Biology subjects

Wong, C. W.

Publications and source records attributed to Wong, C. W..

8 recordsLinked to original sources

bioRxiv2025

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

BackgroundAberrant enhancer dynamics play a critical role in the initiation and progression of colorectal cancer (CRC). BRAFV600E-mutated metastatic CRC may be a unique subtype, exhibiting a strong epigenetic phenotype. Interestingly, bromodomain 2, a reader protein for H3K27ac-marked enhancers, was found to be synthetically lethal in CRC with BRAF + EGFR inhibition. DesignWe evaluated the effectiveness of targeting aberrant enhancers with bromodomain and extraterminal (BET) + MAPK pathway inhibitors in patient-derived xenograft models of metastatic CRC, followed by comprehensive profiling of transcriptomic and chromatin dynamics upon BET inhibitor combination treatment. ResultsThe combination of BET and standard MAPK inhibitors has demonstrated improved efficacy against BRAFV600E CRC and selective improvements against RAS-mutant CRC in vivo. We showed that BET + MAPK inhibition induced a profound downregulation of the MAPK signaling pathway compared to MAPK inhibition alone. The loss of activation signal on enhancers, as determined by H3K27ac, led to dysregulation of core-regulatory circuitries of CRC, especially loss of the auto-regulatory mechanism of the MAPK downstream E26 transformation-specific transcription factor family. Single nucleus multiome (RNA + ATAC) sequencing further distinguished differential transcriptomic and chromatin dynamics at cell type levels. Profound downregulation of well-differentiated cell types confirmed deep inhibition of MAPK signaling and downstream transcription factors. On the other hand, dedifferentiated cell populations were abundant after MAPK or combination inhibition, suggesting therapy-induced cell state switching and adaptation. ConclusionWe are evaluating BET + BRAF + EGFR inhibition in patients with treatment-refractory BRAFV600E metastatic CRC. ClinicalTrial.gov identifier: NCT06102902. What is already known on this topicEnhancer aberrations emerge as critical epigenetic features in the progression of colorectal cancer (CRC). However, the dynamics of active enhancer and the therapeutic potential of enhancer blockade, particularly in CRC tumors with BRAFV600E mutation, is not well understood. What this study addsThis study demonstrates improved efficacy of BET inhibitor combination therapies in diverse patient-derived models and reveals epigenetic reprogramming driven cellular plasticity in BRAFV600E-mutated CRC. How this study might affect research, practice or policyOur findings support treatment with BET + BRAF + EGFR inhibitors for patients with BRAFV600E-mutant mCRC [NCT06102902]. This study also highlights the potential of combining epigenetic agents to standard targeted therapy, offering a novel treatment option for this subset of patients.

cancer biology↗

bioRxiv2025

Adaptive Plasticity Tumor Cells Modulate MAPK-Targeting Therapy Response in Colorectal Cancer

MAPK pathway inhibitors (MAPKi) are increasingly used in the treatment of advanced colorectal cancer, but often produce short-lived responses in patients. Although acquired resistance by de novo mutations in tumors have been found to reduce response in some patients, additional mechanisms underlying the limited response durability of MAPK targeting therapy remain unknown. Here, we denote new contributory tumor biology and provide insight on the impact of tumor plasticity on therapy response. Analysis of MAPKi treated patients revealed activation of stemness programs and increased ASCL2 expression, which are associated with poor outcomes. Greater ASCL2 with MAPKi treatment was also seen in patient-derived CRC models, independent of driver mutations. We find ASCL2 denotes a distinct cell population, arising from phenotypic plasticity, with a proliferative, stem-like phenotype, and decreased sensitivity to MAPKi therapy, which were named adaptive plasticity tumor (APT) cells. MAPK pathway suppression induces the APT phenotype in cells, resulting in APT cell enrichment in tumors and limiting therapy response in preclinical and clinical data. APT cell depletion improved MAPKi treatment efficacy and extended MAPKi response durability in mice. These findings uncover a cellular program that mitigates the impact of MAPKi therapies and highlights the importance of addressing tumor plasticity to improve clinical outcomes.

cancer biology↗

bioRxiv2024

Combined PARP14 Inhibition and PD-1 Blockade Promotes Cytotoxic T Cell Quiescence and Modulates Macrophage Polarisation in Relapsed Melanoma

Programmed Cell Death 1 (PD-1) signaling blockade effectively restores immune surveillance to treat melanoma. However, chronic interferon-gamma (IFN{gamma}) -driven immune homeostatic mechanisms in melanoma cells contribute to immune evasion and acquired resistance. We previously demonstrated that poly ADP ribosyl polymerase 14 (PARP14), an IFN{gamma}-responsive gene product, in part mediates IFN{gamma}-driven resistance, as its inhibition prolonged PD-1 blockade responses in preclinical models. Nevertheless, PARP14 inhibition alone could not achieve full tumor clearance, indicating additional resistance mechanisms. Herein, we identify a robust PARP14 catalytic inhibitor (PARP14i) gene signature associated with improved patient survival. We elucidate immune and tumor cell adaptations to PARP14 inhibition combined with PD-1 blockade using preclinical models. This combination therapy suppressed tumor-associated macrophages while increasing pro-inflammatory memory macrophages. Notably, it preserved cytotoxic T cell function by inducing a quiescent state, mitigating terminal exhaustion. Despite enhancing immune responses, adaptive resistance mechanisms emerged in tumor cells, engaging alternative immune evasion pathways. These findings indicate that this combination therapy primes immune cells for further therapeutic intervention, providing a promising strategy to overcome resistance and optimize treatment outcomes. SummaryWhile immune checkpoint inhibitors, such as -PD-1 therapy, provide significant clinical benefits, many tumors develop resistance and relapse. Re-treatment with -PD-1 often fails because T cells lose their function (a process called exhaustion), and immune-suppressing cells like tumor-associated macrophages (TAMs) increase in the tumor environment, enabling tumors to evade immune attack. Recent studies have shown that a small molecule inhibitor of PARP14 can restore sensitivity to -PD-1 therapy by remodeling the tumor environment. This includes increasing immune cell infiltration and improving antigen presentation, which helps the immune system recognize tumor cells. Using single-cell RNA sequencing, we discovered that this therapy induces a new state of T cell dormancy, where cytotoxic T cells temporarily stop attacking but retain the potential to be reactivated by additional treatments. This finding opens new opportunities to sustain immune responses and improve outcomes for patients who relapse after immunotherapy. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/615178v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e6dcf4org.highwire.dtl.DTLVardef@1b44548org.highwire.dtl.DTLVardef@309cb1org.highwire.dtl.DTLVardef@17f6202_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance

