Biology subjects

Vu, H.

Publications and source records attributed to Vu, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Overexpression of miR-424(322)/-503 induces severe dilated cardiomyopathy by regulating the fatty acid oxidation gene expression program

Fatty acid oxidation (FAO) is a major energy source in the adult heart, and disruption of cardiac metabolism is closely associated with heart failure. Here, we investigated the effects of cardiac-specific overexpression of the H19X-encoded miR-424(322)/-503 cluster using an inducible transgenic mouse model. Sustained miR-424(322)/-503 overexpression caused rapid metabolic and functional deterioration, with early impairment of fatty acid oxidation. Short-term induction reduced FAO activity and downregulated genes involved in lipid metabolism, while glycolytic enzyme activity remained largely unchanged. Continued miR-424(322)/-503 expression subsequently led to severe dilated cardiomyopathy characterized by ventricular dilation, wall thinning, fibrosis, reduced contractility, and high mortality. Importantly, disease progression was dependent on the level and duration of miR-424(322)/-503 expression, as intermittent or lower-dose induction delayed cardiac dysfunction and prolonged survival. Withdrawal of miR-424(322)/-503 expression after the onset of dysfunction promoted substantial functional recovery. Together, these findings identify miR-424(322)/-503 as a potent regulator of cardiac metabolic reprogramming that disrupts fatty acid metabolism and drives progressive heart failure.

molecular biology↗

bioRxiv2026

Medulloblastoma Forms Symbiotic Metabolic Partnerships with Macrophages to Establish Leptomeningeal Metastases

Leptomeningeal metastases are the primary source of morbidity and mortality for pediatric medulloblastoma patients. Due to limited surgical sampling of metastases in patients, little is understood of the mechanisms of metastasis. Here, we identify biologically distinct quiescent small metastases (designated as micrometastases) and mitotically active larger metastases (macrometastases). Macrometastases are more metabolically active than micrometastases and contain higher levels of lipids, particularly cholesterol. Macrometastases secrete CXCL12, which attracts lipid-laden macrophages into the tumor. Lipid-laden macrophages upregulate the cholesterol transporter ABCG1, promoting the efflux of free cholesterol, which is then taken up by tumor cells via the HDL receptor SCARB1. CXCL12-driven macrophage recruitment and exogenous cholesterol are sufficient and necessary to drive progression of medulloblastoma leptomeningeal metastases in vivo. High fat diets drive metastatic progression in vivo. Dietary or pharmacological interventions targeting the CXCL12-SCARB1-cholesterol axis represent therapeutic strategies to either prevent or treat medulloblastoma leptomeningeal metastases.

cancer biology↗

bioRxiv2026

Life-cycle trajectory inference links temperature-gated progenitors to reproductive fate

Temperature shapes reproductive strategies across animals, yet how individuals switch between sexual and asexual reproduction remains unknown. We establish the planarian Phagocata morgani as a model for temperature-dependent reproductive plasticity and adapt multiplexed single-cell transcriptomics to profile >1 million nuclei from >300 animals across body sizes and temperatures. Leveraging individual variation in cell composition, we reconstruct an organism-wide trajectory that bifurcates toward alternative reproductive fates. Temperature extremes constrain worms to one fate, whereas intermediate conditions permit probabilistic commitment to either. At the bifurcation, temperature gates a stem cell pool: warmth suppresses differentiation and promotes progenitor accumulation, whereas cold transcriptionally activates this pool for de novo sexual organogenesis. These findings reveal how environmental inputs act on stem cells to couple body size, temperature, and reproductive fate.

Developmental Biology↗

bioRxiv2026

EpiATLAS - a reference for human epigenomic research

The sequence of the human genome provides a foundation for understanding cellular processes in health and disease1. The organisation of this primary genetic information into cell-specific structure and function is critical to understanding the cell type-specific interpretation and execution of the genome. Epigenetic processes are essential for packaging and higher-level functional organisation of the genome, and changes therein are increasingly recognised as contributors to human disease. Building on primary data generated by multinational consortia, the International Human Epigenome Consortium2 (IHEC) has uniformly processed a collection of more than 2000 comprehensive human reference epigenomes, collectively referred to as EpiATLAS. This effort involved the development of standardised molecular and bioinformatics protocols, metadata models, and analytical tools to manage, integrate, display, and share vast amounts of epigenomic data. This includes the creation of a publicly available Epigenome Reference Registry, which provides a system for accessing protected human subject datasets and facilitates open searching of de-identified samples and experimental data. The integrated EpiATLAS ecosystem and its comprehensive human reference epigenome maps provide an unprecedented resource for the biosciences, expanding the annotated epigenomic landscape while uncovering previously unappreciated relationships among regulatory layers and revealing how epigenetic inputs underpin fundamental cellular functions and disease associations.

