Biology subjects

Harbour, J. W.

Publications and source records attributed to Harbour, J. W..

11 recordsLinked to original sources

bioRxiv2026

BAP1 loss and PRAME expression converge to remodel the tumor-immune ecosystem during uveal melanoma progression

Uveal melanoma (UM) is characterized by a small number of recurrent genetic alterations that determine metastatic propensity. BAP1 loss and PRAME expression define the dominant prognostic axes in UM, yet how they promote malignant progression remains unclear. We profiled 190,535 cells from normal uvea, uveal nevus, primary and metastatic UM using single-cell transcriptomics, T cell receptor sequencing, spatial transcriptomics and isogenic perturbation models. Normal melanocytes, nevus cells and UM cells formed a transcriptional continuum marked by loss of differentiation and emergence of neural crest-like, stress-responsive, hypoxic-glycolytic and immune-interacting states. BAP1 loss and PRAME expression imposed distinct but convergent immunoregulatory programs, inducing interferon and TNF-NFkB signaling and MHC-I expression, with HLA-E showing the strongest response. These alterations were accompanied by macrophage and CD8+ T cell remodeling. PRAME-enriched tumor regions formed spatially organized niches enriched for macrophages and plasma cells. These findings define BAP1 loss and PRAME expression as distinct but convergent axes of tumor-immune coevolution and nominate HLA-E as a candidate mediator of immune resistance.

cancer biology↗

bioRxiv2026

Surface Complex V couples proton gradient across the plasma membrane to ATP production in cancer

Cancer cells alter their metabolism to support growth and survival, most notably by fermenting glucose to lactate even in the presence of oxygen, a phenomenon known as the Warburg effect. Although this metabolic state has been recognized for decades, its bioenergetic advantages remain unclear, as fermentation produces less net ATP than mitochondrial respiration. How aerobic fermentation contributes to cellular energy balance therefore remains unresolved. Here, we show that extracellular acidification generated by lactate export creates a proton gradient across the plasma membrane that is harnessed by ectopic ATP synthases to drive intracellular ATP production. We find that ATP synthase and proton-shuttling components of the mitochondrial respiratory chain translocate to the plasma membrane in cancer cells and are preferentially oriented to exploit this gradient, linking a hallmark of aerobic fermentation directly to energy supplementation. This work provides a mechanistic resolution to the apparent energetic inefficiency of the Warburg paradigm and identifies a previously unrecognized pathway for energy complementation in cancer.

cancer biology↗

bioRxiv2025

A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma

Uveal melanoma (UM) is a highly aggressive intraocular malignancy with limited therapeutic options for metastatic disease. Existing transgenic UM mouse models inadequately recapitulate human disease progression, while transplant models lack immune competence for studying the tumor immune microenvironment and therapeutic interventions. To address these limitations, we developed a genetically engineered mouse model incorporating stepwise genetic alterations implicated in human UM progression. Spatiotemporally controlled expression of mutant GNAQQ209L from the endogenous locus induced choroidal nevi with limited penetrance. Concomitant BAP1 deletion enhanced nevus formation, while further MYC activation led to fully penetrant intraocular tumors with metastatic potential. Single-cell RNA sequencing revealed malignant cells segregated into Melanocytic and Neural Crest-like subpopulations characterized by distinct transcriptional and biosynthetic programs. Trajectory analyses inferred dedifferentiation from the Melanocytic toward the Neural Crest-like state during tumor progression. Comparison to human UM revealed commonalities with highly aggressive Class 2 UM, including gene expression signatures and copy number gains affecting genes that map to human chromosome 8q beyond the activated MYC allele, suggesting cooperative effects of multiple drivers in this chromosomal region. The tumor microenvironment featured immunosuppressive macrophage populations and exhausted T cells, closely resembling human UM. This physiologically relevant, immune-competent model provides a platform for investigating UM biology, functionally characterizing candidate driver genes, and developing immune-based therapeutic strategies. SIGNIFICANCE STATEMENTWe developed a mouse model that resembles the genetic progression and phenotypic plasticity of human UM. This spatially controlled model confirms the critical role of driver mutations in GNAQ and BAP1, proposes MYC as a promoter of malignant transformation in coordination with other chromosome 8q genes, and reveals UM progression through distinct cellular states. This model offers an urgently needed preclinical platform for understanding the immunogenomics of UM and for testing immune and targeted treatments for this lethal cancer.

