Biology subjects

Zimmer, S.

Publications and source records attributed to Zimmer, S..

13 recordsLinked to original sources

bioRxiv2026

Mechanical stress-induced release of mitochondrial double-stranded RNA activates RIG-I to drive osteogenic differentiation in aortic disease

Background: Gain-of-function mutations in RIG-I and MDA5 (RIG-I-like receptors, RLR) cause Singleton-Merten syndrome, an interferonopathy with early aortic calcification. Here we set out to study a possible involvement of RIG-I-like receptor signaling in the formation of aortic valve stenosis in general. Methods and results: We investigated whether mechanical stress-induced RLR activation promotes osteogenic differentiation and calcification of primary human aortic cells, whether such RLR activation drives the development of aortic valve stenosis in vivo, and whether inhibition of downstream JAK/STAT activation ameliorates aortic valve stenosis. We found that activation of primary human aortic interstitial cells by exogenous RIG-I- and MDA5 agonists induced a type I interferon response and an osteogenic program including increased expression of BMP-2 and BSP2, and promoted calcification. These effects were RIG-I/MDA5 or MAVS-dependent, as assessed by CRISPR/Cas9 knockouts. The stress-granule protein G3BP1 and the Wnt receptor FZD5 were induced downstream of RLR activation and were required for osteogenic gene expression and calcification. To assess a potential endogenous source of RIG-I activation, mechanical stretch mimicking valvular tissue stress was applied in cell cuture, which induced a significant RIG-I-dependent interferon response. Sequencing of highly purified preparations of double-stranded RNA from stretched cells demonstrated a predominant mitochondrial origin of double-stranded RNA, and depleting mitochondrial RNA abolished the stretch-dependent response. The JAK/STAT inhibitor ruxolitinib suppressed the RIG-I-induced response including the expression of osteogenic factors in vitro. In a murine wire-injury model of aortic stenosis, MAVS deficiency attenuated valvular morphological changes and improved hemodynamic parameters. Ruxolitinib attenuated hemodynamic progression, prevented aortic stenosis development, and improved survival. Conclusions: Altogether, our results demonstrate that the mechanical-stress-induced release of mitochondrial double-stranded RNA activates RIG-I signaling in aortic interstitial cells, thereby driving osteogenic differentiation and calcification via a MAVS- and G3BP1-dependent pathway. JAK/STAT inhibition with ruxolitinib mitigates this process in a mouse model of aortic valve stenosis, identifying a candidate therapeutic strategy.

cell biology↗

bioRxiv2026

Activation of perivascular thermogenic fat improves aortic stenosis

Aim: Aortic stenosis (AS) is a common condition with exponential increases in incidence in aging populations. Perivascular adipose tissue (PVAT) forms the outer layer of the aortic wall and has - especially in the thoracic area - characteristics of thermogenic adipose tissue, which dissipates energy and releases endocrine factors. Here, we set out to investigate the role of thermogenic PVAT in AS. Methods and results: We studied the role of (PVAT) in the development of AS in a murine model of AS. To specifically delineate the role of PVAT activity in AS, we used a pharmacological {beta}3-adrenergic agonist as well as cold exposure in combination with a genetic mouse model with deficient PVAT development. To investigate the role of thermogenic adipose tissue in human AS, we used 18F-FDG PET-CT imaging. We found that pharmacological activation of thermogenic adipose tissue resulted in an improvement of AS, but not in mice genetically deficient in PVAT. Similarly, PVAT was found to be protective against AS during physiological stimulation of PVAT using cold exposure. Mechanistically, PVAT activation resulted in enhanced aortic distensibility and cellular remodeling of the aortic wall, possibly via release of polyunsaturated fatty acids and oxylipins from perivascular adipocytes. Finally, analysis of thermogenic fat activity in humans revealed that mediastinal thermogenic fat activity correlated negatively with diagnostic criteria of AS severity, suggesting an important role for PVAT activity in human AS. Conclusion: Our data indicate that PVAT activation reduces aortic stenosis and supports aortic remodeling to improve ascending aorta hemodynamics. PVAT activation might be a novel therapeutic target to ameliorate AS progression. Translational perspective: Currently, there are no effective strategies for treating AS other than valve replacement. Since the molecular mechanisms underlying the disease progression remain unclear, there are no pharmacological agents approved for either treatment or prevention of this disease. Furthermore, AS development cannot currently be predicted and is often only diagnosed when patients develop symptoms, which may be 10-20 years after disease onset. Therefore, identifying novel mechanisms that improve aortic valve function and prevent AS is of high medical need. This study identifies activation of PVAT-dependent aortic remodeling as a potential new therapeutic approach to improve or prevent AS.

