Biology subjects

Gracia, J.

Publications and source records attributed to Gracia, J..

6 recordsLinked to original sources

bioRxiv2025

Early overactivation of non-muscle myosin II during adaptation to combined BRAF and MEK inhibitors in dedifferentiating cutaneous melanomas

Cutaneous melanoma is a very aggressive type of skin cancer with remarkable phenotypic plasticity that contributes to adaptation and resistance to targeted therapies against the MAPK pathway. Previous research described that non-muscle myosin II (NMII) of the actomyosin cytoskeleton, which is essential for cell migration and metastasis, is overactivated in BRAF inhibitor-resistant melanomas. Since the combination of BRAF and MEK inhibitors (BMi) is the current standard of care, we investigated if and how NMII activity is regulated during adaptation to BMi. Here, we find that most dedifferentiating BMi-resistant melanomas overactivate NMII compared to their parental counterparts. NMII activity generally increases during the first 2 weeks of BMi treatment, and it is followed by elevated total NMII levels due partly to transcriptional modulation. Although ERK activity rebounds with similar kinetics, NMII overactivation is not prevented by ERK inhibition but by blockade of ROCK. In melanomas that hyperdifferentiate during adaptation to BMi, NMII activity is not increased upon BMi treatment due, in part, to MITF. We also find that co-targeting NMII along BMi in some melanomas reduces survival of drug-tolerant persister cells, which would delay the development of resistance. Therefore, our study identifies elevated NMII activity as a potential marker of adaptation to MAPK in some melanoma subpopulations, and also provide an approach to delay the emergence of resistance to MAPK-targeted therapy.

cancer biology↗

bioRxiv2025

Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation and transcriptional regulation as human S100 proteins

S100 proteins are highly versatile calcium-binding proteins from vertebrates. Following extracellular release, they become instrumental in immune and antimicrobial defenses, initiating the inflammatory response through receptor signaling and providing direct control of bacterial invaders via nutritional immunity. While mammalian S100s have been extensively studied, very little is known about the more recently discovered S100 proteins from teleost fish, including those with no strict orthologs in mammals. Comparable functioning between both clades would allow to expand their study into the highly popular zebrafish model, particularly suited for live imaging and mechanistic exploration of immune and inflammatory processes. To fill the gap of knowledge on teleost S100s, we here provide a detailed structural and biochemical characterization of S100i1 and S100i2 from Danio rerio, two teleost-specific S100s absent in mammals. We demonstrate that they nevertheless share conserved tertiary and quaternary organization with mammalian S100s. In addition, they exhibit comparable calcium binding properties and undergo a similar calcium-dependent activation mechanism. Furthermore, they display analogous expression pattern, being enriched in tissues highly exposed to the environment like gills and skin, the latter constituting an important reservoir of S100 proteins in mammals. Finally, our results show, for the very first time, that s100i2/i2 gene expression is differentially modulated in sterile disease conditions associated with sustained inflammation or high hypoxic state. Altogether, these findings underline the strong parallelism existing between mammalian and teleost-specific S100 proteins despite their divergent evolution, opening up new avenues to explore their biology in the zebrafish model.

immunology↗

bioRxiv2024

Depletion of aneuploid cells is shaped by cell-to-cell interactions

Aneuploidy, the major cause of miscarriages in humans, is pervasive in early embryos but robustly dampened during development, allowing for healthy births. Later in life, aneuploidy correlates with pathological conditions including cancer. Identification of the mechanisms underlying the elimination of aneuploid cells is relevant in development and disease. Here we generated cells carrying molecularly defined segmental monosomies and trisomies and characterized their immediate impact on cellular behavior. Our data reveal signs of out-competition of cells carrying monosomies in genomic regions devoid of previously known haploinsufficient genes. Dose-dependent effects of single genes or a discrete number of genes contribute to the observed cellular behaviors. By simultaneously inducing cells carrying monosomies and trisomies of the same genomic location, we present evidence that segmental trisomies potentiate or alleviate the negative effects of the monosomy on growth, thus revealing a key role of cell interactions in defining the in vivo elimination of aneuploid cells. HighlightsSegmental monosomies cause growth impairment and are out-competed. Growth impairment relies on dose-dependent effects of single genes or a discrete number of genes. Segmental trisomies of up to 1500 genes do not have a major impact on proliferation and survival. Cell competition is modulated by the presence of cells trisomic for the same genomic region. eTOC BlurbAneuploidy has a negative impact on the growth and proliferation of all animal cells analyzed so far. Fusari et al. unravel a role of cell interactions in defining the in vivo elimination of aneuploid cells through cell competition.