cancer biology↗

bioRxiv2025

GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases

Uveal melanoma (UM) results in fatal liver metastasis, yet little is known about the interactions between UM and host cells in the tumor microenvironment that promote this distinctive proclivity. Here, we used single cell (sc)-RNA-Seq analysis of UM-hepatic stellate cell (HSC) co-cultures to demonstrate that HSCs enriched for UM cell states that expressed genes implicated in cell survival, metabolic reprogramming and angiogenesis. A lead candidate driver of HSC reprogramming was the TGF-{beta} family member GDF15, which was associated with a metastatic UM phenotype. Silencing of BAP1 in UM cells led to increased GDF15 expression and accumulation of H3K27ac marks at the GDF15 promoter. Treatment of HSCs with GDF15 led to increased expression extracellular matrix proteins, inflammatory cytokines and angiogenic factors, including IL-8. Both exogenous GDF15, IL-8 and conditioned media from UM-HSC co-cultures increased endothelial cell network formation in vitro, an effect that was blocked by anti-GDF15 antibodies. In multiple models of metastatic UM, silencing of GDF15 inhibited the outgrowth of metastatic lesions, associated with reduced deposition of extracellular matrix and recruitment of endothelial cells. UM liver metastasis development is dependent upon GDF15-mediated remodeling of the liver microenvironment leading to an angiogenic response and matrix deposition that supports tumor growth.

cancer biology↗

bioRxiv2024

Identification of targetable epigenetic vulnerabilities in uveal melanoma

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, with a strong predilection for hepatic metastasis, occurring in approximately 50% of cases. Metastatic UM remains highly resistant to therapy and is almost invariably fatal. The strongest genetic drivers of UM metastasis are loss-of-function mutations in tumor suppressor BAP1, an epigenetic regulator that serves as the ubiquitin hydrolase subunit of the polycomb repressive deubiquitinase (PR-DUB) complex, and a key player in global epigenetic regulation. Inactivation of BRCA Associated Protein 1 (BAP1) has been shown to induce widespread epigenetic alterations across multiple model systems. To identify novel therapeutic strategies, we investigated whether targeting the epigenome could reveal new vulnerabilities in UM. We performed high-throughput compound screening using a curated epigenetic inhibitor library and identified BET (bromodomain and extra-terminal domain) inhibition as a particularly promising approach. Interestingly, we observed significant heterogeneity in the efficacy of different BET inhibitors in UM. While previous clinical trials with two BET inhibitors have failed to show efficacy in UM, our findings highlight substantial differences in the potency of specific BET inhibitors for this malignancy. Notably, the BET inhibitor mivebresib (ABBV-075) significantly improved survival rates by 50% in a metastatic UM xenograft mouse model and completely prevented detectable metastases in the bones, spinal cord, and brain. Unexpectedly, RNA sequencing revealed a strong transcriptional overlap between BET inhibition and histone deacetylase (HDAC) inhibition--an approach currently under clinical evaluation for UM treatment. Both BET and HDAC inhibitors reversed gene expression signatures associated with high metastatic risk and induced a neuronal differentiation-like phenotype in UM cells. Together, our findings demonstrate that UM cells exhibit a distinct vulnerability to BET inhibition and establish BET inhibitors as promising candidates for further clinical evaluation for metastatic UM.

cancer biology↗

bioRxiv2021

RB1 loss triggers dependence on ESRRG in retinoblastoma

Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 16 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify novel Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death which is exacerbated in hypoxia. These findings reveal a novel dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.

