Biology subjects

Cabral, J. M. S.

Publications and source records attributed to Cabral, J. M. S..

6 recordsLinked to original sources

bioRxiv2026

Transcriptomic Analysis Identifies Transient Mesendodermal State and Lineage Divergence in Human Pluripotent Stem Cell Differentiation

Human pluripotent stem cells serve as a vital model for studying early human lineage specification, yet conventional assessments relying on endpoint canonical markers of the three germ layers may overlook transient intermediate states and broader cellular programs. Here we combined directed differentiation of human induced pluripotent stem cells toward neuroectodermal, cardiac mesodermal, and hepatic endodermal lineages with comparative transcriptomic profiling across timepoints. Our analyses revealed a transient primitive streak-like mesendodermal state shared by mesodermal and endodermal trajectories, followed by lineage-specific divergence characterized by distinct transcriptional, metabolic, proliferative, and chromatin remodeling dynamics. Notably, endodermal differentiation exhibited rapid definitive endoderm commitment with enriched oxidative metabolism, whereas cardiac mesoderm differentiation showed progressive transcriptional remodeling and cardiac progenitor activation. These findings demonstrate that comparative transcriptomics can resolve developmental intermediates and cellular-state dynamics during human germ layer specification, providing a framework for evaluating lineage commitment beyond endpoint canonical marker expression, and to inform strategies for optimizing or redirecting differentiation.

bioengineering↗

bioRxiv2025

Gradient-Based Regulation of Activin A Directs Multilineage Liver Organoid Development from Human Pluripotent Stem Cells

Morphogen gradients critically regulate the coordinated emergence of endodermal and mesodermal lineages during liver bud formation, yet current human hepatic organoid models inadequately replicate these spatial cues. Here we demonstrate that precise modulation of Activin A concentrations within a dynamic 3D vertical-wheel bioreactor system enables the co-emergence and spatial organization of hepatic epithelium and septum transversum mesenchyme-like populations from human pluripotent stem cells. High Activin levels induce uniform definitive endoderm and enhanced hepatic maturation, whereas low levels promote epithelial tube-like structures encased by mesenchymal cells, recapitulating early liver diverticulum architecture. This gradient-based approach autonomously generates parenchymal and non-parenchymal hepatic lineages, providing a scalable platform to model human liver organogenesis and engineer ventral foregut-derived tissues.

bioengineering↗

bioRxiv2023

Cell-derived ECM loaded electrospun Polycaprolactone/Chitosan nanofibrous scaffolds for periodontal regeneration

Periodontitis is an inflammatory infection caused by bacterial plaque accumulation that affects the periodontium, a complex structure of different tissues (cementum, periodontal ligament and alveolar bone) that surrounds and supports the teeth. Current treatments lack bioactive signals to induce tissue repair and coordinated regeneration of the periodontium, thus alternative strategies are needed to improve clinical outcomes. Cell-derived extracellular matrix (ECM) has been combined with biomaterials to enhance their biofunctionality for various tissue engineering (TE) applications. In this work, bioactive cell-derived ECM loaded electrospun polycaprolactone/chitosan (PCL/CTS) nanofibrous scaffolds were developed combining polymer solutions with lyophilized decellularized ECM (dECM) derived from human Periodontal Ligament Stem/Stromal Cells (PDLSCs). The works aims were to fabricate and characterize cell-derived ECM electrospun PCL/CTS scaffolds in terms of morphology, physico-chemical, thermal and mechanical properties and assess their ability to enhance the osteogenic differentiation of PDLSCs, envisaging periodontal TE applications. PDLSCs were cultured and used for dECM production. PDLSCs-derived dECM was characterized regarding morphology, protein expression, DNA removal efficiency, and glycosaminoglycans and collagen contents. Osteogenic differentiation of PDLSCs was performed on PCL, PCL/CTS and PCL/CTS/ECM electrospun scaffolds for 21 days. The obtained results demonstrate that PCL/CTS/ECM scaffolds promoted cell proliferation compared to PCL and PCL/CTS scaffolds, while maintaining similar physical and mechanical properties of PCL/CTS scaffolds. PCL/CTS/ECM scaffolds enhanced the osteogenic differentiation of PDLSCs, confirmed by increased alkaline phosphatase activity, calcium deposition, and bone-specific marker genes expression. Moreover, PCL/CTS scaffolds showed higher levels of cell mineralization than PCL scaffolds. Overall, this work describes the first use of lyophilized cell-derived ECM loaded electrospun scaffolds for periodontal TE applications and highlights its potential as a promising therapeutic strategy for periodontitis treatment.