physiology↗

bioRxiv2026

Targeting soluble immunoglobulins ameliorates idiopathic multicentric Castleman disease in a mouse model

Idiopathic multicentric Castleman disease (iMCD) is a rare lymphoproliferative disorder that affects lymph nodes at multiple sites and can progress to life-threatening organ dysfunction. While curative therapies remain unavailable, largely due to a critical gap in understanding the diseases underlying etiology, the cytokine interleukin-6 (IL-6) is recognized as a major pathogenic driver, particularly in iMCD patients with plasmacytic lymphadenopathy. Here, we demonstrate the presence of Foxp3-expressing cells alongside plasma cells within germinal centers of lymph nodes from such iMCD patients. Based on this observation, we directed IL-6 overexpression specifically to Foxp3+ Treg cells and established a novel preclinical mouse model of iMCD. This targeted approach successfully recapitulated the key characteristics of iMCD in mice, including multifocal lymphadenopathy, splenomegaly, anemia, thrombocytopenia, marked plasmacytosis, and mortality in young adults. Advanced disease was characterized by renal pathology, including proteinuria and elevated creatinine levels. In this model, IL-6 directly promoted plasmacytosis, resulting in profound IgG1 hyperimmunoglobulinemia. Genetic ablation of soluble immunoglobulin production ameliorated iMCD symptoms, prevented renal dysfunction, and significantly extended survival. Our findings identify IL-6-driven IgG1 plasmacytosis as a critical pathogenic factor in iMCD, shedding light on the mechanisms underlying its development. Key pointsO_LITransgenic IL-6 expression in Foxp3+ cells models iMCD in mice and drives lethal IgG1 plasmacytosis C_LIO_LILoss of soluble immunoglobulins prevented renal impairment and prolonged survival in iMCD-like mice C_LI

immunology↗

bioRxiv2026

Vitamin K2 Limits Ferroptosis-Associated Lipid Peroxidation and Attenuates Aortic Valve Stenosis

BackgroundCalcific aortic valve stenosis (AS) is the most common valvular heart disease in the aging population and lacks effective pharmacological therapy. Oxidative stress is a key feature of valvular remodeling, yet the mechanisms linking oxidative injury to calcification remain unclear. Ferroptosis, a lipid peroxidation-driven form of regulated cell death, has emerged as a key mediator of oxidative tissue injury and may contribute to cardiovascular disease. Vitamin K was recently identified as a suppressor of ferroptosis and cardiovascular calcification, but whether ferroptosis links vitamin K status to disease progression in AS remains unknown. Methods and ResultsWe investigated the role of lipid peroxidation and ferroptosis in AS and their modulation by vitamin K2 using a translational approach. In human stenotic aortic valves, lipid peroxidation was markedly increased and localized to calcified regions, consistent with a ferroptosis-associated microenvironment. In primary human valvular interstitial cells (VICs), pro-calcific conditions induced lipid peroxidation and a pro-ferroptotic state. Pharmacological induction of ferroptosis enhanced VIC calcification, whereas its inhibition attenuated mineralization, supporting a causal role in osteogenic remodeling. Impaired vitamin K status was associated with increased valvular lipid peroxidation in AS patients. Conversely, vitamin K2 attenuated lipid peroxidation, preserved cell viability under ferroptotic stress, and partially normalized pro-ferroptotic and inflammatory transcriptional programs in VICs. In a murine model of AS, dietary vitamin K2 supplementation attenuated disease progression, reduced transvalvular gradients, and decreased valvular inflammation and lipid peroxidation-associated pathways. Finally, in a prospective cohort of patients with aortic sclerosis to moderate AS (n = 157), circulating undercarboxylated osteocalcin, a marker of impaired vitamin K status, was independently associated with accelerated disease progression. ConclusionsVitamin K2 counteracts ferroptosis-associated lipid peroxidation in AS and attenuates disease severity in vivo. Impaired vitamin K status is independently associated with accelerated progression in patients. These findings position vitamin K2 as a potential disease-modifying strategy and vitamin K status as a prognostic marker in AS. What Is New?O_LIFerroptotic lipid peroxidation is enriched in calcified regions of human stenotic aortic valves. Pharmacological induction of ferroptosis increases, and its inhibition reduces, calcification of human valvular interstitial cells, indicating a causal contribution to valvular mineralization. C_LIO_LIVitamin K2 suppresses ferroptotic lipid peroxidation, preserves cell viability under ferroptotic stress, and shifts pro-oxidative and pro-inflammatory transcriptional programs in human valvular interstitial cells toward a protective state. C_LIO_LIIn an in vivo model of aortic stenosis, dietary vitamin K2 attenuated hemodynamic progression, with lower peak transvalvular velocity and mean gradient, and reduced valvular inflammation and lipid peroxidation, without affecting coagulation C_LIO_LIIn a prospective cohort of 157 patients with aortic sclerosis to moderate stenosis, impaired vitamin K status, reflected by higher circulating undercarboxylated osteocalcin, was independently associated with accelerated disease progression and with higher rates of mortality. C_LI What Are the Clinical Implications?O_LIAortic stenosis currently has no medical therapy. Vitamin K2, an inexpensive, safe nutrient that does not interfere with anticoagulation, emerges as a candidate disease-modifying strategy that warrants testing in randomized trials. C_LIO_LICirculating undercarboxylated osteocalcin may serve as a biomarker to identify patients at risk of rapid progression and to enrich future vitamin K trials for those most likely to benefit. C_LIO_LITargeting valvular lipid peroxidation, through antioxidant repletion and/or inhibition of lipid-peroxidation enzymes, may be a mechanistically grounded approach to slow calcific aortic valve disease. C_LI