genomics↗

bioRxiv2026

Potassium-Selective Nanoelectrode Arrays for Single-Cell Profiling of human iPSC-Derived Cardiomyocytes

Potassium ion (K) dynamics are central to cardiac electrophysiology, with early disruptions in K flux often preceding arrhythmia and contractile dysfunction. However, current sensing technologies, such as patch-clamp, Microelectrode arrays (MEAs), and fluorescent indicators, either lack chemical specificity for K or are unsuitable for long-term, single-cell analysis. Conventional ion-selective electrodes (ISEs), while more selective, are limited by bulk-phase design and poor spatial resolution. To address these limitations, we present KINESIS (K-Ion Nano-Electrode Selective Interface System), a nanofabricated, cell-compliant platform that enables direct, label-free potentiometric measurement of K gradients with subcellular precision. KINESIS features high-aspect-ratio nanopillars coated with a valinomycin-based K recognition membrane, forming a stable, non-invasive interface with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). This architecture allows localized, Nernstian sensing of K efflux or depletion without disrupting cell membranes. Pharmacological validation shows distinct potential shifts in response to caffeine and ouabain. KINESIS thus offers a highly selective, spatially resolved approach for studying K handling in cardiotoxicity screening and patient-specific disease modeling.

pharmacology and toxicology↗

bioRxiv2026

Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma

Single-cell and spatial transcriptomic studies have provided insights into the developmental origins and intratumoural heterogeneity of SHH medulloblastoma (SHH-MB) and suggested how targeted drugs such as CDK4/6 inhibitors remodel tumour ecosystems, yet the interplay between local drug exposure, metabolism, cell state, and drug resistance remains poorly understood. Here we developed a same-section spatial pharmaco-multiomics framework that integrates MALDI-MSI-based spatial metabolomics with Visium whole-transcriptome profiling and high-resolution Xenium imaging to map palbociclib distribution, metabolite landscapes, and transcriptional programs within the same histological contexts of an SHH-MB PDOX model and primary human tumours. Palbociclib-rich tumour bulk exhibited broad suppression of E2F-driven proliferation and a shift toward neuronal differentiation, corroborating and extending prior findings. In contrast, drug-poor tumour-brain interfaces and perivascular regions retained E2F-high proliferative states and were enriched for mesenchymal-like stromal cells and ECM-remodelling genes, indicating anatomically constrained reservoirs of tolerance. Spatial metabolomics linked these interface niches to ganglioside (GM2) and sphingomyelin enrichment, while differentiated, drug-exposed regions displayed phosphatidylcholine, phosphatidic-acid signatures consistent with neuronal maturation. Integrated pathway analysis further revealed a "mitochondrial tuning" program, with upregulation of histidine, folate/one-carbon, CoA, and lipoate metabolism with redox and oxidative-phosphorylation support. These signatures were specific to therapy-exposed border cells. Rare palbociclib-positive, E2F-high resistant spots additionally exhibited mitotic checkpoint and DNA-repair signatures, implying a drug-induced resistance axis independent of scarcity. Together, our study provides a generalisable same-section spatial pharmaco-multiomics pipeline and a spatially resolved model of CDK4/6 response, nominating interface-focused metabolic and cell-intrinsic vulnerabilities for combination therapy.

cancer biology↗

bioRxiv2026

Whole-genome profiling of native 5-hydroxymethylation in human neurons with long-read sequencing

