Biology subjects

Steiner, D.

Publications and source records attributed to Steiner, D..

4 recordsLinked to original sources

bioRxiv2026

Galectin-9 drives thrombo-inflammatory circuits initiating venous thrombosis

Background: Venous thromboembolism is increasingly recognized as a thrombo-inflammatory disease, yet the pathways linking inflammation to venous thrombus initiation remain incompletely defined. Galectin-9 (Gal-9), a {beta}-galactoside-binding lectin elevated in inflammatory disorders, has no defined role in venous thrombosis. Methods: Using plasma from patients with deep vein thrombosis (DVT), Gal-9-deficient mice, an inferior vena cava stenosis model, intravital microscopy, microfluidics, and ex vivo platelet and neutrophil assays, we assessed the functional contribution of Gal-9 to venous thrombosis. Results: Plasma Gal-9 was elevated in DVT patients, correlated with D-dimer at presentation, and declined over 3-month follow-up. Gal-9 deletion did not alter hemostasis but markedly impaired thrombus initiation, with reduced platelet and neutrophil recruitment to the vessel wall and reduced intra-thrombus neutrophil extracellular trap (NET) formation. TNF-/IFN-{gamma}-stimulated endothelial cells upregulated Gal-9 and promoted platelet adhesion and fibrin(ogen) deposition, which Gal-9 neutralization partially reversed. Under venous shear, immobilized recombinant Gal-9 potentiated platelet activation and thrombus formation, particularly alongside collagen, whereas Gal-9 inhibition suppressed these responses. Gal-9-activated platelets promoted NETosis and shifted thrombus composition toward a NET-rich inflammatory phenotype. Conclusions: Gal-9 is a previously unrecognized driver of venous thrombo-inflammation, linking vascular inflammation to platelet activation, NET formation, and thrombosis. Genetic deletion attenuated these responses in vivo, and antibody-mediated Gal-9 neutralization suppressed platelet activation and thrombus formation in vitro, identifying the Gal-9 glycan-binding pathway as a therapeutic target that disrupts thrombosis without impairing hemostasis.

immunology↗

bioRxiv2025

Methylation-Based Deconvolution Unveils Glioblastoma Heterogeneity and Cell-Type Composition Linked to Patient Survival

BackgroundIDH-wildtype glioblastoma (GBM) is an aggressive, heterogeneous brain tumor with limited treatment options. DNA methylation profiling allows detailed tumor characterization. This study applies methylation-based deconvolution to define GBMs cellular composition and its association with patient outcomes. MethodsWe generated oligodendroglial precursor cells at various developmental stages from enriched human neural progenitor cultures and used their DNA methylation signatures, along with published signatures of brain tumor and tumor microenvironment-relevant cell types, to deconvolve 263 adult GBMs (Heidelberg-cohort). Tumor purity was estimated using RF_Purify. An independent cohort of 199 GBMs from TCGA and GEO, all treated with standard-of-care therapy, was similarly deconvolved, followed by Kaplan-Meier survival analysis to assess the prognostic value of neoplastic component proportions. ResultsDeconvolution uncovered distinct cellular compositions, consistent with single-cell RNA sequencing findings. Tumor purity analysis showed neoplastic fractions averaged 70% of tumor bulk, predominantly oligodendrocyte-like (43%), oligodendrocyte precursor-like (27%), astrocyte-like (19%), and mesenchymal stem cell-like (11%) populations. Non-neoplastic fractions were enriched for macrophages, vascular cells, and immune populations. A higher oligodendrocyte-like signature was linked to poorer survival (median survival 14.3 vs. 15.3 months; p = 0.017), while a higher astrocyte-like signature correlated with improved outcomes (15.3 vs. 13.4 months; p = 0.044). The astrocyte-to-oligodendrocyte ratio emerged as a strong prognostic marker, with a higher ratio predicting significantly longer survival (15.8 vs. 11.9 months; p < 0.00011). ConclusionsMethylation-based deconvolution provides insight into GBM heterogeneity, highlighting the prognostic relevance of the astrocyte-to-oligodendrocyte ratio, which may guide personalized treatment strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/640603v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@942af0org.highwire.dtl.DTLVardef@18f2626org.highwire.dtl.DTLVardef@111a756org.highwire.dtl.DTLVardef@1194b_HPS_FORMAT_FIGEXP M_FIG A. We generated oligodendroglial precursor cells (OPs) at various developmental stages from enriched human neural progenitor cultures. A reference atlas of methylation signatures from 14 normal cell types, including the in vitro-generated cells, combined with published profiles of brain tumor and tumor microenvironment-relevant cell types, was applied to deconvolve 263 GBM samples based on their methylation profiles (Heidelberg cohort). Cell type proportions were analyzed with RF_Purify to estimate tumor purity and distinguish neoplastic from non-neoplastic components. B. An independent cohort of 199 GBMs from TCGA and GEO, with available clinical data and all treated with standard-of-care therapy, was similarly deconvolved based on methylation profiles. Kaplan-Meier survival analysis assessed the prognostic impact of cell type proportions, identifying the astrocyte-to-oligodendrocyte ratio as the most significant marker. (Created with BioRender.com) C_FIG Key pointsO_LIMethylation-based deconvolution incorporating in-vitro-derived oligodendrocyte precursor differentiation data reveals GBM heterogeneity C_LIO_LIGBMs neoplastic fraction is dominated by oligodendrocyte-lineage cells C_LIO_LIAstrocyte/oligodendrocyte ratio is a strong prognostic marker for patient survival C_LI Importance of the studyThis study advances neuro-oncology research by using methylation-based deconvolution to uncover the cellular heterogeneity of glioblastoma. By constructing a comprehensive reference atlas and identifying cell-type-specific methylation signatures, it provides prognostic insights into the distinct cellular compositions of glioblastoma. Combining deconvolution results with purity analysis enables the differentiation between neoplastic and non-neoplastic tumor components. This approach complements single-cell RNA sequencing while offering greater clinical applicability, as DNA methylation profiling can be performed on FFPE or fresh frozen samples, unlike the more costly and tissue-sensitive single-cell methods. Importantly, the identification of the astrocyte-to-oligodendrocyte ratio as a strong prognostic marker highlights key cellular determinants of glioblastoma survival. These findings deepen our understanding of glioblastoma biology and offer a practical tool for patient stratification.

