Biology subjects

Garcia Garcia, A.

Publications and source records attributed to Garcia Garcia, A..

9 recordsLinked to original sources

bioRxiv2026

Multi-omics profiling links epigenetic and lncRNA changes to early human endochondral ossification priming

Differentiation programs remain incompletely understood across stem cell types, including for human bone marrow mesenchymal stromal/stem (BM-MSCs) cells, a heterogenous population orchestrating bone formation and establishing a functional hematopoietic niche in the bone marrow. BM-MSCs form and repair bone through the evolutionarily conserved process of endochondral ossification (EO), initiated by deposition of a transient cartilage template subsequently remodeled into bone and bone marrow tissues. Despite their considerable potential for skeletal regeneration, the early molecular and cellular events underlying BM-MSCs commitment to EO remain elusive. To overcome donor dependent variability in chondrogenic potential that limits mechanistic studies, we here exploit OssiGel as a potent chondro-inductive extracellular matrix offering robust recapitulation of EO by BM-MSCs. Through multi-omics profiling of OssiGel-primed BM-MSCs, we identify rapid chromatin remodeling at chondrogenic loci as concomitant for lineage commitment. The emergence of a chondro-progenitor population is detected as early as 3 days in vivo and correlates with successful EO recapitulation. Mechanistically, we identify LINC02511 as novel enhancer-associated element involved in the onset of EO. We confirm presence of LINC02511 in human skeletal atlases, and its CRISPR-mediated silencing significantly impaired EO. By integrating human tissue engineering strategies with single cell multi-omics profiling, our study provides a framework for deciphering BM-MSCs fate decisions, highlighting the role of enhancer and non-coding elements as key determinants of early lineage specification. These findings advance our understanding of BM-MSCs biology and will prompt their translational exploitation in regenerative medicine.

cell biology↗

bioRxiv2026

Engineering autologous ossicles for the personalized modeling of acute myeloid leukemia

Acute Myeloid Leukemia (AML) is the most lethal hematological malignancy in adults and is characterized by significant genetic and cytogenetic heterogeneity. This diversity drives substantial patient-to-patient variability in disease progression and therapeutic response. Increasing evidence indicates that bone marrow mesenchymal stem/stromal cells (MSCs) play a critical role in AML emergence, evolution and treatment resistance. However, progress in the field is challenged by the lack of experimental models supporting sustained AML survival while faithfully recapitulating the human bone marrow niche. Humanized ossicles (hOss) have recently emerged as ectopic human bone/bone marrow microenvironments composed of MSCs and hematopoietic elements, enabling improved AML engraftment in vivo. Nonetheless, those models typically exploit healthy MSCs largely because primary patient-derived cells exhibit diminished ossification potential. Here, we introduce OssiGel, a novel engineered human cartilage extracellular matrix produced by a mesenchymal cell line. We hypothesized that combining OssiGel with primary MSCs would enable the robust formation of hOss in healthy and malignant settings. We report that OssiGel supports fast and reproducible formation of hOss through endochondral ossification using MSCs isolated from both healthy and AML bone marrow samples. Within hOss, AML-MSCs were shown to persist long-term and to generate a human stromal microenvironment supporting the establishment of autologous AML hematopoietic cells, enabling the generation of autologous (autologOss). Single-cell RNA sequencing (scRNA-seq) revealed that autologOss recapitulate the majority of the AML blood populations observed in the corresponding patient bone marrow samples. Moreover, proof-of-concept sequencing of AML-MSCs from autologOss allowed predictive interrogation of interactions with leukemic populations and revealed the acquisition of an inflammatory-like phenotype, characteristic of AML. Taken together, our study establishes OssiGel as a novel platform for the robust engineering of autologous ossicles from AML patient samples. This provides a relevant tool to decipher patient-specific cellular interactions and drug responses, with potential translational value to broad hematological malignancies.

bioengineering↗

bioRxiv2025

Pre-clinical validation of in vitro engineered but cell-free human tissue grafts for skeletal regeneration

