Biology subjects

Cuadrado, A.

Publications and source records attributed to Cuadrado, A..

5 recordsLinked to original sources

bioRxiv2026

GATA4 loss promotes mutant Kras-driven pancreatic ductal adenocarcinoma in the absence of canonical precursor lesions

ABSTRACTGATA6 and GATA4 play key roles in pancreatic development and are essential to maintain the classical transcriptional program in pancreatic ductal adenocarcinoma (PDAC). Using genetic mouse models we show that, in contrast to GATA6, GATA4 is dispensable for the maintenance of acinar homeostasis in the adult pancreas. Deletion of Gata4 in mice expressing mutant Kras in the embryonic pancreas (KG4C) leads to PDAC development in the absence of tissue remodeling, pancreatic intraepithelial neoplasia (PanIN), or other canonical precursor lesions present in Gata4-proficient (KC) mice. Similar observations were made when Gata4 was selectively inactivated in adult, Kras-mutant, acinar cells. We identify Pale Acinar Lesions (PALes) as a previously unrecognized pancreatic lesion, distinct from acino-ductal metaplasia (ADM) and PanINs, present in KC and KG4C mice but not in wild type mice. PALes display weak expression of acinar and ductal markers and lack mucins; they have lower proliferation rates than PanINs. RNA-seq and ChIP-seq reveal that GATA4 and GATA6 partially share genomic binding sites and transcriptomic effects, but they exert opposing influences on mutant Kras-induced, haematopoietic cell-dependent, transcriptional inflammatory programs. Adenoviral-mediated pancreatic expression of IL17 restored the formation of ductal lesions in KG4C mice but failed to rescue PanIN development. Our data indicate that GATA4 functions through the coordinated action of multiple inflammatory factors that are required for ADM/PanIN formation but are dispensable for PDAC development. Collectively, these findings challenge current paradigms of PDAC initiation and progression.

cancer biology↗

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

NRF2 drug repurposing using a question-answer artificial intelligence system

Drug repurposing represents an innovative approach to reduce the drug development timeline. Text mining using artificial intelligence methods offers great potential in the context of drug repurposing. Here, we present a question-answer artificial intelligence (QAAI) system that is capable of repurposing drug compounds. Our system employs a Google semantic AI universal encoder to compute the sentence embedding of an imposed text question in relation to publications stored in our RedBrain JSON database. Sentences similarity is calculated using a sorting function to identify drug compounds. We demonstrate our systems ability to predict new indications for already existing drugs. Activation of the NRF2 pathway seems critical for enhancing several diseases prognosis. We experimentally validated the prediction for the lipoxygenase inhibitor drug zileuton as a modulator of the NRF2 pathway in vitro, with potential applications to reduce macrophage M1 phenotype and ROS production. This novel computational method provides a new approach to reposition of known drugs in order to treat neurodegenerative diseases. Github for the database and the code can be downloaded from https://gist.github.com/micheledw/5a165b44345d45105d715340b88c756b

neuroscience↗