Biology subjects

Brich, S.

Publications and source records attributed to Brich, S..

4 recordsLinked to original sources

bioRxiv2026

Histone deacetylase activity limits the response to EZH2 inhibition-based therapy in epithelioid sarcoma and is targetable by epigenetic combination

Epithelioid sarcoma (EpS) is an ultra-rare, aggressive soft tissue sarcoma (STS) driven by INI1 loss and consequent hyperactivation of the chromatin-modifying enzyme EZH2. Although the EZH2 inhibitor tazemetostat has shown clinical activity, responses remain limited, highlighting the need for improved treatment strategies. Here, using two in-house generated patient-derived xenograft models and matched cell lines derived from INI-1 deficient EpS, we investigated EZH2 inhibition in combination with doxorubicin, the first-line standard for advanced STSs, identifying distinct patterns of response and resistance. Integrated transcriptomic and functional analyses revealed that response to EZH2 inhibition-based therapy was associated with chromatin remodeling, characterized by increased H3K27 acetylation and downregulation of histone deacetylase (HDAC)-related transcriptional programs. Conversely, the intrinsically resistant model failed to undergo this epigenetic transition despite EZH2 inhibition. Pharmacological HDAC inhibition restored H3K27 acetylation, promoted apoptosis, and enhanced the activity of EZH2 inhibition-based therapy. These findings identify failure to accumulate H3K27 acetylation as a hallmark of resistance to EZH2 inhibition-based treatment, and show that pharmacological HDAC inhibition can restore this chromatin transition and re-sensitize resistant tumors, providing a rationale for combined epigenetic targeting strategies in INI1-deficient malignancies. Translational relevanceProspective trials are challenging in rare tumors such as epithelioid sarcoma (EpS), limiting the level of evidence for existing therapies and the development of new agents. This is particularly relevant for EpS, where drug regimens are those used for all soft tissue sarcomas (STSs), and the specific mechanisms of drug response remain poorly understood. This preclinical study of tazemetostat in combination with doxorubicin shows differential outcomes in two INI1-deficient proximal-type EpS models, providing evidence of the heterogeneity that exists even within the same tumor subtype and fostering the need to better understand the molecular mechanisms driving drug sensitivity/resistance in this disease. In addition, we demonstrated the potential to treat EpS models through modulation of epigenetic mechanisms, showing that HDAC inhibition may restore sensitivity to EZH2-targeted therapy. These findings support the rationale for developing combination strategies incorporating epigenetic modulators and provide a preclinical framework for overcoming resistance to current therapies in EpS.

cancer biology↗

bioRxiv2022

The nanomechanical fingerprint of colorectal-derived peritoneal metastasis

Peritoneal metastases (PM) are one of the most common routes of dissemination for colorectal cancer (CRC) and remain a lethal disease with a poor prognosis. The compositional, mechanical and structural properties of the extracellular matrix (ECM) play an important role in cancer development; studying how these properties change during the progression of the disease is crucial to understand CRC-PM development. The elastic properties of ECMs derived from human samples of normal and neoplastic PM in different pathological conditions were studied by atomic force microscopy (AFM); results were correlated to patients clinical data and to the expression of ECM components related to metastatic spread. Our results show that PM progression is accompanied by stiffening of ECM as a common feature; spatially resolved mechanical analysis highlighted significant spatial heterogeneity of the elastic properties of both normal and neoplastic ECMs, which show significant overlap in the two conditions. On the micrometre scale, ECMs that are considered normal according to the pathological classification possess stiffer spatial domains, which are typically associated with cancer associated fibroblasts (CAF) activity and tumour development in neoplastic matrices; on the other hand, softer regions are found in neoplastic ECMs on the same scales. Our results support the hypothesis that local changes (stiffening) in the normal ECM can create the ground for growth and spread from the tumour of invading metastatic cells. Mechanical changes correlate well with the presence of CAF and an increase in collagen deposition, which are well known markers of cancer progression. Furthermore, we have found correlations between the mechanical properties of the ECM and patients clinical data like age, sex, presence of mutations in BRAF and KRAS genes and tumour grade. Overall, our findings suggest that the mechanical phenotyping of the PM-ECM has the potential for predicting tumour development.