The 5-hydroxymethylcytosine (5hmC) modification of DNA is particularly prevalent in neurons and thereby a hallmark of the brains epigenetic landscape. While 5mC DNA methylation is a well-known player in genome stability and transcriptional regulation, the role of 5hmC remains largely unknown. Here, we used long-read Oxford Nanopore Technology (ONT) to profile whole-genome, native 5mC and 5hmC levels in sorted neuronal nuclei samples from human post-mortem brain tissue. We applied different models for DNA modification calling and compared with array-based 5mC and 5hmC levels derived from the same samples, demonstrating high sample-wise correlations. Annotation across genomic and regulatory features, as well as chromatin states, generated by the International Human Epigenome Consortium, revealed high levels of 5hmC in introns, actively transcribed genes and (distal) enhancers. Pathway analysis of genes with high levels of 5hmC (> 60%) were enriched in neuron-related terms, with functional variety when stratifying across chromatin states. Analysis of transcription factor motifs in highly methylated regions, demonstrated 5hmC- and 5mC-specific enrichment affecting downstream regulatory networks. Altogether, our study demonstrates the potential of ONT to characterize whole-genome, native 5hmC and 5mC DNA modifications in human neurons, specifically highlighting the enrichment of 5hmC in actively transcribed regions and enhancers in the human brain.

neuroscience↗

bioRxiv2025

Genetic Ablation and Multi-Omics Profiling Reveal CEP55 as a Key Driver of Tumorigenesis in Diverse Cancer Models

BackgroundCEP55 is a centrosomal protein with emerging oncogenic roles. It is overexpressed in many cancers, where it drives genomic instability, phenocopies PTEN loss and hyperactivates the PI3K/AKT pathway, thereby promoting aggressive and therapy-resistant tumors. MethodsWe developed an inducible Cep55 knockout (KO) mouse model as well as generated primary, immortalized (SV40), and transformed (E1A/Ras) mouse embryonic fibroblasts (MEFs) for functional and proteomic assays. Tumorigenesis was studied using E1A/Ras MEF transplantation and a Pten-deficient genetically engineered mouse model (GEMM). Multi-omics apparatus including proteomics, and spatial transcriptomics, histopathology, immunobloting and functional assays were employed to elucidate underlying mechanisms. Findings were cross-validated using human cancer datasets. ResultsCep55 ablation remodeled the extracellular matrix (ECM), disrupted integrin and oncogenic signaling, reduced AKT/ERK activation, and induced stress pathways. Cep55 knockouts (KO) cells showed impaired proliferation, migration, invasion, and adhesion. In vivo, unlike the embryonic lethality observed in constitutive KOs, the inducible Cep55 deletion was well-tolerated in adult mice. Strikingly, tumors derived from Cep55-null EIA/RAS-transformed MEFs exhibited delayed onset and progression. In the genetically engineered cancer-prone mouse model, Cep55 deletion on a Pten-deficient background led to a greater than seven-fold increase in median survival. Spatial transcriptomics on cancerous tissues revealed that CEP55 regulates ECM remodeling, integrin expression, trafficking, and cell adhesion, supporting its critical role in tumor progression to metastasis. ConclusionCEP55 is dispensable for adult homeostasis but essential for tumorigenesis, especially with PTEN loss. Its deletion suppresses transformation, delays tumor growth, and prolongs survival, supporting CEP55 as a therapeutic target in PTEN-deficient cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/685219v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@3d81e8org.highwire.dtl.DTLVardef@1bd5a7org.highwire.dtl.DTLVardef@167ecf3org.highwire.dtl.DTLVardef@1f57b95_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma - the three major skin cancers - collectively comprise over 70% of all cancer cases. Despite their prevalence, much understanding of cellular interactions in the skin cancer microenvironment is needed, both in the outer skin layer where the cancer originates and at the deeper junctional and dermal layers into which it progresses. To address this gap, we integrated 12 complementary spatial and single-cell technologies to generate orthogonally-validated cell signatures, spatial maps, and interactomes for cSCC, BCC, and melanoma. Through comprehensive comparisons and integrating these spatial methods, we provided practical benchmarking guidelines for experimental design and analysis. By identifying keratinocyte cancer cells and melanomas, we found distinct signatures of these cells compared to non-cancer keratinocytes and melanocytes. Spatial integration of transcriptomics, proteomics and glycomics uncovered cancer niches enriched for cancer initiating cells (melanocytes or keratinocytes) and fibroblast and T-cell (MKFT) clusters, with altered tyrosine and pyrimidine metabolism. Ligand-receptor analysis across >700 cell-type combinations and >1.5 million interactions highlighted key roles for CD44, integrins, and collagens, with CD44-FGF2 emerging as a potential therapeutic target. Consistently, melanoma showed strong MFT interactions, validated by Opal Polaris, RNAScope, Proximal Ligation Assay and two additional single-cell spatial platforms (making a total of 14 technologies). For population-scale generalisation, genetic associations from >500,000 individuals were mapped onto spatial skin tissues, identifying SNPs enriched in domains containing melanocytes and T cells and their ligand-receptor pairs, shedding light on functional mechanisms linking genetic heritability to cells within cancer tissue. We built an interactive multiomics resource for exploring spatially-resolved molecular signatures and cellular crosstalk in skin cancer, available at https://skincanceratlas.com.