Tissue engineering strategies predominantly consist of the autologous generation of living substitutes capable of restoring damaged body parts. Persisting challenges with patient-specific approaches include inconsistent performance, high costs and delayed graft availability. Towards developing a one-for-all solution, a more attractive paradigm lies in the exploitation of dedicated cell lines for the fabrication of human tissue grafts. Following decellularization, this new class of biomaterials relies on the sole extracellular matrix and embedded growth factors instructing endogenous repair. This conceptual approach was previously validated using a custom mesenchymal line for the manufacturing of human cartilage, exhibiting remarkable osteoinductive capacity following lyophilization. Key missing criteria to envision clinical translation include proper decellularization as well as stringent assessment of both immunogenicity and regenerative performance. Here, we report the engineering and subsequent decellularization of human cartilage tissue with minimal matrix impairment. Ectopic evaluation in immunocompetent and immunocompromised animals reveal preservation of osteoinductivity predicted by macrophage kinetic of polarization. By establishing in vitro human allogeneic co-culture models, we evidenced the immuno-evasive properties of cell-free human cartilages, controlling macrophages and dendritic cells maturation as well as T cell activation. Lastly, regenerative performance was stringently assessed in an immunocompetent rat orthotopic model whereby decellularized human cartilage grafts achieved morphological and mechanical restoration of all critical-sized femoral defects. Taken together, our study compiles robust safety and efficacy pre-requisites prompting a first-in-human trial for engineered and decellularized human tissue grafts.

bioengineering↗

bioRxiv2025

Human mitochondrial transfer modeling reveals biased delivery from mesenchymal-to-hematopoietic stem cells

Within the bone marrow (BM), the intercellular communication between hematopoietic stem and progenitor cells (HSPCs) and mesenchymal stem/stromal cells (MSCs) is critical for the life-long maintenance of functional hematopoiesis. In recent years, the transfer of mitochondria between MSCs and HSPCs has emerged as a key aspect of this communication, occurring both in stress and homeostatic conditions. In human, the mesenchymal-to-hematopoietic transfer process and functional impact remain cryptic, primarily due to a lack of robust models. To this end, we here describe the development and exploitation of iMSOD-mito, an immortalized human MSCs line bearing an inducible mCherry mitochondrial tag. Co-culture with primary healthy HSPCs or a leukemic cell line revealed a high mitochondrial transfer rate (>15%), exclusively relying on cell-to-cell contact. While all CD34+ blood cells received mitochondria, a preferential transfer towards phenotypic hematopoietic stem cells was identified. Similarly, using primary MSCs with genetically labelled mitochondria we confirmed a transfer to all CD34+ populations, albeit occurring at a lower frequency than with the iMSOD-mito (3.38%). By engineering 3D bone marrow niches in perfusion bioreactor, this transfer rate could be significantly increased, while the biased towards HSC as receiver was maintained. Functionally, mitochondria-receiving cells exhibited an increased mitochondria membrane potential and reactive oxygen species (ROS) production, which in HSPCs was associated with retained quiescence in single cell divisional assay. In summary, we propose the iMSOD-mito as a standardized tool to model human mesenchymal-to-hematopoietic mitochondria transfer in 2D or 3D culture systems. Our work prompts the study of mitochondria transfer in both healthy or disease conditions, towards the design of regenerative therapies or identification of new targets in a malignant context.

cell biology↗

bioRxiv2024

ELOVL6 as a Therapeutic Target: Disrupting c-MYC-Driven Lipid Metabolism to Enhance Chemotherapy in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease, marked by a survival rate of only 12%. Consequently, the exploration of novel therapeutic strategies becomes a critical clinical imperative. Among the genetic alterations contributing to PDAC, c-MYC overexpression arises due to upstream mutations, amplifications, and copy number alterations. c-MYC serves as a key regulator in the tumors metabolic reprogramming, playing a pivotal role in proliferation, migration, and metastasis. This study delves into the investigation of the role of the elongase ELOVL6 in c-MYC-induced cell transformation and its potential as a therapeutic target in PDAC. Here, we demonstrate that c-MYC regulates lipid elongation to promote cell transformation, offering a new avenue for therapeutic intervention. Initially, we show the direct regulation of ELOVLs expression by c-MYC in various PDAC mouse models and cell lines, elucidating its upregulation during transformation and tumor progression. Genetic or chemical inhibition of ELOVL6 results in decreased proliferation and migration, accompanied by alterations in fatty acid elongation. These changes in fatty acid composition led to modifications in membrane rigidity, permeability, and thickness, which collectively affect micropinocytosis and macropinocytosis. Importantly, we observe an increase in Abraxane uptake and a synergistic effect when combined with ELOVL6 interference in vitro. In vivo validation demonstrates that ELOVL6 inhibition significantly reduces tumor growth and enhances the response to Abraxane, thereby increasing overall survival. Altogether, these results position ELOVL6 as a promising therapeutic target in the treatment of PDAC.