physiology↗

bioRxiv2026

In vitro effects of tensile strain on cancer-associated and matched normal fibroblasts derived from oral squamous cell carcinoma: an exploratory study

BackgroundMechanical forces, particularly tensile stress, influence tumor progression by modulating cancer-associated fibroblast (CAF) behaviour and extracellular matrix remodelling, yet their role in oral cancer remains insufficiently defined. To our knowledge, this is the first study investigating in vitro tensile stress responses in CAF and normal fibroblasts (NF) derived from oral squamous cell carcinoma (OSCC). ObjectiveTo assess how tensile stress affects fibroblast gap closure, proliferation, metabolic activity, and paracrine signalling relevant to tumor-stroma interactions. MethodsCAFs and NFs were isolated from OSCC tissue and matched healthy mucosa and exposed to cyclic tensile strain (3%, 0.02 Hz, 96 h) using the FX-6000T system. Gap closure was assessed by wound-healing assay, proliferation by cell counting, metabolic activity by AlamarBlue, and paracrine effects on A549 tumor cell gap closure using fibroblast-conditioned supernatants. ResultsTensile loading significantly increased CAF gap closure capacity compared with both stimulated NFs (p<0.0001) and unstimulated CAF controls (p=0.0167). Metabolic activity showed a non-significant trend toward higher values in CAFs. Proliferation did not differ between groups up to 48 h, arguing against a major early contribution of proliferation to the observed group differences in the fibroblast scratch assays; however, because proliferation was not inhibited and was not quantified beyond 48 h, later time points should be interpreted conservatively as composite gap closure. Supernatants from mechanically stimulated CAFs increased A549 gap closure by [~]40% compared with non-stimulated controls (p=0.0485), whereas stimulated NFs did not enhance the tumor cells capacity to close the cell-free gap. ConclusionsTensile strain was associated with increased fibroblast gap closure and enhanced gap-closure-promoting paracrine effects of oral CAFs under the conditions tested. These exploratory findings support the concept that biomechanical cues can modulate CAF functional behaviour in OSCC. Given the limited cohort size and inter-patient variability, these results should be interpreted as hypothesis-generating and require confirmation in larger studies. Mechanistic pathways were not interrogated in this study and should be addressed in future work using more complex tumor-stroma models. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/737904v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@d275c6org.highwire.dtl.DTLVardef@13249c5org.highwire.dtl.DTLVardef@8964b9org.highwire.dtl.DTLVardef@33e767_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Aortic valve stenosis promotes pathological shear stress-dependent epigenomic dysregulation in circulating T cells.

