Biology subjects

Becker, J. C.

Publications and source records attributed to Becker, J. C..

4 recordsLinked to original sources

bioRxiv2025

Redirecting resistance evolution in BRAFV600 melanoma by inhibition of the peroxiredoxin-thioredoxin system

Drug-tolerant persister cells (DTPs) exhibit remarkable cell state heterogeneity and phenotypic evolvability. However, the central question of how DTPs epigenetically coordinate their metabolic flexibility to adapt early to therapeutic stress remains unanswered. We have recently shown that the histone demethylase KDM5B, which is intrinsically expressed in differentiated melanoma DTPs, reprograms the metabolic cell landscape. However, the exact mechanism by which KDM5B affects underlying metabolic enzymes, and whether this reveals new druggable vulnerabilities, remain unknown. By transcriptional and epigenetic profiling of BRAFV600 melanoma cells following KDM5B gene silencing, we discovered a direct molecular axis between the epigenetic regulator KDM5B and the PRDX/TXN ROS detoxification system. This metabolic axis is regulated independently of KDM5Bs demethylase activity. Furthermore, RNAi approaches and the pharmacological inhibition of the PRDX/TXN system led to ROS-induced cell death in differentiated melanoma DTPs and a delay of resistance development to MAPK inhibition. This process was independent of lipid-ROS-driven ferroptosis. Additionally, single-cell transcriptome analyses from pre-clinical melanoma models under continuous MAPK inhibitory treatment demonstrated altered cellular differentiation dynamics, with a reduction in the early evolution into the mesenchymal DTP state under concomitant PRDX inhibition. Interestingly, the degree of melanoma cell state differentiation at the onset of treatment was a major determinant for the transition towards the neural crest-like DTP state. Our study identified a high degree of epigenetic-metabolic connectivity and flexibility within the melanoma DTP pool and urges caution with single redox pathway-targeted strategies for tumor elimination in the future. Prospectively, our results point towards a new resistance targeting strategy for BRAFV600 melanoma patients based on pharmacological re-direction of the evolution of melanoma cell states already at therapy onset. HighlightsO_LITranscriptional and epigenetic profiling identified KDM5B as a regulator of the PRDX/TXN-ROS detoxification system C_LIO_LIPRDX inhibition increases the vulnerability of KDM5Bhigh DTPs to ROS, independent of ferroptosis C_LIO_LIPRDX inhibition delays resistance to MAPK inhibition in BRAFV600 melanoma cells C_LIO_LILongitudinal single-cell transcriptome analysis reveals that PRDX inhibition re-directs early DTP evolution C_LIO_LIPRDX/TXN gene expression is predictive for melanoma patient survival C_LI

cancer biology↗

bioRxiv2022

Single-cell transcriptomics reveals varying degrees of epithelial-mesenchymal plasticity in lymph node metastasis from oral cavity squamous cell carcinoma

