Biology subjects

Fong, L.

Publications and source records attributed to Fong, L..

11 recordsLinked to original sources

bioRxiv2026

IL-1β/IL-6 signaling circuit in the tumor microenvironment drives prostate cancer development

Despite considerable progress in elucidating mechanisms leading to castration-resistant prostate cancer (CRPC), insight into the early stages of prostate cancer initiation and progression remains limited. Genomic drivers of prostate cancer initiation have been defined through patient tumor sequencing, but the subsequent events responsible for local tissue invasion are poorly understood. Here we leverage a well-studied genetically engineered mouse prostate cancer model (Hi-Myc) that, based on robust and reproducible kinetics for transitioning from pre-invasive prostatic intraepithelial neoplasia (PIN) to invasive prostate adenocarcinoma (PCa), provides an ideal system to systematically address this question using single-cell analysis. Surprisingly, the transcriptomic profiles of early PIN lesions are indistinguishable from those of late-stage, highly invasive tumor cells, suggesting that MYC activation at the PIN stage establishes a transcriptional program that is fully capable of driving invasion but is restrained by the local tumor microenvironment (TME). Indeed, we find that progression to PCa is associated with progressive infiltration of IL-1{beta}+ tumor-infiltrating macrophages at the PIN stage that, based on immunodepletion and cytokine neutralization experiments, are required for the PIN-to-PCa transition. Mechanistically, IL-1{beta} from macrophages acts directly on prostate fibroblasts, leading to the release of IL-6, which drives invasion by activating IL-6R in tumor cells. Collectively, these findings identify a pro-tumorigenic IL-1{beta}/IL-6 signaling circuit mediated through local macrophages and fibroblasts that unleashes the full oncogenic potential of a cancer driver (MYC) activated at the PIN stage. We also find evidence of this circuit in other (non-MYC-driven) prostate cancer models as well as human prostate and lung adenocarcinoma, with implications for TME-specific targeted therapeutics in early-stage disease.

cancer biology↗

bioRxiv2025

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Treatment-related neuroendocrine prostate cancer (NEPC) is an increasingly frequent mechanism of resistance to androgen receptor pathway inhibitor (ARPI) therapy in prostate adenocarcinoma (PRAD). This lineage transition is dependent on upregulation of the NE-specifying transcription factor ASCL1, typically in a genetic background of RB1 and TP53 loss. Here we identify extracellular matrix-integrin-YAP1/TEAD signaling as a critical brake on NEPC lineage transition. Deletion of Itgb1, the shared B1 subunit required for collagen and laminin-mediated integrin activation, is sufficient to induce ASCL1 and NE lineage gene expression, by activating LATS1/2 kinases with subsequent inactivation of YAP1/TEAD signaling. Conversely, restoration of YAP1/TEAD signaling by pharmacological LATS1/2 inhibition, or by expression of constitutively active YAP1/TAZ mutants, prevents or reverts NEPC lineage transition. NOTCH and AR cooperate with YAP/TEAD to repress ASCL1, such that combined inhibition leads to complete reprograming of PRAD into NEPC in vitro, providing a dynamic platform to dissect the molecular events responsible for lineage transition over time. We find that lineage transition is accompanied by a redistribution of FOXA1 and TEAD cistromes from PRAD to NEPC-specific enhancers and requires the pioneering activity of FOXA1. Thus, extracellular matrix/integrin signaling in the PRAD tumor microenvironment restrains NE lineage plasticity, highlighting a potential path for pharmacological inhibitors in modulating treatment-induced lineage change.

cancer biology↗

bioRxiv2024

PVRL2 Suppresses Anti-tumor Immunity Through PVRIG- and TIGIT-Independent Pathways

