Biology subjects

Pampou, S.

Publications and source records attributed to Pampou, S..

6 recordsLinked to original sources

bioRxiv2025

Ras-Responsive Element Binding Protein 1 regulates survival of Group 3 medulloblastoma

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, and Group 3 (G3, MYC-driven) MB has the worst prognosis. Despite advances in molecular classification, oncogenic drivers of G3 MB remain poorly defined. To identify such drivers, we profiled transcription factor expression across MB subgroups. Our analysis revealed Ras-responsive element binding protein 1 (RREB1) as one of the most highly expressed transcription factors in G3 MB. RREB1 knockdown impaired cell proliferation in vitro and prolonged survival in orthotopic xenograft models, suggesting it plays a key role in regulating tumor growth. Mechanistically, RREB1 acts by enhancing transcription of TGF-{beta} pathway genes. Upstream, RREB1 expression is controlled by c-MET signaling, and the MET inhibitor SU11274 decreased RREB1 levels and MB cell viability. Local delivery of SU11274 in tumor-bearing mice suppressed RREB1 expression and extended survival. These results establish the c-MET/RREB1 axis as a critical oncogenic regulator and a promising therapeutic target in in high-risk MB.

cancer biology↗

bioRxiv2024

Multiwell-based G0-PCC assay for radiation biodosimetry

In cytogenetic biodosimetry, assessing radiation exposure typically requires over 48 hours for cells to reach mitosis, significantly delaying the administration of crucial radiation countermeasures needed within the first 24 hours post-exposure. To improve medical response times, we incorporated the G0-Premature Chromosome Condensation (G0-PCC) technique with the Rapid Automated Biodosimetry Tool-II (RABiT-II), creating a faster alternative for large-scale radiation emergencies. Our findings revealed that using a lower concentration of Calyculin A (Cal A) than recommended effectively increased the yield of highly-condensed G0-PCC cells (hPCC). However, integrating recombinant CDK1/Cyclin B kinase, vital for chromosome condensation, proved challenging due to the properties of these proteins affecting interactions with cellular membranes. Interestingly, Cal A alone was capable of inducing chromosome compaction in some G0 cells even in the absence of mitotic kinases, although these chromosomes displayed atypical morphologies. This suggests that Cal A mechanism for compacting G0 chromatin may differ from condensation driven by mitotic kinases. Additionally, we observed a correlation between radiation dose and extent of hPCC chromosome fragmentation, which allowed us to automate radiation damage quantification using a Convolutional Neural Network (CNN). Our method can address the need for a same-day cytogenetic biodosimetry test in radiation emergency situations.

cell biology↗

bioRxiv2023

Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium

Drug Mechanism of Action (MoA) is often represented as a small repertoire of tissue-independent, high-affinity binding targets. Yet drug activity and polypharmacology are also manifested through a broad range of off-target and tissue-specific effector proteins. To address this dichotomy, we generated a compendium of drug perturbation profiles for >700 oncology drugs in cell lines representing high-fidelity models of 23 aggressive tumor subtypes, as well as an integrative framework for the proteome-wide assessment of drug-mediated, tissue-specific differential protein activity. Extending MoA and polypharmacology assessment via proteome-wide, multi-tissue analyses revealed novel polypharmacology, including for MAPK, PI3K, and folate pathways inhibitors--as supported by Western blots, thermal shift assays, and structural analysis--as well as functional inhibitors of challenging oncoprotein targets, including MYC, CTNNB1, CENPF and UHRF1. The dataset and associated computational framework might be extensible to additional compound libraries, supporting global, quantitative approaches to defining the mechanisms of action of many drugs.

systems biology↗

bioRxiv2023

Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis

Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies, over the past decade, we developed VESPA--an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations--and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.

systems biology↗

bioRxiv2021

Network-based identification and pharmacological targeting of host cell master regulators induced by SARS-CoV-2 infection

Precise characterization and targeting of host cell transcriptional machinery hijacked by SARS-CoV-2 remains challenging. To identify therapeutically targetable mechanisms that are critical for SARS-CoV-2 infection, here we elucidated the Master Regulator (MR) proteins representing mechanistic determinants of the gene expression signature induced by SARS-CoV-2. The analysis revealed coordinated inactivation of MR-proteins linked to regulatory programs potentiating efficiency of viral replication (detrimental host MR-signature) and activation of MR-proteins governing innate immune response programs (beneficial MR-signature). To identify MR-inverting compounds capable of rescuing activity of inactivated host MR-proteins, with-out adversely affecting the beneficial MR-signature, we developed the ViroTreat algorithm. Overall, >80% of drugs predicted to be effective by this methodology induced significant reduction of SARS-CoV-2 infection, without affecting cell viability. ViroTreat is fully generalizable and can be extended to identify drugs targeting the host cell-based MR signatures induced by virtually any pathogen.

microbiology↗

bioRxiv2020

The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States

Most antiviral agents are designed to target virus-specific proteins and mechanisms rather than the host cell proteins that are critically dysregulated following virus-mediated reprogramming of the host cell transcriptional state. To overcome these limitations, we propose that elucidation and pharmacologic targeting of host cell Master Regulator proteins--whose aberrant activities govern the reprogramed state of infected-coronavirus cells--presents unique opportunities to develop novel mechanism-based therapeutic approaches to antiviral therapy, either as monotherapy or as a complement to established treatments. Specifically, we propose that a small module of host cell Master Regulator proteins (ViroCheckpoint) is hijacked by the virus to support its efficient replication and release. Conventional methodologies are not well suited to elucidate these potentially targetable proteins. By using the VIPER network-based algorithm, we successfully interrogated 12h, 24h, and 48h signatures from Calu-3 lung adenocarcinoma cells infected with SARS-CoV, to elucidate the time-dependent reprogramming of host cells and associated Master Regulator proteins. We used the NYS CLIA-certified Darwin OncoTreat algorithm, with an existing database of RNASeq profiles following cell perturbation with 133 FDA-approved and 195 late-stage experimental compounds, to identify drugs capable of virtually abrogating the virus-induced Master Regulator signature. This approach to drug prioritization and repurposing can be trivially extended to other viral pathogens, including SARS-CoV-2, as soon as the relevant infection signature becomes available.

systems biology↗