biophysics↗

bioRxiv2022

Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy

BackgroundInnovative cancer immunotherapy approaches aim at combining immune checkpoint inhibitors with other immunomodulatory agents. Epigenetic regulators can control immune-related genes, therefore targeting them with specific inhibitors may be a potential way forward. Here we identified immune-related signatures induced by four classes of epigenetic drugs in human melanoma cells to define the most promising agent and to understand its biological activity in-vitro, in-vivo and in clinical samples. MethodsHuman melanoma cell lines were characterized for mutational and differentiation profile and treated with inhibitors of DNA methyltransferases (guadecitabine), histone deacetylases (givinostat), bromodomain and extraterminal domain proteins (JQ1 and OTX-015) and enhancer of zeste homolog 2 (GSK126). Drug-specific gene signatures were identified by Clariom S and Nanostring platforms. Modulation of 14 proteins was determined by quantitative western blot. Ingenuity Pathway Analysis (IPA) identified Upstream Regulator (UR) molecules explaining changes in gene expression and biological activity of drugs. Gene set enrichment and IPA were used to test modulation of guadecitabine-specific gene and UR signatures, respectively, in on-treatment tumor biopsies from melanoma patients enrolled in the Phase Ib NIBIT-M4 Guadecitabine + Ipilimumab Trial. ResultsDrug-specific gene and UR signatures were identified for each of the four inhibitors. Immune-related genes were frequently upregulated by guadecitabine, to a lesser extent by givinostat, but downregulated by JQ1 and OTX-015. GSK126 was the least active drug. Treatment of melanoma cells with combination of two epigenetic drugs revealed a dominant effect of guadecitabine and JQ1 on immune-related gene modulation. Drug-specific modulatory profiles were confirmed at the protein level. The guadecitabine-specific UR signature was characterized by activated molecules of the TLR, NF-kB, and IFN innate immunity pathways and was induced in drug-treated melanoma, mesothelioma, hepatocarcinoma cell lines and human melanoma xenografts. Most of the guadecitabine-specific signature genes (n>160) were upregulated in on-treatment tumor biopsies from NIBIT-M4 trial. Progressive activation of guadecitabine UR signature molecules was observed in on-treatment tumor biopsies from responding compared to non-responding patients. ConclusionsGuadecitabine was the most promising immunomodulatory agent among those investigated. This DNA methyltransferases inhibitor emerged as a strong inducer of innate immunity pathways, supporting the rationale for its use in combinatorial immunotherapy approaches.

immunology↗

bioRxiv2021

Decellularized Normal and Tumor Scaffolds for Cancer Organoid Cultures as a Model of Colorectal Peritoneal Metastases

Peritoneal metastases (PM) from colorectal cancer (CRC) are associated with poor survival. The extracellular matrix (ECM) plays a fundamental role in modulating the homing of CRC metastases to the peritoneum. The mechanisms underlying the interactions between metastatic cells and the ECM, however, remain poorly understood and the number of in vitro models available for the study of the peritoneal metastatic process is limited. Here, we show that decellularized ECM of the peritoneal cavity allows the growth of organoids obtained from PM, favoring the development of three-dimensional nodules that maintain the characteristics of in vivo PM. Organoids preferentially grow on scaffolds obtained from neoplastic peritoneum, which are characterized by greater stiffness than normal scaffolds. A gene expression analysis of organoids grown on different substrates reflected faithfully the clinical and biological characteristics of the organoids. An impact of the ECM on the response to standard chemotherapy treatment for PM was also observed. SignificanceEvidence of the value of ex vivo 3D models obtained by combining patient-derived extracellular matrices depleted of cellular components and organoids to mimic the metastatic niche, to be used as a tool to develop new therapeutic strategies in a biologically relevant context, to personalize treatments and increase their efficacy.

cancer biology↗