PVRL2 is believed to act as an immune checkpoint protein in cancer; however, most insight into PVRL2s role is inferred from studies on its known receptor PVRIG. Here, we directly study PVRL2. PVRL2 levels are high in tumor cells and tumor-derived exosomes. Deletion of PVRL2 in multiple syngeneic mouse models of cancer shows a dramatic reduction in tumor growth that is immune dependent. This effect can be even greater than seen with deletion of PD-L1. PVRL2 functions by suppressing CD8 T and NK cells in the tumor microenvironment. Unexpectedly, the effect of PVRL2 loss on tumor growth remains in the absence of PVRIG. In contrast, PVRIG loss shows no additive effect in the absence of PVRL2. TIGIT blockade combined with PVRL2 deletion results in the greatest reduction in tumor growth. This effect is not recapitulated by the combined deletion of PVRL2 with its paralog PVR, the ligand for TIGIT. These data uncover PVRL2 as a distinct inhibitor of the anti-tumor immune response with functions beyond that of its known receptor PVRIG. Importantly, the data provide a strong rationale for combinatorial targeting of PVRL2 and TIGIT for cancer immunotherapy.

immunology↗

bioRxiv2023

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma

Intratumoral heterogeneity (ITH)--defined as genetic and cellular diversity within a tumor--is linked to failure of immunotherapy and an inferior anti-tumor immune response. The underlying mechanism of this association is unknown. To address this question, we modeled heterogeneous tumors comprised of a pro-inflammatory ("hot") and an immunosuppressive ("cold") tumor population, labeled with YFP and RFP tags respectively to enable precise spatial tracking. The resulting mixed-population tumors exhibited distinct regions comprised of YFP+ (hot) cells, RFP+ (cold) cells, or a mixture. We found that tumor regions occupied by hot tumor cells (YFP+) harbored more total T cells and a higher frequency of Th1 cells and IFN{gamma}+ CD8 T cells compared to regions occupied by cold tumor cells (RFP+), whereas immunosuppressive macrophages showed the opposite spatial pattern. We identified the chemokine CX3CL1, produced at higher levels by our cold tumors, as a mediator of intratumoral macrophage accumulation, particularly immunosuppressive CD206Hi macrophages. Furthermore, we examined the response of heterogeneous tumors to a therapeutic combination of PD-1 blockade and CD40 agonist on a region-by-region basis. While the combination successfully increases Th1 abundance in "cold" tumor regions, it fails to bring overall T cell activity to the same level as seen in "hot" regions. The presence of the "cold" cells thus ultimately leads to a failure of the therapy to induce tumor rejection. Collectively, our results demonstrate that the organization of heterogeneous tumor cells has a profound impact on directing the spatial organization and function of tumor-infiltrating immune cells as well as on responses to immunotherapy.

cancer biology↗

bioRxiv2023

Analysis of evolutionary dynamics and clonal architecture in prostate cancer

The extent to which clinical and genomic characteristics associate with prostate cancer clonal architecture, tumor evolution, and therapeutic response remains unclear. Here, we reconstructed the clonal architecture and evolutionary trajectories of 845 prostate cancer tumors with harmonized clinical and molecular data. We observed that tumors from patients who self-reported as Black had more linear and monoclonal architectures, despite these men having higher rates of biochemical recurrence. This finding contrasts with prior observations relating polyclonal architecture to adverse clinical outcomes. Additionally, we utilized a novel approach to mutational signature analysis that leverages clonal architecture to uncover additional cases of homologous recombination and mismatch repair deficiency in primary and metastatic tumors and link the origin of mutational signatures to specific subclones. Broadly, prostate cancer clonal architecture analysis reveals novel biological insights that may be immediately clinically actionable and provide multiple opportunities for subsequent investigation. Statement of significanceTumors from patients who self-reported as Black demonstrate linear and monoclonal evolutionary trajectories yet experience higher rates of biochemical recurrence. In addition, analysis of clonal and subclonal mutational signatures identifies additional tumors with potentially actionable alterations such as deficiencies in mismatch repair and homologous recombination.