cancer biology↗

bioRxiv2024

Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics

Microscopic vascular invasion (VI) is predictive of recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and microenvironment features associated with angioinvasive LUAD we profiled 162 resected stage I tumors with and without VI by RNA-seq and explored spatial patterns of gene expression in a subset of 15 samples by high-resolution spatial transcriptomics (stRNA-seq). Despite the small size of invaded blood vessels, we identified a gene expression signature of VI from the bulk RNA-seq discovery cohort (n=103) and found that it was associated with VI foci, desmoplastic stroma, and high-grade patterns in our stRNA-seq data. We observed a stronger association with high-grade patterns from VI+ compared with VI- tumors. Using the discovery cohort, we developed a transcriptomic predictor of VI, that in an independent validation cohort (n=60) was associated with VI (AUROC=0.86; p=5.42x10-6) and predictive of recurrence-free survival (HR=1.98; p=0.024), even in VI- LUAD (HR=2.76; p=0.003). To determine our VI predictors robustness to intra-tumor heterogeneity we used RNA-seq data from multi-region sampling of stage I LUAD cases in TRACERx, where the predictor scores showed high correlation (R=0.87, p<2.2x10-16) between two randomly sampled regions of the same tumor. Our study suggests that VI-associated gene expression changes are detectable beyond the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from biopsy specimens, allowing for more tailored medical and surgical management of stage I LUAD.

cancer biology↗

bioRxiv2021

Multi-specific DARPin(R) therapeutics demonstrate very high potency against mutated SARS-CoV-2 variants in vitro

SARS-CoV-2 has infected millions of people globally and continues to undergo evolution. Emerging variants can be partially resistant to vaccine induced immunity and therapeutic antibodies, emphasizing the urgent need for accessible, broad-spectrum therapeutics. Here, we report a comprehensive study of ensovibep, the first trispecific clinical DARPin candidate, that can simultaneously engage all three units of the spike protein trimer to potently inhibit ACE2 interaction, as revealed by structural analyses. The cooperative binding of the individual modules enables ensovibep to retain inhibitory potency against all frequent SARS-CoV-2 variants, including Omicron BA.1 and BA.2, as of February 2022. Moreover, viral passaging experiments show that ensovibep, when used as a single agent, can prevent development of escape mutations comparably to a cocktail of monoclonal antibodies (mAb). Finally, we demonstrate that the very high in vitro antiviral potency also translates into significant therapeutic protection and reduction of pathogenesis in Roborovski dwarf hamsters infected with either the SARS-CoV-2 wild-type or the Alpha variant. In this model, ensovibep prevents fatality and provides substantial protection equivalent to the standard of care mAb cocktail. These results support further clinical evaluation and indicate that ensovibep could be a valuable alternative to mAb cocktails and other treatments for COVID-19.

immunology↗