survival only when tumors expressed high levels of RIP140. ConclusionsOur data identify RIP140 as a key regulator of the Notch/HES1 signaling pathway with a dual effect on HES1 gene expression at the transcriptional level and a strong impact on colon cancer cell proliferation.

cancer biology↗

bioRxiv2021

Massive export of diazotrophs across the tropical south Pacific Ocean

Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, regulating marine productivity. Yet, their contribution to organic matter export has not been quantified, making an assessment of their impact on the biological carbon pump impossible. Here, we demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are massively exported down to 1000 m-depth in the western subtropical South Pacific Ocean (WTSP), accounting for up to 52-100% of the total particulate nitrogen export fluxes. We further demonstrate that small size unicellular diazotrophs (UCYN, 1-8 {micro}m) are exported more efficiently than filamentous diazotrophs (>100-1000 {micro}m) under the form of large (>50 {micro}m) aggregates linked by an extracellular organic matrix. Beyond the WTSP, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, showing that diazotrophs are systematically detected in mesopelagic waters when present at the surface. We thus conclude that diazotrophs are key players in carbon sequestration in the ocean and need to be considered in future studies to improve the accuracy of current regional and global estimates of export.

microbiology↗

bioRxiv2020

Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean

Diazotrophs are important contributors to reactive nitrogen availability in the ocean. Oceanographic cruise data accumulated along decades has revealed a heterogeneous distribution of diazotroph species at regional to global scales. However, the role of dynamic fine scale structures in distributing diazotrophs is not well understood. This is due to typical insufficient spatiotemporal resolution sampling and the lack of detailed physical studies in parallel. Here we show the distribution of five groups of diazotrophs in the South Pacific at an unprecedented resolution of 7-16 km. We find a patchy distribution of diazotrophs, with each group being differently affected by parameters describing fine scale structures. The observed variability could not have been revealed with a lower resolution sampling, highlighting the need to consider fine scale physics to resolve the distribution of diazotrophs in the ocean.

microbiology↗