cancer biology↗

bioRxiv2022

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted by metastasis

CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment (TME), recent studies in mice identified responses in lymph nodes (LN) as essential; however, the role of LN in human cancer patients remains unknown. We examined CD8+ T cells in human head and neck squamous cell carcinomas, regional LN, and blood using mass cytometry, single-cell genomics, and multiplexed ion beam imaging. We identified progenitor exhausted CD8+ T cells (Tpex) that were abundant in uninvolved LN and clonally related to terminally exhausted cells in the TME. After anti-PD-L1 immunotherapy, Tpex in uninvolved LN reduced in frequency but localized near dendritic cells and proliferating intermediate-exhausted CD8+ T cells (Tex-int), consistent with activation and differentiation. LN responses coincided with increased circulating Tex-int. In metastatic LN, these response hallmarks were impaired by immunosuppressive cellular niches. Our results identify important roles for LN in anti-tumor immune responses in humans.

immunology↗

bioRxiv2021

Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics

Given the growing number of clinically integrated cancer single-cell transcriptomic studies, robust differential enrichment methods for gene signatures to dissect tumor cellular states for discovery and translation are critical. Current analysis strategies neither adequately represent the hierarchical structure of clinical single-cell transcriptomic datasets nor account for the variability in the number of recovered cells per sample, leading to results potentially confounded by sample-driven biology with high false positives instead of accurately representing true differential enrichment of group-level biology (e.g., treatment responders vs. non-responders). This problem is especially prominent for single-cell analyses of the tumor compartment, because high intra-patient similarity (as opposed to inter-patient similarity) results in stricter hierarchical structured data that confounds enrichment analysis. Furthermore, to identify signatures which are truly representative of the entire group, there is a need to quantify the robustness of otherwise statistically significant signatures to sample exclusion. Here, we present a new nonparametric statistical method, BEANIE, to account for these issues, and demonstrate its utility in two cancer cohorts stratified by clinical groups to reduce biological hypotheses and guide translational investigations. Using BEANIE, we show how the consideration of sample-specific versus group biology greatly decreases the false positive rate and guides identification of robust signatures that can also be corroborated across different cell type compartments.

bioinformatics↗

bioRxiv2021

Sex Chromosome Heteromorphism and the Fast-X Effect in Poeciliids

Accelerated rates of sequence evolution on the X chromosome compared to autosomes, known as Fast-X evolution, have been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast-X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across Poeciliid fish species. The common guppy, Poecilia reticulata, Endlers guppy, P. wingei, swamp guppy, P. picta, and para guppy, P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. This sex chromosome system is absent in recent outgroups. We combined analyses of sequence divergence and polymorphism data across Poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast-X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast-X evolution, in P. picta and P. parae, while no change in the rate of evolution of X-linked relative to autosomal genes in P. reticulata. In P. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test different models for the origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast-X and suggests a single, recent origin of the sex chromosome system in this clade.

evolutionary biology↗

bioRxiv2020

Deep immune profiling reveals targetable mechanisms of immune evasion in checkpoint blockade-refractory glioblastoma