cancer biology↗

bioRxiv2025

Souporcell3: Robust Demultiplexing for High-Donor Single-Cell RNA-seq Datasets

MotivationAccurate demultiplexing of pooled single-cell RNA-seq (scRNAseq) data is critical for large-scale studies. However, existing methods like vireo, while effective up to [~]16 donors, often struggle with poor clustering due to local optima as donor numbers rise. In high-donor scenarios, overlapping genotypes, a dense genotype space, and increased doublet formation make demultiplexing challenging, requiring methods that are robust to sparse, high-dimensional data and maintain reliable accuracy even as sample complexity grows. ResultsWe present an enhanced version of souporcell capable of demultiplexing up to 64 donors. The method uses 10x merge for initialization, K-Harmonic Means for robust clustering, and iterative refinement with reinitialization of low-quality clusters and locking of high-quality ones. Compared to vireo, vireo with overclustering, and the original souporcell, our approach completely eliminates duplicate clusters and achieves consistently high Adjusted Rand Index (ARI) scores across various doublet rates, demonstrating improved accuracy and scalability. AvailabilitySouporcell3 source code and documentation are released on GitHub: https://github.com/wheaton5/souporcell

bioinformatics↗

bioRxiv2025

Spatial Transcriptomic Signature of Progressive Fibrosis in Human MASLD: Role of Senescence and Metabolic Reprogramming.

Granular detail about the location and nature of liver cell interactions and the metabolic, inflammatory and fibrogenic pathways driving progressive fibrosis in metabolic dysfunction-associated steatotic liver disease (MASLD) is needed to deliver novel therapeutic targets. Here we used spatial transcriptomic data from human MASLD liver biopsies to identify the major cell types and their potential interconnected activities within specific tissue regions across the spectrum of MASLD. Gene expression data were generated using 10X Genomics Visium technology from 33 formalin-fixed paraffin-embedded liver biopsy samples and overlaid with annotated anatomical regions. Differential gene expression (DEG) and pathway analyses, cellular deconvolution and ligand-receptor interactions were conducted for each annotated anatomical category, with specific protein expression validated using CODEX spatial proteomics and immunohistochemistry staining. Unsupervised gene expression data grouped the annotated spots into 2 main clusters enriched for early/intermediate vs late fibrosis and transcriptome-based cellular deconvolution was well aligned with annotated histopathological features. In addition to extracellular matrix/receptor interactions and immune cell recruitment and trafficking, several genes encoding immunoglobulins were highly upregulated in late-stage fibrosis and were spatially associated with a senescence signature. Upregulated DEGs for early/intermediate-stage fibrosis were significantly enriched for metabolic pathways, oxidative phosphorylation and fatty acid metabolism. In contrast glycolysis genes were strongly co-expressed with late stage fibrosis. MASLD progression is accompanied by a decline in normal liver metabolic function and significant reprogramming of metabolic fuel utilisation. The spatial association of a senescence signature with expression of genes encoding immunoglobulins and complement has been linked to aging and is associated with progressive fibrosis. This work provides a valuable discovery dataset spanning different stages of human liver fibrosis and highlights the complex crosstalk between metabolic perturbations and inflammation underpinning fibrosis progression.

genomics↗

bioRxiv2024

SpaMTP: Integrative Statistical Analysis and Visualisation of Spatial Metabolomics and Transcriptomics data.