developmental biology↗

bioRxiv2024

How do we respond to the next SARS CoV epidemic/pandemic? A bioinformatics approach with the promise of preventing or reducing the severity of future SARS CoV related pandemics

In this work, we develop a Bayesian weighted scheme to generate evolutionary lineages of a particular viral protein sequence of interest and through a process of clustering and choosing representative lineages from the different clusters according to an evolutionary fitness objective function, we demonstrate it is possible to have anticipated the emergence of the SARS-CoV 2 (2019) strain from the SARS-CoV 1(2004) strain and having shown this retrospectively, we discuss the possibility of applying this approach along with continuous genomic surveillance of SARS-CoVs to prevent or reduce severity of future SARS-CoV related pandemics by being prepared with broad neutralization strategies for anticipated future lineages of SARS-CoVs identified through bioinformatics approaches such as that reported in this work.

bioinformatics↗

bioRxiv2020

A program to automate the discovery of drugs for West Nile and Dengue virus -- programmatic screening of over a billion compounds on PubChem, generation of drug leads and automated In Silico modelling

Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning based AutoQSAR algorithm to generate drug leads for the flaviviruses - Dengue and West Nile. The drug leads generated by the program are feed as programmatic inputs to AutoDock Vina package for automated In Silico modelling of interaction between the compounds generated as drug leads by the program and the chosen Dengue and West Nile drug target methyltransferase, whose inhibition leads to the control of viral replication. The machine learning based AutoQSAR algorithm involves feature selection, QSAR modelling, validation and prediction. The drug leads generated each time the program is run is reflective of the constantly growing PubChem database is an important dynamic feature of the program which facilitates fast and dynamic drug lead generation against the West Nile and Dengue virus in way which is reflective of the constantly growing PubChem database. The program prints out the top drug leads after screening PubChem library which is over a billion compounds. The leads generated by the program are fed as programmatic inputs to an In Silico modelling package. The interaction of top drug lead compounds generated by the program and drug targets of West Nile and Dengue virus, was modelled in an automated way through programmatic commands. Thus our program ushers in a new age of automatic ease in the virtual drug screening and drug identification through programmatic data mining of chemical data libraries and drug lead generation through machine learning based AutoQSAR algorithm and an automated In Silico modelling run through the program to study the interaction between the drug lead compounds and the drug target protein of West Nile and Dengue virus

bioinformatics↗

bioRxiv2019

Isolation and quantification of blood apoptotic bodies in neurological patients

Dysregulation of apoptosis may contribute to the etiology and/or progression of several prevalent diseases, including stroke and neurodegenerative pathologies. So, detection of the apoptotic processes in patients would be useful in daily clinical practice, However, the in vivo analysis of apoptosis that occurs in tissue has limitations. We therefore propose to use circulating apoptotic bodies as biomarkers for measuring apoptotic death in patients. Since there is no scientific literature establishing the most appropriate method for measuring apoptotic bodies from human blood samples, we here describe a reproducible centrifugation-based method combined with electron microscopy, dynamic light scattering and flow cytometry studies to isolate, characterize and quantify plasma apoptotic bodies of patients with ischemic stroke, multiple sclerosis and Parkinsons disease. The analysis revealed that our isolation protocol achieves notable recovery rates of highly-purified intact apoptotic bodies. This easy and rapid procedure would help physicians to implement the use of plasma apoptotic bodies analysis as a non-invasive tool to monitor apoptotic death in neurological patients for prognostic purposes and for following disease activity and assessing drug effectiveness.

neuroscience↗