Showing papers by "Mehdi Bouhaddou published in 2022"

Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19

Abstract: This proof-of-concept study shows that plitidepsin, a marine peptide that inhibits SARS-CoV-2 replication, has a favorable safety profile and may be an efficacious treatment for patients with COVID-19. Plitidepsin, a marine-derived cyclic-peptide, inhibits SARS-CoV-2 replication at nanomolar concentrations by targeting the host protein eukaryotic translation elongation factor 1A. Here, we show that plitidepsin distributes preferentially to lung over plasma, with similar potency against across several SARS-CoV-2 variants in preclinical studies. Simultaneously, in this randomized, parallel, open-label, proof-of-concept study (NCT04382066) conducted in 10 Spanish hospitals between May and November 2020, 46 adult hospitalized patients with confirmed SARS-CoV-2 infection received either 1.5 mg (n = 15), 2.0 mg (n = 16), or 2.5 mg (n = 15) plitidepsin once daily for 3 d. The primary objective was safety; viral load kinetics, mortality, need for increased respiratory support, and dose selection were secondary end points. One patient withdrew consent before starting procedures; 45 initiated treatment; one withdrew because of hypersensitivity. Two Grade 3 treatment-related adverse events were observed (hypersensitivity and diarrhea). Treatment-related adverse events affecting more than 5% of patients were nausea (42.2%), vomiting (15.6%), and diarrhea (6.7%). Mean viral load reductions from baseline were 1.35, 2.35, 3.25, and 3.85 log10 at days 4, 7, 15, and 31. Nonmechanical invasive ventilation was required in 8 of 44 evaluable patients (16.0%); six patients required intensive care support (13.6%), and three patients (6.7%) died (COVID-19-related). Plitidepsin has a favorable safety profile in patients with COVID-19.

A functional map of HIV-host interactions in primary human T cells

Abstract: Abstract Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Abstract: Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.

Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories

Abstract: A series of SARS-CoV-2 variants of concern (VOCs) have evolved in humans during the COVID-19 pandemic—Alpha, Beta, Gamma, Delta, and Omicron. Here, we used global proteomic and genomic analyses during infection to understand the molecular responses driving VOC evolution. We discovered VOC-specific differences in viral RNA and protein expression levels, including for N, Orf6, and Orf9b, and pinpointed several viral mutations responsible. An analysis of the host response to VOC infection and comprehensive interrogation of altered virus-host protein-protein interactions revealed conserved and divergent regulation of biological pathways. For example, regulation of host translation was highly conserved, consistent with suppression of VOC replication in mice using the translation inhibitor plitidepsin. Conversely, modulation of the host inflammatory response was most divergent, where we found Alpha and Beta, but not Omicron BA.1, antagonized interferon stimulated genes (ISGs), a phenotype that correlated with differing levels of Orf6. Additionally, Delta more strongly upregulated proinflammatory genes compared to other VOCs. Systematic comparison of Omicron subvariants revealed BA.5 to have evolved enhanced ISG and proinflammatory gene suppression that similarly correlated with Orf6 expression, effects not seen in BA.4 due to a mutation that disrupts the Orf6-nuclear pore interaction. Our findings describe how VOCs have evolved to fine-tune viral protein expression and protein-protein interactions to evade both innate and adaptive immune responses, offering a likely explanation for increased transmission in humans. One sentence summary Systematic proteomic and genomic analyses of SARS-CoV-2 variants of concern reveal how variant-specific mutations alter viral gene expression, virus-host protein complexes, and the host response to infection with applications to therapy and future pandemic preparedness.

Abstract B011: Network propagation of the kinase activity signatures of therapy-resistant tumors reveals novel druggable targets in BRAF(V600E)-mutated colorectal cancer

Abstract: Despite combination therapies targeting BRAF and EGFR, metastatic colorectal cancer (mCRC) with a BRAF(V600E) mutation confers poor prognosis with early development of drug resistance in a majority of patients. Treatment with a current standard of care (encorafenib plus panitumumab) temporarily suppresses tumor growth, but fails to promote regression and leads to eventual disease progression. Consequently, there is a need to better characterize the compensatory resistance pathways that are activated in response to treatment. To identify these parallel resistance mechanisms and novel druggable targets, we analyzed the effects of combination treatment with encorafenib (a BRAF-inhibitor) and panitumumab (an anti-EGFR antibody) in BRAF(V600E) mCRC patient-derived xenograft (PDX) tumor samples via a high throughput kinase activity mapping (HT-KAM) platform and advanced computational tools. HT-KAM uses libraries of peptides as combinatorial sensors that identify and measure the activity of >160 kinases involved in oncogenic pathways (Coppé et al 2019). As these key kinases provide an informative yet filtered view of proteome-wide signaling effects, we developed a network-based workflow to further analyze our HT-KAM results. Network propagation methods were applied to integrate this data into ReactomeFI, a well-validated gene/protein interaction network. Significant genes from the network propagation results were clustered and enriched for pathway analysis using additional scripts, and results were visualized using Cytoscape. Based on HT-KAM results comparing the kinase signatures of PDX tumors treated with encorafenib + panitumumab versus vehicle, EGFR was confirmed to be downregulated. Moreover, several kinases previously identified as (re-)activated upon treatment and progression were significantly upregulated, including kinases in the RAF–MEK–ERK cascade as well as AKTs and downstream effectors. In addition, STK11, a tumor suppressor also known as LKB1, was significantly downregulated, while the activity of several kinases involved in cell surface signaling were upregulated, including PKA and PKCs. Network propagation of this data and enrichment of network subclusters resulted in a broad range of pathways implicated in persistent cell survival. Among top hits, signaling networks orchestrated by GPCRs, MTOR, WNT and beta-catenin were significantly enriched, suggesting that multiple interacting pathways coordinate the response and resistance to BRAF/EGFR joint inhibition. Our workflow implementing network propagation and enrichment analysis of HT-KAM data pinpoints essential pathways that contain druggable targets. We are in the process of validating these dependencies in PDX models and translating these mechanisms into novel combinatorial targeted therapy interventions designed to overcome drug resistance in BRAF(V600E) mCRC. Citation Format: Yeonjoo Hwang, Mehdi Bouhaddou, Christina Moelders, Denise P. Muñoz, Chloe E. Atreya, Jean-Philippe Coppé. Network propagation of the kinase activity signatures of therapy-resistant tumors reveals novel druggable targets in BRAF(V600E)-mutated colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B011.

How can systems approaches help us understand and treat infectious disease?

Abstract: Leading researchers at the intersection of infectious disease and systems biology speak about how systems approaches have influenced modern infectious disease research and what these tools can offer for the future of the field.