The ability to spatially measure multi-modal data provides an unprecedented opportunity to comprehensively explore molecular regulation at transcriptional, translational and metabolic levels to acquire insights on cellular activities underpinning health and disease. However, there is currently a lack of analytical tools to integrate complementary information across different spatial-omics data modalities, particularly with respect to spatial metabolomics data, which is becoming increasingly invaluable. We introduce SpaMTP, a versatile software that implements an end-to-end integrative analysis of spatial metabolomics and transcriptomics data. Based in R, SpaMTP bridges processing functionalities for metabolomics data from Cardinal with user-friendly cell-centric analyses implemented in Seurat. Furthermore, SpaMTPs comprehensive analysis pipeline covers (1) automated mass-to-charge ratio (m/z) metabolite annotation; (2) a wide range of metabolite-gene based downstream statistical analyses including differential expression, pathway analysis, and correlation analysis; (3) integrative spatial-omics analysis; and (4) a suite of visualisation functions. For flexibility and interoperability, SpaMTP includes various functions for data import/export and object conversion, enabling seamless integration with other R and Python packages. We demonstrated the utility of SpaMTP to draw new biological understandings through analysing two biological system. We believe this software and implemented methods will be broadly utilised in spatial multi-omics and spatial metabolomics analyses.

bioinformatics↗

bioRxiv2024

Spatial analysis of HPV associated cervical intraepithelial neoplastic tissues demonstrate distinct immune signatures associated with cervical cancer progression

Cervical cancer remains the fourth most common cancer affecting women worldwide, and incidences of other HPV-related cancers continue to rise. For the development of effective prevention strategies in high-risk patients, we aimed to better understand the roles of inflammatory pathways and the tumour microenvironment as the main driver of progression to malignancy in HPV-infected tissues. We analysed the spatial organisation of seven samples of HPV+ high-grade squamous intraepithelial lesion (HSIL) and cervical intraepithelial neoplasia 3 (CIN3), comparing tumour heterogeneity and immune microenvironments between pre-malignant (neoplastic) and adjacent cervical tissues. We observed evidence of immune suppression within the neoplastic regions across all samples and identified distinct immune clusters for each dysplastic lesion. Previous single-cell data analyses in an HPV16 E7 oncoprotein-driven transgenic mouse model suggested a potential role for IL34-CSF1R signalling in immune modulation, where low IL34 expression was associated with Langerhans cell dysfunction, and, in cervical cancer, with poor patient outcome. Here, we observed that IL34-CSF1R co-expression was absent within HPV-associated neoplastic tissues but present in adjacent normal tissue regions. Additionally, we identified enrichment of an M2 gene signature in neoplastic tissue, while adjacent tissue was enriched with a pro-inflammatory M1 gene signature. Our findings provide bio-pathological insights into the spatial cellular and molecular mechanisms underlying HPV-associated cervical cancer immune regulation and suggest a strategy to modulate the immune system in HPV-positive neoplastic cervical and other tissues.

genomics↗

bioRxiv2024

Unraveling lncRNA Diversity at a Single Cell Resolution and in a Spatial Context across Different Cancer Types

Long non-coding RNAs (lncRNAs) play pivotal roles in gene regulation and disease, including cancer. Overcoming the limitations of lncRNA analysis with bulk data, we analyzed single-cell and spatial transcriptomics data to uncover 354937 novel lncRNAs and their functions across 13 cancer types. LncRNA functions were assessed by identifying their cell-type specificity and distinct spatial distributions across different tissue regions. First, lncRNAs were computationally validated by comparing to existing databases, and experimentally validated using spatial long read sequencing methods. Further, genome-wide computation of spatial-autocorrelation identified coexpression of lncRNAs with cancer-associated protein coding genes across the tissue. Additionally, genomic co-localization of lncRNAs with regulatory features and disease-associated genetic variants suggest possible functional association. The identified lncRNAs were analyzed for responses to immunotherapy and prognostic value, revealing cancer-outcome associated lncRNAs. We have made this novel resource available as an open website SPanC-Lnc hosted on AWS cloud to serve as a pan-cancer atlas of single cell- and spatially-resolved lncRNAs. These can complement established biomarkers because they reflect the unique characteristics of specific cell populations within tumors, offering new insights into disease progression and treatment response.

cancer biology↗

bioRxiv2024

Interferon-Induced PARP14-Mediated ADP-Ribosylation in p62 Bodies Requires an Active Ubiquitin-Proteasome System