BackgroundOral squamous cell carcinoma (OSCC), an HPV-negative head and neck cancer, frequently metastasizes to the regional lymph nodes but only occasionally beyond. Initial phases of metastasis are associated with an epithelial-mesenchymal transition (EMT), the consolidation phase is associated with mesenchymal-epithelial transition (MET). This dynamic is referred to as epithelial-mesenchymal plasticity (EMP). While it is known that EMP is essential for cancer cell invasion and metastatic spread, less is known about the heterogeneity of EMP states within a tumor and even less about the heterogeneity between the primary and metastatic lesions. MethodsTo capture heterogeneity of EMP states in OSCC, we performed single-cell RNA sequencing (scRNAseq) of 5 primary tumors and 9 matching lymph node metastases and re-analyzed publicly available scRNAseq data of 9 additional primary tumors. To account for possible bias in cell type compositions by scRNAseq, these were also deconvoluted from bulk transcriptome analyses. Protein expression of selected genes were confirmed by immunohistochemistry. ResultsFrom the 23 OSCC lesions the single cell transcriptome of a total of 7,263 carcinoma cells was available for in-depth analyses. We initially focused on one lesion to avoid inter-patient heterogeneity as a confounding factor and identified OSCC cells expressing genes characteristic of different epithelial and partial EMT stages, such as keratins and SPRR1B (cornifin B) or vimentin and matrix metallopeptidases. RNA velocity information together with the increase in inferred copy number variations indicated a progressive trajectory towards epithelial differentiation in this metastatic lesion. Extension to all samples revealed a less stringent but essentially similar pattern. Interestingly, cells undergoing MET show increased activity of the EMT activator ZEB1. Immunohistochemistry confirmed that ZEB1 was co-expressed with the epithelial marker cornifin B in individual tumor cells - more frequently in lymph node metastases. The lack of E-cadherin mRNA expression suggests this is a partial MET. ConclusionsThis study reveals that EMP enables different partial EMT and epithelial phenotypes of OSCC cells, which are endowed with capabilities essential for the different stages of the metastatic process, including maintenance of cellular integrity. During MET, ZEB1 appears to be functionally active, indicating a more complex role of ZEB1 than mere induction of EMT.

cancer biology↗

bioRxiv2020

The Janus-faced role of KDM5B heterogeneity in melanoma: differentiation as a situational driver of both growth arrest and drug-resistance

Melanoma is a highly plastic tumor characterized by dynamic interconversion of different cell identities depending on the biological context. For example, melanoma cells with high expression of the H3K4 demethylase KDM5B (JARID1B) rest in a slow-cycling, yet reversible persister state. Over time, KDM5Bhigh cells can promote rapid tumor repopulation with equilibrated KDM5B expression heterogeneity. The cellular identity of KDM5Bhigh persister cells has not been studied so far, missing an important cell state-directed treatment opportunity in melanoma. Here, we have established a doxycycline-titratable system for genetic induction of permanent intratumor expression of KDM5B and screened for chemical agents that phenocopy this effect. Transcriptional profiling and cell functional assays confirmed that the dihydropyridine phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxylate (termed Cpd1) supports high KDM5B expression and directs melanoma cells towards differentiation along the melanocytic lineage and to cell cycle-arrest. The high KDM5B state additionally prevents cell proliferation through negative regulation of cytokinetic abscission. Moreover, treatment with Cpd1 promoted the expression of the melanocyte-specific tyrosinase gene specifically sensitizing melanoma cells for the tyrosinase-processed antifolate prodrug 3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin (TMECG). In summary, our study provides proof-of-concept for a new dual hit strategy in melanoma, in which persister state-directed transitioning limits tumor growth and plasticity and primes melanoma cells towards lineage-specific elimination.

cancer biology↗

bioRxiv2019

Highly expressed miR-375 is not an intracellular oncogene in Merkel cell polyomavirus-associated Merkel cell carcinoma

miR-375 is a highly abundant miRNA in Merkel cell carcinoma (MCC), in other cancers it acts either as a tumor suppressor or oncogene. While free-circulating miR-375 serves as surrogate marker for tumor burden in patients with advanced MCC, its function within MCC cells has not been established. Nearly complete miR-375 knockdown in MCC cell lines was achieved using antagomiRs via nucleofection. Neither cell viability, growth characteristics nor morphology were altered by this knockdown. miR-375 target genes and related signaling pathways were determined using ENCORI revealing Hippo signaling and EMT-related genes likely to be regulated. Thus, their expression was analyzed by multiplexed qRT-PCR after miR-375 knockdown demonstrating only a limited change in expression. In summary, highly effective miR-375 knockdown in classical MCC cell lines did neither significantly change cell viability, morphology, nor oncogenic signaling pathways. These observations render miR-375 an unlikely intracellular oncogene in MCC cells, thus suggesting to address likely functions of miR-375 for intercellular communication of MCC.

cancer biology↗