BackgroundCalcific aortic valve stenosis (AVS) is the most prevalent valvular heart disease in Western adults, yet no disease-modifying therapy exists. High shear stress (HSS) generated by progressive valvular obstruction drives endothelial injury and immune-mediated inflammation, but the contribution of circulating T cells to AVS pathogenesis remains poorly defined. ObjectivesWe tested whether chronic HSS corresponds with epigenomic reprogramming of peripheral T cells proportionate with hemodynamic severity to yield a clinically informative proxy of disease. MethodsA prospective cohort of 70 participants was recruited for peripheral blood sampling, including 34 with severe symptomatic AVS (aortic valve area <1.0 cm2, mean gradient [≥]40 mmHg) scheduled for transcatheter aortic valve implantation and 36 age- and sex-matched controls. Peripheral T cells were isolated and profiled by genome-wide CpG methylation (Illumina MethylationEPIC) and RNA-sequencing. To test whether HSS directly activates inflammatory signaling, Jurkat T cells were exposed to 20 dyn/cm2 HSS via parallel-plate microfluidic chamber and concomitant CD3/CD28 stimulation, followed by assessment of NFAT nuclear translocation and NFAT target gene expression. ResultsUnsupervised clustering of the 5,000 most-variable CpG loci resolved an epigenomic axis segregating AVS from control T cells (PC1, 15.8% variance explained; P = 3.9x10-6). Multivariable-adjusted analysis identified 3,950 differentially methylated positions (1,889 hyper-, 2,061 hypo-methylated), enriched in promoter-associated CpG islands implicating aortic valve morphogenesis (P = 6.0 x 10-10) and cell-cell adhesion pathways (P = 9.5 x 10-5). Multi-omics factor analysis isolated a latent factor that independently associated with AVS (adjusted P = 1.8x10-3; AUC = 0.79), enriched for chemokine receptor binding and TNF-family signaling, and correlated with canonical HSS-responsive transcripts, consistent with a T cell-mediated shear stress activation. An 18-CpG elastic-net methylation risk score discriminated AVS from controls (AUC = 0.89) and independently predicted hemodynamic severity ({beta} = 7.05 mmHg/SD, 95% CI 2.31-11.79). HSS augmented NFAT nuclear translocation in CD3/CD28-activated Jurkat T cells and induced NFAT-responsive inflammatory transcripts. ConclusionsSevere AVS is associated with promoter-enriched epigenomic remodeling of circulating T cells that converges on hemodynamic stress-dependent inflammatory programs. An 18-CpG methylation risk score outperforms clinical covariates and tracks hemodynamic severity, establishing peripheral T cell DNA methylation as a molecular corollary of AVS.

molecular biology↗

bioRxiv2026

Migration of dI5 Reelin-Lmx1b-Zfhx3 and Disabled-1-Lmx1b-Zfhx3 neurons contribute to the superficial dorsal horn and lamina V

In adult superficial dorsal horn, 90% of Reelin (Reln+) and 70% of Disabled-1 (Dab1+) neurons co-express the transcription factor LIM-homeobox 1-beta (Lmx1b+) and therefore are glutamatergic neurons. Here we asked if embryonic Reln+Lmx1b+ and Dab1+Lmx1b+ dorsal horn neurons are derived from Lmx1b-expressing early-born dI5 or late-born dILB dorsal neurons. On Embryonic day (E)11.5, Reln+ and Dab1+ neurons appear to be part of the migration of early-born dI5 Lmx1b-expressing neurons. Between E12.5-E15.5, the lateral Reln+Lmx1b+ and Dab1+Lmx1b+ neurons migrate circumferentially along the rim of what will become the superficial dorsal horn, whereas medial Reln+Lmx1b+ and Dab1+Lmx1b+ neurons move into the dorsal midline and then migrate into lamina V. The small, late-born dILB Reln+Lmx1b+ and Dab1-Lmx1b+ neurons fill the superficial dorsal horn. In Reln mutants, large Dab1+Lmx1b+ neurons were mispositioned in lamina I and at the border between the superficial and deep dorsal horn. To confirm the identity of the circumferential and midline Reln+Lmx1b+ and Dab1+Lmx1b+ neurons, we asked if they expressed the transcription factor Zfhx3, a marker of dI5 projection neurons. We detected examples of Reln+Lmx1b+Zfhx3+ and Dab1+Lmx1b+Zfhx3+ projection neurons that migrated along the outer rim of the superficial dorsal horn and others that migrated from the midline into lamina V. Taken together, our study demonstrates that the larger Reln+Lmx1b+Zfhx3+ and Dab+Lmx1b+Zfhx3+ neurons represent two subsets of dI5 projections neurons, whereas smaller Reln+Lmx1b+ and Dab1+Lmx1b+ neurons concentrated in lamina II are likely dILB interneurons.