Adaptive resistance limits immune checkpoint blockade therapy (ICBT) response duration and magnitude. Interferon {gamma} (IFN{gamma}), a critical cytokine that promotes cellular immunity, also induces adaptive resistance to ICBT. Using syngeneic mouse tumour models, we confirmed that chronic IFN{gamma} exposure confers resistance to anti-Programmed cell death protein 1 (-PD-1) therapy. We identified consistent upregulation of poly-ADP ribosyl polymerase 14 (PARP14) in both chronic IFN{gamma}-treated cancer cells and patient melanoma with elevated IFNG expression. Knockdown or pharmacological inhibition of PARP14 increased effector T cell infiltration into tumours derived from cells pre-treated with IFN{gamma} and decreased the presence of regulatory T cells, leading to restoration of -PD-1 sensitivity. Finally, we determined that tumours which spontaneously relapsed following -PD-1 therapy could be re-sensitised upon receiving PARP14 inhibitor treatment, establishing PARP14 as an actionable target to reverse IFN{gamma}-driven ICBT resistance.

cancer biology↗

bioRxiv2020

Single-cell regulatory landscape and disease vulnerability map of adult Macaque cortex

Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell chromatin accessibility (single-cell ATAC) and transcriptomic data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult cynomolgus monkey brain, and integrated this dataset with Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.

neuroscience↗

bioRxiv2020

Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

Stopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans. Bullet pointsO_LIWe generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19. C_LIO_LIACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2. C_LIO_LIACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities. C_LIO_LIWe unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry. C_LI

cell biology↗

bioRxiv2018

In Vitro Expansion of Keratinocytes on Human Dermal Fibroblast-Derived Matrix Retains Their Stem-Like Characteristics

The long-term expansion of keratinocytes under serum- and feeder free conditions generally results in diminished proliferation and an increased commitment to terminal differentiation. Here we present a serum and xenogeneic feeder free culture system that retains the self-renewal capacity of primary human keratinocytes. In vivo, the tissue microenvironment is a major contributor to determining cell fate and a key component of the microenvironment is the extracellular matrix (ECM). Accordingly, acellular ECMs derived from human dermal fibroblasts, cultured under macromolecular crowding conditions to facilitate matrix deposition and organisation, were used as the basis for a xenogeneic-free keratinocyte expansion protocol. A phospholipase A2 decellularisation procedure produced matrices which, by proteomics analysis, resembled in composition the core matrix proteins of skin dermis. On these ECMs keratinocytes proliferated rapidly, retained their small size, expressed p63, did not express keratin 10 and rarely expressed keratin 16. Moreover, the colony forming efficiency of keratinocytes cultured on these acellular matrices was markedly enhanced. Collectively these data indicate that the dermal fibroblast-derived matrices support the in vitro expansion of keratinocytes that maintained stem-like characteristics under serum free conditions.

cell biology↗

bioRxiv2017

Template-based prediction of vigilance fluctuations in resting-state fMRI

Changes in vigilance or alertness during a typical resting state fMRI scan are inevitable and have been found to affect measures of functional brain connectivity. Since it is not often feasible to monitor vigilance with EEG during fMRI scans, it would be of great value to have methods for estimating vigilance levels from fMRI data alone. A recent study, conducted in macaque monkeys, proposed a template-based approach for fMRI-based estimation of vigilance fluctuations. Here, we use simultaneously acquired EEG/fMRI data to investigate whether the same template-based approach can be employed to estimate vigilance fluctuations of awake humans across different resting-state conditions. We first demonstrate that the spatial pattern of correlations between EEG-defined vigilance and fMRI in our data is consistent with the previous literature. Notably, however, we observed a significant difference between the eyes-closed (EC) and eyes-open (EO) conditions finding stronger negative correlations with vigilance in regions forming the default mode network and higher positive correlations in thalamus and insula in the EC condition when compared to the EO condition. Taking these correlation maps as \"templates\" for vigilance estimation, we found that the template-based approach produced fMRI-based vigilance estimates that were significantly correlated with EEG-based vigilance measures, indicating its generalizability from macaques to humans. We also demonstrate that the performance of this method was related to the overall amount of variability in a subjects vigilance state, and that the template-based approach outperformed the use of the global signal as a vigilance estimator. In addition, we show that the template-based approach can be used to estimate the variability across scans in the amplitude of the vigilance fluctuations. We discuss the benefits and tradeoffs of using the template-based approach in future fMRI studies.

neuroscience↗