Biology subjects

Egan, D.

Publications and source records attributed to Egan, D..

5 recordsLinked to original sources

bioRxiv2024

A TEMPORAL MODEL OF TUMOR-IMMUNE DYNAMICS IN HIGH GRADE SEROUS OVARIAN CANCER

Patients with high-grade serous ovarian cancer (HGSOC) typically present with widespread metastasis, obscuring a temporal understanding of tumor-immune dynamics. We performed multi-site global proteomics and matched immunohistochemistry (IHC) of CD4+ and CD8+ tumor infiltrating lymphocytes (TILs) in patient samples. The protein expression profiles were ordered by pseudotime, recapitulating metastatic progression observed in the clinic, and providing a framework to explore tumor-immune dynamics from localized to metastatic disease. Metastatic progression correlated with immune cell infiltration and the recruitment of Tregs to counterbalance the effect of {gamma}{delta} and CD4+ T cells. Whilst later-stage metastases recruited Tregs via chemokines induced by SNX8, early-stage tumors relied more on antigen presentation. The exclusion of CD4+ TILs from the epithelium was correlated with metastatic progression, whereas CD8+ TILs were not, likely due to a predominance of exhausted CD8+ T cells. In early-stage tumors, keratin-expressing cancer cells recruited Tregs via MHC class II, resulting in an inflammatory phenotype characterized by limited IFN{gamma} production and non-clonally expanded T cells. Additionally, IFI44L expression on macrophages caused immune exclusion by downregulating CD53 on T cells. Our findings reveal novel mechanisms of immune escape associated with localized disease and metastatic progression in HGSOC, highlighting potential targets to improve the efficacy of immunotherapy.

cancer biology↗

bioRxiv2024

Diphenyleneiodonium chloride inhibits MYCN-amplified neuroblastoma by targeting MYCN induced mitochondrial alterations

High-risk neuroblastoma is one of the most lethal childhood cancers. Half of these tumors are driven by MYCN gene amplification (MNA). Despite intensive chemo- and radiotherapy, only 40% of patients survive, and they often suffer from severe long-term side effects of these genotoxic treatments. Thus, new therapies are needed that are less toxic and more efficacious. Here, we identified diphenyleneiodonium (DPI) as a tool compound that preferentially targets MNA neuroblastoma. Using proteomic assays we investigated the DPI mode of action, finding that DPI induces the proteasomal degradation of MYCN and could reverse some alterations induced by high levels of MYCN. These include profound changes in the expression of proteins participating in the mitochondrial electron transport chain. Metabolic and biological assays suggested that alterations in mitochondrial function and the associated production of reactive oxygen species (ROS) are critical DPI targets in the context of MNA. DPI reduced the survival, and malignant transformation of neuroblastoma across a panel of cell lines at clinically achievable concentrations. DPI also shrank tumors and prevented metastatic spread in zebrafish models of MYCN-driven neuroblastoma. These findings suggest that processes impacted by complex I inhibitors could be valuable new targets for the development of non-genotoxic drugs against high-risk MNA neuroblastoma. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/619268v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@167e953org.highwire.dtl.DTLVardef@10749e4org.highwire.dtl.DTLVardef@1842598org.highwire.dtl.DTLVardef@c05d82_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