neuroscience↗

bioRxiv2025

Cadherin Regulation of Endoplasmic Reticulum-Plasma Membrane Contact Sites

The spatial organization and dynamics of the endoplasmic reticulum (ER) govern when and where ER tubules engage with other organelles and the plasma membrane. We previously found that ER tubules are closely associated with desmosomes, but the mechanisms of ER recruitment to these adhesive intercellular junctions were unclear. Here, we demonstrate that adherens junctions recruit ER tubules to intercellular junctions in a manner dependent upon E-cadherin association with -catenin and vinculin. During cell-cell junction assembly, adherens junctions and ER appear nearly simultaneously at nascent cell-cell contacts, followed by desmosome formation. ER recruitment to cell-cell contacts allows the formation of ER-plasma membrane contact sites (ER-PMCS) and the assembly of a complex comprising adherens junctions, ER-PMCS, and desmosomes. Ablating adherens junctions disrupts this tripartite complex and perturbs global cellular lipid levels. Collectively, our findings identify cadherins as key organizers of ER-PMCS positioning and suggest that this complex integrates cellular mechanical elements with plasma membrane homeostasis.

cell biology↗

bioRxiv2025

Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment

Merkel cell carcinoma (MCC) is an aggressive skin cancer with high propensity for metastasis, caused by Merkel-cell-polyomavirus (MCPyV), or chronic UV-light-exposure. How MCPyV spatially modulates immune responses within the tumor microenvironment and how such are linked to patient outcomes remains unknown. We interrogated the cellular and transcriptional landscapes of 60 MCC-patients using a combination of multiplex proteomics, in-situ RNA-hybridization, and spatially oriented transcriptomics. We identified a spatial co-enrichment of activated CD8+ T-cells and CXCL9+PD-L1+ macrophages at the invasive front of virus-positive MCC. This spatial immune response pattern was conserved in another virus-positive tumor, HPV+ head-and-neck cancer. Importantly, we show that virus-negativity correlated with high risk of metastasis through low CD8+ T-cell infiltration and the enrichment of cancer-associated-fibroblasts at the tumor boundary. By contrast, responses to immune-checkpoint blockade (ICB) were independent of viral-status but correlated with the presence of a B-cell-enriched spatial contexts. Our work is the first to reveal distinct immune-response patterns between virus-positive and virus-negative MCC and their impact on metastasis and ICB-response.

immunology↗

bioRxiv2024

The Single-Stranded DNA-Binding Factor SUB1/PC4 Alleviates Replication Stress at Telomeres and is a Vulnerability of ALT Cancer Cells