BackgroundGlioblastoma (GBM) is refractory to checkpoint blockade immunotherapy (CPI). We sought to determine to what extent this immune evasion is due to intrinsic properties of the tumor cells versus the specialized immune context of the brain, and if it can be reversed. MethodsWe used CyTOF mass cytometry to compare the tumor immune microenvironments (TIME) of human tumors that are generally CPI-refractory (GBM and sarcoma) or CPI-responsive (renal cell carcinoma), as well as mouse models of GBM that are CPI-responsive (GL261) or CPI-refractory (SB28). We further compared SB28 tumors grown intracerebrally versus subcutaneously to determine how tumor site affects TIME and responsiveness to dual CTLA-4/PD-1 blockade. Informed by these data, we explored rational immunotherapeutic combinations. ResultsCPI-sensitivity in human and mouse tumors was associated with increased T cells and dendritic cells, and fewer myeloid cells, in particular PD-L1+ tumor associated macrophages. The SB28 mouse model of GBM responded to CPI when grown subcutaneously but not intracerebrally, providing a system to explore mechanisms underlying CPI resistance in GBM. The response to CPI in the subcutaneous SB28 model required CD4 T cells and NK cells, but not CD8 T cells. Recombinant FLT3L expanded dendritic cells, improved antigen-specific T cell priming, and prolonged survival of mice with intracerebral SB28 tumors, but at the cost of increased Tregs. Targeting PD-L1 also prolonged survival, especially when combined with stereotactic radiation. ConclusionsOur data suggest that a major obstacle for effective immunotherapy of GBM is the low antigenicity of the tumor cells coupled with poor antigen presentation in the brain, rather than intrinsic immunosuppressive properties of GBM tumor cells. Deep immune profiling identified dendritic cells and PD-L1+ tumor-associated macrophages as promising targetable cell populations, which was confirmed using therapeutic interventions in vivo. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/404939v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@bdd0e4org.highwire.dtl.DTLVardef@1dd335forg.highwire.dtl.DTLVardef@157bfa6org.highwire.dtl.DTLVardef@1e76151_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefIn mice and humans, tumors that were sensitive to checkpoint blockade had consistent immunological features. A mouse model of glioma that is refractory to checkpoint blockade was sensitized by increasing antigen presentation through a variety of approaches.

cancer biology↗

bioRxiv2020

Transcriptional mediators of treatment resistance in lethal prostate cancer

Metastatic castration resistant prostate cancer (mCRPC) is primarily treated with therapies that prevent transcriptional activity of the androgen receptor (AR), cause DNA damage, or prevent cell division. Clinical resistance to these therapies, including second-generation androgen-targeting compounds such as enzalutamide and abiraterone, is nearly universal. Other treatment modalities, including immune checkpoint inhibitors, have provided minimal benefit except in rare subsets of patients1,2. Both tumour intrinsic and extrinsic cellular programs contributing to therapeutic resistance remain areas of active investigation. Here we use full-length single-cell RNA-sequencing (scRNA-seq) to identify the transcriptional states of cancer and immune cells in the mCRPC microenvironment. Within cancer cells, we identified transcriptional patterns that mediate a significant proportion of inherited risk for prostate cancer, extensive heterogeneity in AR splicing within and between tumours, and vastly divergent regulatory programs between adenocarcinoma and small cell carcinoma. Moreover, upregulation of TGF-{beta} signalling and epithelial-mesenchymal transition (EMT) were both associated with resistance to enzalutamide. We found that some lymph node metastases, but no bone metastases, were heavily infiltrated by dysfunctional CD8+ T cells, including cells undergoing dramatic clonal expansion during enzalutamide treatment. Our findings suggest avenues for rational therapeutic approaches targeting both tumour-intrinsic and immunological pathways to combat resistance to current treatment options.

genomics↗

bioRxiv2019

TCR convergence in individuals treated with immune checkpoint inhibition for cancer

Tumor antigen-driven selection may expand T cells having T cell receptors (TCRs) of shared antigen specificity but different amino acid or nucleotide sequence in a process known as TCR convergence. Substitution sequencing errors introduced by TCR{beta} (TCRB) repertoire sequencing may create artifacts resembling TCR convergence. Given the anticipated differences in substitution error rates across different next-generation sequencing platforms, the choice of platform could be consequential. To test this, we performed TCRB sequencing on the same peripheral blood mononuclear cells (PBMC) from individuals with cancer receiving anti-CTLA-4 or anti-PD-1 using an Illumina-based approach and an Ion Torrent-based approach. While both approaches found similar TCR diversity, clonality, and clonal overlap, we found that Illumina-based sequencing resulted in higher TCR convergence than with the Ion Torrent approach. Using the latter approach, we found that clonality and convergence independently predicted response and could be combined to improve the accuracy of a logistic regression classifier. These results demonstrate the importance of the sequencing platform in assessing TCRB convergence.

cancer biology↗