cancer biology↗

bioRxiv2023

Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines

Tissue engineering strategies predominantly rely on the production of living substitutes, whereby implanted cells actively participate in the regenerative process. Beyond cost and delayed graft availability, the patient-specific performance of engineered tissues poses serious concerns on their clinical translation ability. A more exciting paradigm consists in exploiting cell-laid, engineered extracellular matrices (eECM), which can be used as off-the-shelf materials. Here, the regenerative capacity solely relies on the preservation of the eECM structure and embedded signals to instruct an endogenous repair. We recently described the possibility to exploit custom human stem cell lines for eECM manufacturing. In addition to the conferred standardization, the availability of such cell lines opened avenues for the design of tailored eECMs by applying dedicated genetic tools. In this study, we demonstrated the exploitation of CRISPR/Cas9 as a high precision system for editing the composition and function of eECMs. Human mesenchymal stromal/stem cell (hMSC) lines were modified to knockout VEGF and RUNX2 and assessed for their capacity to generate osteoinductive cartilage matrices. We report the successful editing of hMSCs, subsequently leading to targeted VEGF and RUNX2-knockout cartilage eECMs. Despite the absence of VEGF, eECMs retained full capacity to instruct ectopic endochondral ossification. Conversely, RUNX2-edited eECMs exhibited impaired hypertrophy, reduced ectopic ossification and superior cartilage repair in a rat osteochondral defect. In summary, our approach can be harnessed to identify the necessary eECM factors driving endogenous repair. Our work paves the road towards the compositional eECMs editing and their exploitation in broad regenerative contexts.

bioengineering↗

bioRxiv2021

Engineering of human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia and solid tumor metastasis

The bone marrow microenvironment provides indispensable factors to sustain blood production throughout life. It is also a hotspot for the progression of hematologic disorders and the most frequent site of solid tumor metastasis. Pre-clinical research relies on xenograft mouse models, precluding the human-specific functional interactions of stem cells with their bone marrow microenvironment. Human mesenchymal cells can be exploited for the in vivo engineering of humanized ossicles (hOss). Those mini-bones provide a human niche conferring engraftment of human healthy and malignant blood samples, yet suffering from major reproducibility issue. Here, we report the standardized generation of hOss by developmental priming of a custom-designed human mesenchymal cell line. We demonstrate superior engraftment of cord blood hematopoietic cells and primary acute myeloid leukemia samples, but also validate our hOss as metastatic site for breast cancer cells. Finally, we report the first engraftment of neuroblastoma patient-derived xenograft cells in a humanized model, recapitulating clinically reported osteolytic lesions. Collectively, our hOss constitute a powerful standardized and malleable platform to model normal hematopoiesis, leukemia and solid tumor metastasis.

bioengineering↗

bioRxiv2021

Modeling Vertical Migrations of Zooplankton Based on Maximizing Fitness

The purpose of the work is to calculate the evolutionarily stable strategy of zooplankton diel vertical migrations from known data of the environment using principles of evolutionary optimality and selection. At the first stage of the research, the fitness function is identified using artificial neural network technologies. The training sample is formed based on empirical observations. It includes pairwise comparison results of the selective advantages of a certain set of species. Key parameters of each strategy are calculated: energy gain from ingested food, metabolic losses, energy costs on movement, population losses from predation and unfavorable living conditions. The problem of finding coefficients of the fitness function is reduced to a classification problem. The single-layer neural network is built to solve this problem. The use of this technology allows one to construct the fitness function in the form of a linear convolution of key parameters with identified coefficients. At the second stage, an evolutionarily stable strategy of the zooplankton behavior is found by maximizing the identified fitness function. The maximization problem is solved using optimal control methods. A feature of this work is the use of piecewise linear approximations of environmental factors: the distribution of food and predator depending on the depth. As a result of the study, mathematical and software tools have been created for modeling and analyzing the hereditary behavior of living organisms in an aquatic ecosystem. Mathematical modeling of diel vertical migrations of zooplankton in Saanich Bay has been carried out.

evolutionary biology↗

bioRxiv2020

Mathematical modelling evolutionarily stablebehavior of zooplankton with state constraints

The purpose of this work is to create mathematical base and software for solving the problem of finding an evolutionarily stable strategy of zooplankton diel vertical migrations and explaining the observed effects in aquatic ecosystems using this software (in particular, in the northeastern part of the Black Sea). An essential feature of this study is the inclusion in the mathematical model of state constraints on the strategy of behavior, which reflect the vertical limited zone of zooplankton habitat. The presence of state constraints creates the main mathematical difficulties for solving the optimal control problem used in the analysis of the model. The general methodological basis for defining evolutionarily stable behavior is the Darwinian principle "survival of the fittest". However, it remains a problem to construct a mathematical expression for the fitness function of hereditary elements. The efforts of the authors were aimed at creating a software package that allows predicting the evolutionarily stable behavior of zooplankton based on the actual universal extreme principle. The created software package includes, as a main component, a computational module for solving the set optimal control problem with state constraints.

evolutionary biology↗