AO_SCPLOWBSTRACTC_SCPLOWTo achieve replicative immortality, cancer cells must activate telomere maintenance mechanisms. In 10-15% of cancers, this is enabled by recombination-based alternative lengthening of telomeres pathways (ALT). ALT cells display several hallmarks including heterogeneous telomere length, extrachromosomal telomeric repeats and ALT-associated PML bodies. ALT cells also have high telomeric replication stress (RS) enhanced by fork-stalling structures (R-loops, G4s) and altered chromatin states. In ALT cells, telomeric RS promotes telomere elongation but above a certain threshold becomes detrimental to cell survival. Manipulating RS at telomeres has thus been proposed as a therapeutic strategy against ALT cancers. Through analysis of genome-wide CRISPR fitness screens, we identified ALT-specific vulnerabilities and describe here our characterization of the roles of SUB1, a ssDNA-binding protein, as a novel regulator of telomere stability. SUB1 depletion further increases RS at ALT telomeres, profoundly impairing ALT cell growth without impacting telomerase-positive cancer cells. During RS, SUB1 is recruited to stalled forks and ALT telomeres via its ssDNA-binding domain. This recruitment is potentiated by RPA depletion, suggesting that these factors may compete for ssDNA. The viability of ALT cells and their resilience towards RS also requires ssDNA-binding by SUB1. SUB1 depletion accelerates cell death induced by FANCM depletion, triggering unsustainable levels of telomeric damage specifically in ALT cells. Finally, combining SUB1 depletion with RS-inducing drugs rapidly induces replication catastrophe in ALT cells. Altogether, our work identifies SUB1 as a new ALT susceptibility with important roles in the mitigation of RS at ALT telomeres and suggests new therapeutic strategies for a host of still poorly managed cancers. SO_SCPLOWIGNIFICANCEC_SCPLOW SO_SCPLOWTATEMENTC_SCPLOWCurrently, there are few treatment options for ALT cancers with chemotherapy still occupying center stage despite often limited efficacy. ALT cancer cells experience high levels of replication stress at telomeres and its enhancement (e.g. via ATR inhibition) is a promising therapeutic strategy. Sensitivity to ATR inhibition varies amongst ALT cell lines/tumors warranting the development of additional ways to modulate telomeric replication stress. Here we identify SUB1, a single-stranded DNA-binding protein, as a vulnerability of ALT cells. SUB1 localizes to ALT telomeres and mitigates deleterious replication stress. SUB1 depletion synergizes with ATR inhibition and FANCM downregulation suggesting that co-targeting SUB1 with other regulators of replication stress at telomeres may kill ALT cancer cells more effectively.

cancer biology↗

bioRxiv2022

Porcine and human aortic valve endothelial and interstitial cell isolation and characterization

BackgroundCalcific aortic valve stenosis is defined by pathological changes in the aortic valve and their predominant cell types: valvular interstitial (VICs) and endothelial cells (VECs). Understanding the cellular and molecular mechanisms of this disease is a prerequisite to identify potential pharmacological treatment strategies. In this study, we present a unique aortic valve cell isolation technique to acquire specific human and porcine cell populations and compared VICs and VECs of these species with each other for the first time. Methods and ResultsAortic valve cells were isolated from human explants from patients undergoing surgical aortic valve replacement or porcine valvular tissue. Pure VEC and VIC populations could be verified by gene expression analysis and immunofluorescence staining showing a highly significant upregulation of endothelial markers in VECs and mesenchymal markers in VICs, respectively. Further analysis and comparison of cells in in vitro experiments revealed that endothelial-to-mesenchymal transition could be induced in hVECs, leading to significant increase of mesenchymal markers. In vitro calcification experiments of VICs induced by osteogenic medium or pro-calcifying medium demonstrated a pronounced calcification marker expression and visible calcific deposition in Alizarin red staining in both species. ConclusionThis study aims to initiate a first step towards standardization of a reproducible isolation technique for pure human and porcine VEC and VIC populations. Comparison of human and porcine aortic valve cells demonstrated that porcine cells might serve as an alternative cellular model system, in settings, where human tissues are difficult to obtain. Statements and DeclarationsThe authors declare no relevant financial or non-financial interests to disclose.

cell biology↗

bioRxiv2022

Aortic valve disease augments vesicular microRNA-145-5p to regulate the calcification of valvular interstitial cells via cellular crosstalk

