Biology subjects

Vlahos, L.

Publications and source records attributed to Vlahos, L..

4 recordsLinked to original sources

bioRxiv2024

pyVIPER: A fast and scalable Python package for rank-based enrichment analysis of single-cell RNASeq data

SummarySingle-cell sequencing has revolutionized biomedical research by offering insights into cellular heterogeneity at unprecedented resolution. Yet, the low signal-to-noise ratio, characteristic of single-cell RNA sequencing (scRNASeq), challenges quantitative analyses. We have shown that gene regulatory network (GRN) analysis can help overcome this obstacle and support mechanistic elucidation of cellular state determinants, for example by using the VIPER algorithm to identify Master Regulator (MR) proteins from gene expression data. A key challenge, as the size and complexity of scRNASeq datasets grow, is the need for highly scalable tools supporting the analysis of large-scale datasets with up to hundreds of thousands of cells. To address it, we introduce pyVIPER, a fast, memory-efficient, and highly scalable Python toolkit for assessing protein activity in large-scale scRNASeq datasets. pyVIPER supports multiple enrichment analysis algorithms, data transformation/postprocessing modules, a novel data structure for GRNs manipulation, and seamless integration with AnnData, Scanpy and several widely adopted machine learning libraries. Compared to VIPER, benchmarking reveals orders of magnitude runtime reduction for large datasets--i.e., from hours to minutes-- thus supporting VIPER-based analysis of virtually any large-scale single-cell dataset, as well as integration with other Python-based tools. Availability and ImplementationpyVIPER is available on GitHub (https://github.com/alevax/pyviper) and PyPI (https://pypi.org/project/viper-in-python/). Contactav2729@cumc.columbia.edu Supplementary informationSupplementary data are available at Bioinformatics online. Accompanying data for the tutorials are available on Zenodo (https://zenodo.org/records/10059791).

bioinformatics↗

bioRxiv2024

Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations

Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis--whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations--including avapritinib, larotrectinib, and ruxolitinib--produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.

systems biology↗

bioRxiv2023

Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression

The sparse vascularity of Pancreatic Ductal Adenocarcinoma (PDAC) presents a mystery: what prevents this aggressive malignancy from undergoing neoangiogenesis to counteract hypoxia and better support growth? An incidental finding from prior work on paracrine communication between malignant PDAC cells and fibroblasts revealed that inhibition of the Hedgehog (HH) pathway partially relieved angiosuppression, increasing tumor vascularity through unknown mechanisms. Initial efforts to study this phenotype were hindered by difficulties replicating the complex interactions of multiple cell types in vitro. Here we identify a cascade of paracrine signals between multiple cell types that act sequentially to suppress angiogenesis in PDAC. Malignant epithelial cells promote HH signaling in fibroblasts, leading to inhibition of WNT signaling in fibroblasts and epithelial cells, thereby limiting VEGFR2-dependent activation of endothelial hypersprouting. This cascade was elucidated using human and murine PDAC explant models, which effectively retain the complex cellular interactions of native tumor tissues.

cancer biology↗

bioRxiv2022

Therapeutic modulation of the blood-brain barrier and ischemic stroke by a bioengineered FZD4-selective WNT surrogate

Derangements of the blood-brain barrier (BBB) or blood-retinal barrier (BRB) occur in disorders ranging from stroke, cancer, diabetic retinopathy, and Alzheimers disease. The Norrin/FZD4/TSPAN12 pathway activates WNT/{beta}-catenin signaling, which is essential for BBB and BRB function. However, systemic pharmacologic FZD4 stimulation is hindered by obligate palmitoylation and insolubility of native WNTs and suboptimal properties of the FZD4-selective ligand Norrin. Here, we developed L6-F4-2, a non-lipidated, FZD4-specific surrogate with significantly improved sub-picomolar affinity versus native Norrin. In Norrin knockout (NdpKO) mice, L6-F4-2 not only potently reversed neonatal retinal angiogenesis deficits, but also restored BRB and BBB function. In adult C57Bl/6J mice, post-stroke systemic delivery of L6-F4-2 strongly reduced BBB permeability, infarction, and edema, while improving neurologic score and capillary pericyte coverage. Our findings reveal systemic efficacy of a bioengineered FZD4-selective WNT surrogate during ischemic BBB dysfunction, with general applicability to adult CNS disorders characterized by an aberrant blood-brain barrier.

physiology↗