Biology subjects

Gimenez-Llorente, D.

Publications and source records attributed to Gimenez-Llorente, D..

4 recordsLinked to original sources

bioRxiv2025

Integrative multi-omics reveals PARP14 as a key IFNγ-regulated mediator of metastatic progression in Ewing sarcoma.

Metastatic Ewing sarcoma (EwS) remains a major clinical challenge, highlighting the need to identify molecular drivers of disease dissemination. Through integrated transcriptomic, functional, and mechanistic analyses, we identify PARP14 as a key regulator of EwS metastatic progression. PARP14 is consistently upregulated in metastatic lesions across spontaneous and xenograft mouse models as well as in patient samples. Genetic and pharmacologic depletion of PARP14 (via siRNA knockdown, CRISPR-Cas9 knockout, or PROTAC-mediated degradation) significantly impaired EwS cell migration and invasion in vitro, without affecting proliferation or clonogenic capacity. In vivo, PARP14 loss delayed tumor growth and reduced metastatic burden, supporting a functional role in disease progression. Conversely, IFN{gamma}-induced PARP14 upregulation and stable overexpression enhanced EwS cell migration and increased lung metastasis formation. Transcriptomic profiling of PARP14-deficient cells revealed downregulation of invasive signatures and enrichment of inflammatory and p53-related pathways, together with gene sets associated with chromatin remodeling. Subcellular fractionation and interactome analyses showed that PARP14 localizes to cytoplasmic, nuclear, and chromatin-associated compartments, and interacts with chromatin, cytoskeletal and ECM regulators. ChlP analyses further demonstrated PARP14 binding to promoters enriched for NRF1 motifs, suggesting a role as a transcriptional co-regulator influencing gene networks relevant to EwS progression. Together, our results establish PARP14 as a contributor to EwS dissemination and uncover a previously unappreciated chromatin-associated role for this protein, supporting its potential as both a biomarker and therapeutic target in metastatic EwS. STATEMENT OF SIGNIFICANCEWe identify PARP14 as a novel driver of Ewing sarcoma metastasis through integrated multi-omics profiling. Genetic and pharmacological interrogation establishes PARP14 as a promising therapeutic target for this understudied malignancy.

cancer biology↗

bioRxiv2022

Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2

Cohesin organizes the genome through the formation of chromatin loops. NIPBL activates cohesins ATPase and is essential for loop extrusion, but its requirement for cohesin loading is currently unclear. Here we have examined the effect of reducing NIPBL levels on the behavior of the two cohesin variants carrying STAG1 or STAG2 by combining a flow cytometry assay to measure chromatin-bound cohesin with analyses of its genome-wide distribution and genome contacts. We show that NIPBL depletion results in increased cohesin-STAG1 on chromatin that further accumulates at CTCF positions while cohesin-STAG2 diminishes genome-wide. Our data support a model in which NIPBL is not required for initial association of cohesin with chromatin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 is loaded and stabilized at CTCF sites even under low NIPBL levels, but genome folding is severely impaired.

cell biology↗

bioRxiv2021

Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF

The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes.

developmental biology↗

bioRxiv2019

STAG2 cohesin is essential for heart morphogenesis

The distinct functions of cohesin complexes carrying STAG1 or STAG2 need to be unraveled. STAG2 is commonly mutated in cancer and germline mutations have been identified in cohesinopathy patients. To better understand the underlying pathogenic mechanisms, we here report the consequence of Stag2 ablation in mice. STAG2 is largely dispensable in adults and its tissue-wide inactivation does not lead to tumors but reduces fitness and affects both hematopoiesis and intestinal homeostasis. STAG2 is also dispensable for murine embryonic fibroblasts in vitro. In contrast, null embryos die by mid gestation showing global developmental delay and heart defects. Histopathological analysis and RNA-sequencing unveiled that STAG2 is required both for proliferation and regulation of cardiac transcriptional programs and in its absence, secondary heart field progenitors fail to enter the heart tube. These results provide compelling evidence on cell- and tissue-specific roles of the two cohesin complexes and how their dysfunction contributes to disease.

developmental biology↗