OXPHOS TARGETING OF MYCN-AMPLIFIED NEUROBLASTOMA

SummaryHigh risk - neuroblastoma (HR-NB) is a pediatric solid tumor with high lethality. Half of HR-NB are driven by MYCN gene amplification (MNA). These HR-NBs require high dosage chemotherapy and often relapse. Moreover, current therapies can cause severe long-term side effects and new therapies are urgently needed. This study investigates a novel therapeutic approach targeting the metabolic vulnerabilities of MNA NB cells. We discovered that Diphenyleneiodonium chloride (DPI), an inhibitor of flavoprotein enzymes and mitochondrial complex I, synergizes with mitoquinone mesylate (MitoQ), a mitochondria-targeted antioxidant in 2D and 3D in vitro models of NB. Similarly to DPI, MitoQ affects MNA cells in a MYCN-dependent fashion, being more toxic when MYCN levels are high. Furthermore, low nanomolar concentrations of MitoQ significantly decrease MYCN protein expression and induce differentiation of MNA cells. The DPI and MitoQ combination further synergizes with vincristine, a chemotherapeutic agent used in NB treatment. Phosphoproteomics and proteomics analysis suggests that the drug combination induces MNA NB cell death by arresting the cell cycle and inhibiting oxidative phosphorylation (OXPHOS) in the mitochondria. Thus, interference with mitochondrial metabolism may represent an effective strategy to enhance the activity of chemotherapeutic drugs in MNA-NB.

cancer biology↗

bioRxiv2022

Small gene networks can delineate immune cell states and characterize immunotherapy response in melanoma

BackgroundSingle-cell sequencing studies have elucidated some of the underlying mechanisms responsible for immune checkpoint inhibitor (ICI) response, but are difficult to implement as a general strategy or in a clinical diagnostic setting. In contrast, bulk RNAseq is now routine for both research and clinical applications. Therefore, our analysis extracts small transcription factor-directed co-expression networks (regulons) from single-cell RNA-seq data and uses them to deconvolute immune functional states from bulk RNA-seq data to characterize patient responses. MethodsRegulons were inferred in pre-treatment CD45+ cells from metastatic melanoma samples (n=19) treated with first-line ICI therapy (discovery dataset). A logistic regression-based classifier identified immune cell states associated with response, which were characterized according to differentially active, cell-state specific regulons. The complexity of these regulons was reduced and scored in bulk RNAseq melanoma samples from four independent studies (n=209, validation dataset). Patients were clustered according to their regulon scores, and the associations between cluster assignment, response, and survival were determined. Intercellular communication analysis of cell states was performed, and the resulting effector genes were analyzed by trajectory inference. ResultsRegulons preserved the information of gene expression data and accurately delineated immune cell phenotypes, despite reducing dimensionality by > 100-fold. Four cell states, termed exhausted T cells, monocyte lineage cells, memory T cells, and B cells, were associated with therapeutic responses in the discovery dataset. The cell states were characterized by seven differentially active and specific regulons that showed low specificity in non-immune cells. Four clusters with significantly different response outcomes (P <0.001) were identified in the bulk RNAseq validation cohort. An intercellular link between exhausted T cells and monocyte lineage cells was established, whereby their cell numbers were correlated, and exhausted T cells predicted prognosis as a function of monocyte lineage cell number. Analysis of ligand - receptor expression suggested that monocyte lineage cells drive exhausted T cells into terminal exhaustion through programs that regulate antigen presentation, chronic inflammation, and negative co-stimulation. ConclusionsRegulon-based characterization of cell states provides robust and functionally informative markers that can deconvolve bulk RNA-seq data to identify ICI responders.

immunology↗

bioRxiv2017

A quantitative PCR based environmental DNA assay for detecting Atlantic salmon (Salmo salar L.)

O_LIThe Atlantic salmon (Salmo salar L.) has worldwide ecological, cultural and economic importance. The species has undergone extensive decline across its native range, yet concerns have been raised about its invasive potential in the Pacific. Knowledge on the distribution of this species is vital for addressing conservation goals.\nC_LIO_LIThis study presents an eDNA assay to detect S. salar in water samples, using quantitative PCR (qPCR) technology. Species-specific primers and a minor groove binding (MGB) probe were designed for the assay, based on the mitochondrial cytochrome oxidase I (COI) gene.\nC_LIO_LIThe results of this study indicate that eDNA is a highly sensitive tool for detecting S. salar in situ, and could potentially provide an alternative, non-invasive method for determining the distribution of this species.\nC_LI

genetics↗