cancer biology↗

bioRxiv2020

PieParty: Visualizing cells from scRNA-seq data as pie charts

Single cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of gene expression across the plots, for instance to distinguish cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, and every slice in the pie charts corresponds to the gene expression of individual genes. This allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub at https://github.com/harbourlab/PieParty.

bioinformatics↗

bioRxiv2020

UPhyloplot2: Visualizing Phylogenetic Trees from Single-Cell RNA-seq Data

Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs), which can be inferred from single cell RNA-seq (scRNA-seq) data using applications such as inferCNV. Inferences regarding tumor clonality are frequently visualized using phylogenetic plots, which previously required time-consuming and tedious manual analysis. Here, we present UPhyloplot2, a python script that generates phylogenetic plots directly from inferCNV output files. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/.

bioinformatics↗

bioRxiv2020

Kinetics characterization of ASXL1/2-mediated allosteric regulation of BAP1 deubiquitinase

BAP1 is a ubiquitin hydrolase whose deubiquitinase activity is mediated by polycomb group-like protein ASXL2. Cancer-related mutations/deletions of BAP1 lead to loss-of-function either by directly targeting the catalytic (UCH) or ULD domains of BAP1, the latter disrupts binding to ASXL2, an obligate partner for BAP1 enzymatic activity. However, the biochemical and biophysical properties of the domains involved in forming the enzymatically active complex are unknown. Here we investigate the molecular dynamics, kinetics and stoichiometry of these interactions. We demonstrate that the BAP1 and ASXL2 domain/proteins or protein complexes produced in either bacteria or baculovirus are structurally and functionally active. The interaction between BAP1 and ASXL2 is direct, specific, and stable to in vitro biochemical and biophysical manipulations as detected by isothermal titration calorimetry, GST association, and optical biosensor assays. Association of the ASXL2-AB box greatly stimulates BAP1 deubiquitinase activity. A stable ternary complex can be formed comprised of the BAP1-UCH, BAP1-ULD, and ASXL2-AB domains. Binding of the BAP1-ULD domain to the ASXL2-AB box is rapid, with fast association and slow dissociation rates. Stoichiometric analysis revealed that one molecule of the ULD domain directly interacts with one molecule of the AB Box. Real-time kinetics analysis of ULD/AB protein complex to the UCH domain of BAP1, based on SPR, indicated that formation of the ULD/AB complex with the UCH domain is a single-step event with fast association and slow dissociation rates. These structural and dynamic parameters implicate the possibility for future small-molecule approaches to reactivate latent wild-type UCH activity in BAP-mutant malignancies.

cancer biology↗

bioRxiv2019

SparK: A Publication-quality NGS Visualization Tool

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

bioinformatics↗

bioRxiv2019

Fate of developmental mechanisms of myocardial plasticity in the postnatal heart

Whether the hearts organ-founding, progenitor cell gene regulatory networks (CPC-GRNs) are sustained after birth and can be therapeutically evoked for regeneration in response to disease, remains elusive. Here, we report a spatiotemporally resolved analysis of CPC-GRN deployment dynamics, through the pan-CPC-GRN gene Isl1. We show that the Isl1-CPC-GRNs that are deployed during early cardiogenesis and generate the cardiomyocyte majority from mesoderm, undergo programmed silencing through proteasome- and PRC2-mediated Isl1 repression, selectively in the arterial pole. In contrast, we identify a neural crest (CNC)-specific Wnt/{beta}-catenin/Isl1-CPC-GRN that is deployed through the venous pole during cardiac growth and partitioning, and contributes a minority of cardiomyocytes which, in turn, expand massively to build ~10% of the biventricular myocardium. These "dorsal CNCs" continue to sporadically generate cardiomyocytes throughout postnatal growth which, however, are non-proliferative, suggesting that partitioning-like, fetal proliferation signals could be therapeutically targeted to evoke clonal expansion capacity in postnatal CNC-cardiomyocytes for heart regeneration.

developmental biology↗