RationaleAortic valve stenosis (AVS) is a major contributor to cardiovascular death in the elderly population worldwide. MicroRNAs (miRNAs) are highly dysregulated in patients with AVS undergoing surgical aortic valve replacement (SAVR). However, miRNA-dependent mechanisms regulating inflammation and calcification or miRNA-mediated cell-cell crossstalk during the pathogenesis of AVS are still poorly understood. Here, we explored the role of extracellular vesicles (EV)-associated miR-145-5p, which we showed to be highly upregulated upon valvular calcification in AVS in mice and humans. MethodsHuman TaqMan miRNA arrays identified dysregulated miRNAs in aortic valve tissue explants from AVS patients compared to non-calcified valvular tissue explants of patients undergoing SAVR. Echocardiographic parameters were measured in association with the quantification of dysregulated miRNAs in a murine AVS model. In vitro calcification experiments were performed to explore the effects of EV-miR-145-5p on calcification and crosstalk in valvular cells. To dissect molecular miRNA signatures and their effect on signaling pathways, integrated OMICS analyses were performed. RNA sequencing (RNA-seq), high-throughput transcription factor (TF) and proteome arrays showed that a number of genes, miRNAs, TFs, and proteins are crucial for calcification and apoptosis, which are involved in the pathogenesis of AVS. ResultsAmong several miRNAs dysregulated in valve explants of AVS patients, miR-145-5p was the most highly gender-independently dysregulated miRNA (AUC, 0.780, p-value, 0.01). MiRNA arrays utilizing patient-derived- and murine aortic-stenosis samples demonstrated that the expression of miR-145-5p is significantly upregulated and correlates positively with cardiac function based on echocardiography. In vitro experiments confirmed that miR-145-5p is encapsulated into EVs and shuttled into valvular interstitial cells. Based on the integrated OMICs results, miR-145-5p interrelates with markers of inflammation, calcification, and apoptosis. In vitro calcification experiments demonstrated that miR-145-5p regulates the ALPL gene, a hallmark of calcification in vascular and valvular cells. EV-mediated shuttling of miR-145-5p suppressed the expression of ZEB2, a negative regulator of the ALPL gene, by binding to its 3 untranslated region to inhibit its translation, thereby diminishing the calcification of target valvular interstitial cells. ConclusionElevated levels of pro-calcific and pro-apoptotic EV-associated miR-145-5p contribute to the progression of AVS via the ZEB2-ALPL axis, which could potentially be therapeutically targeted to minimize the burden of AVS. Clinical SignificanceO_ST_ABSWhat is known?C_ST_ABSO_LIAortic valve stenosis (AVS) is the most prevalent structural heart valve disease requiring surgical or interventional valve replacement. Currently, no medical treatment option is available to slow, halt, or reverse the progression of the disease. C_LIO_LIAVS induces pressure overload on the left ventricle (LV), resulting in concentric hypertrophy and LV dysfunction. C_LIO_LIAVS is not an exclusively degenerative disease that leads to fibrosis and calcification of the valve cusps but rather a chronic inflammatory disease, in which mechanical strain and shear stress lead to endothelial dysfunction and immune cell infiltration, which induces chronic inflammation, apoptosis and differentiation of valvular interstitial cells into osteoblast-like cells. C_LIO_LIIncreasing osteoblastic differentiation and the formation of macrocalcifications are hallmarks of the later stages of AVS. C_LI What is the new information we provide?O_LIDuring aortic valve stenosis, expression pattern of vesicle-associated regulatory miRNAs is altered. C_LIO_LIPatient-derived aortic valve tissue demonstrated an increased expression of miR-145-5p in humans, as well as in aortic valve explants from an experimental murine AVS model. C_LIO_LIMiR145-5p contributes to calcification of the aortic valve through ZEB2, a transcriptional repressor of ALPL, in valvular interstitial cells. C_LIO_LIExtracellular vesicular shuttling of miR-145-5p contributes to valvular cell-cell crosstalk and plays a role in the pathogenesis of AVS. C_LI

cell biology↗

bioRxiv2021

Chemical-induced Gene Expression Ranking and its Application to Pancreatic Cancer Drug Repurposing

Chemical-induced gene expression profiles provide critical information on the mode of action, off-target effect, and cellar heterogeneity of chemical actions in a biological system, thus offer new opportunities for drug discovery, system pharmacology, and precision medicine. Despite their successful applications in drug repurposing, large-scale analysis that leverages these profiles is limited by sparseness and low throughput of the data. Several methods have been proposed to predict missing values in gene expression data. However, most of them focused on imputation and classification settings which have limited applications to real-world scenarios of drug discovery. Therefore, a new deep learning framework named chemical-induced gene expression ranking (CIGER) is proposed to target a more realistic but more challenging setting in which the model predicts the rankings of genes in the whole gene expression profiles induced by de novo chemicals. The experimental results show that CIGER significantly outperforms existing methods in both ranking and classification metrics for this prediction task. Furthermore, a new drug screening pipeline based on CIGER is proposed to select approved or investigational drugs for the potential treatments of pancreatic cancer. Our predictions have been validated by experiments, thereby showing the effectiveness of CIGER for phenotypic compound screening of precision drug discovery in practice.

bioinformatics↗