Biomolecular condensates are cellular compartments without enveloping membranes, enabling them to dynamically adjust their composition in response to environmental changes through post-translational modifications. A recent study has revealed that interferon-induced ADP-ribosylation (ADPr), which can be reversed by a SARS-CoV-2-encoded hydrolase, is enriched within a condensate. However, the identity of the condensate and responsible host ADP-ribosyltransferase remain elusive. Here, we demonstrate that interferon induces ADPr through transcriptional activation of PARP14, requiring both its physical presence and catalytic activity for condensate formation. Interferon-induced ADPr colocalizes with PARP14, and these PARP14/ADPr condensates contain key components of p62 bodies--including the selective autophagy receptor p62 and its binding partner NBR1, along with K48-linked and K63-linked polyubiquitin chains--but lack the autophagosome marker LC3B. Knockdown of p62 disrupts the formation of these ADPr condensates. Importantly, these structures are unaffected by autophagy inhibition but depend on both ubiquitin activation and proteasome activity. Taken together, these findings demonstrate that interferon triggers PARP14-mediated ADP-ribosylation in p62 bodies, which requires an active ubiquitin-proteasome system.

cell biology↗

bioRxiv2023

Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation

Development of embryonic stem cells (ESCs) into neurons requires intricate regulation of transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) alters splicing of DPF2, a subunit of BAF chromatin remodeling complexes. Dpf2 exon 7 is inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss of PTBP1 allows exon 7 splicing, resulting in a longer DPF2-L isoform. Gene expression changes are induced by DPF2-L in ESC, and by DPF2-S in neurons. In ESC, chromatin immunoprecipitation locates DPF2-S but not DPF2-L at sites bound by pluripotency transcription factors. In neuronal progenitors, DPF2-S sites coincide with NFI protein binding, and DPF2-L sites with CTCF. DPF2-S sites show enhancer chromatin modifications, while DPF2-L sites show modifications associated with promoters. In sum, alternative splicing events during neuronal development impact chromatin organization by altering BAF complex targeting.

molecular biology↗

bioRxiv2022

In-vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma

Targeting metabolic vulnerabilities has been proposed as a therapeutic strategy in renal cell carcinoma (RCC). Here, we analyzed metabolism in patient-derived xenografts (tumorgrafts) from diverse forms of RCC. Tumorgrafts from VHL-mutant clear cell RCC (ccRCC) retained metabolic features of human ccRCC and engage in oxidative and reductive glutamine metabolism. We used several approaches to suppress glutamine metabolism and test the effect on tumor growth. Genetic silencing of isocitrate dehydrogenase-1 or -2 impaired reductive labeling of TCA cycle intermediates and suppressed tumor growth. Glutaminase inhibition resulted in modest growth suppression and variable effects on glutamine metabolism in vivo. Infusions with [amide-15N]glutamine revealed persistent amidotransferase activity during glutaminase inhibition, and blocking these activities with the amidotransferase inhibitor JHU-083 also reduced tumor growth. We conclude that ccRCC tumorgrafts catabolize glutamine via multiple pathways, perhaps explaining why it has been challenging to achieve therapeutic responses in patients by inhibiting glutaminase. TeaserGlutamine fuels the TCA cycle and amidotransferase pathways in clear cell renal cell carcinoma.

cancer biology↗

bioRxiv2022

ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes

The transcription of stress-inducible genes requires synchronized and robust activation, which is critical for organismal survival and homeostasis. The function of the mitogen-activated protein kinase (MAPK) signaling pathway is required for the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth and proliferation1-3. In addition, recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs4-6. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at the EGR1 gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK1 can relax the DNA by itself and produces a semi-relaxed DNA, which is apparently resistant to TOP2B catalysis. Inhibition of ERK2 kinase activity or ERK2 knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we obtained the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with the EGR1 transcriptional start site (50 nt; -30 to +20) that has the strongest affinity to TOP2B within -423 to +332. The structure elucidated in our studies showed TOP2B-mediated breakage and dramatic bending of the double-stranded DNA, comparable to previously reported structures of TOP2. Our cell-based analyses showed transcriptional activation by etoposide and transcriptional inhibition by ICRF193 at EGR1 and FOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.

molecular biology↗