bioengineering↗

bioRxiv2022

Bio-inspired artificial printed bioelectronic cardio-3D-cellular constructs

Bioelectronics is a growing field where novel smart materials are required to interface biology with electronic components. Conductive hydrogels have recently emerged as a promising material for biosensing/actuating applications as they can provide a wet, nanostructured and electrically conductive environment, minimising the mismatch between biological and electronic systems. In this work, we propose a strategy to develop conductive bioinks compatible with the freeform reversible embedding of suspended hydrogels (FRESH) extrusion bioprinting method. These bioinks are based on decellularized extracellular matrix (dECM), extracted from three different tissues (small intestine submucosa, liver and bone) and were characterised. 3D structures were manufactured containing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), exhibiting cell viabilities >80%. Multi-walled carbon nanotubes (MWCNTs) were selected as an additional component of the bioinks. The addition of the MWCNTs enhanced the conductive features of the hydrogels and the morphology of the dECM fibres. Electrical stimulation (ES) through alternating currents was applied to hPSC-CMs encapsulated in 3D structures manufactured with the previous material and our results indicated two main findings: (1) in the absence of external ES, the conductive properties of the materials can improve the contractile behaviour of the hPSC-CMs and (2) this effect is significantly enhanced under the application of external ES. Genetic markers analysed showed a trend towards a more mature state of the cells evaluated by the TNNI3/TNNI1 ratio, with upregulated SERCA2 and RYR2 calcium handling proteins when compared to controls and downregulation of calcium channels involved in the generation of pacemaking currents (CACNA1H). These results demonstrate the potential of our strategy to manufacture conductive hydrogels in complex geometries for bioactuating purposes. However, further development of the 3D bioprinting techniques is required to achieve higher control over the nano- and microarchitectures of the structures to improve their biomimicry.

bioengineering↗

bioRxiv2021

Transcriptome profiling of human pluripotent stem cell-derived cerebellar organoids reveals fastercommitment under dynamic conditions

Human induced pluripotent stem cells (iPSCs) have great potential for disease modeling. However, generating iPSC-derived models to study brain diseases remains a challenge. In particular, the ability to recapitulate cerebellar development in vitro is still limited. We presented a reproducible and scalable production of cerebellar organoids by using the novel Vertical-Wheel single-use bioreactors, in which functional cerebellar neurons were obtained. Here, we evaluate the global gene expression profiles by RNA sequencing (RNA-seq) across cerebellar differentiation, demonstrating a faster cerebellar commitment in this novel dynamic differentiation protocol. Furthermore, transcriptomic profiles suggest a significant enrichment of extracellular matrix (ECM) in dynamic-derived cerebellar organoids, which can better mimic the neural microenvironment and support a consistent neuronal network. Thus, an efficient generation of organoids with cerebellar identity was achieved for the first time in a continuous process using a dynamic system without the need of organoids encapsulation in ECM-based hydrogels, allowing the possibility of large-scale production and application in high-throughput processes. The presence of factors that favors angiogenesis onset was also detected in dynamic condition, which can enhance functional maturation of cerebellar organoids. We anticipate that large-scale production of cerebellar organoids may help developing models for drug screening, toxicological tests and studying pathological pathways involved in cerebellar degeneration.

bioengineering↗

bioRxiv2018

Complex human gut microbiome cultured in anaerobic human intestine chips

The diverse bacterial populations that comprise the commensal microbiota of the human intestine play a central role in health and disease, yet no method is available to sustain these complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro. Here we describe a human Organ-on-a-Chip (Organ Chip) microfluidic platform that permits control and real-time assessment of physiologically-relevant oxygen gradients, and which enables co-culture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota. When compared to aerobic co-culture conditions, establishment of a transluminal hypoxia gradient sustained higher microbial diversity with over 200 unique operational taxonomic units (OTUs) from 11 different genera, and an abundance of obligate anaerobic bacteria with ratios of Firmicutes and Bacteroidetes similar to those observed in human feces, in addition to increasing intestinal barrier function. The ability to culture human intestinal epithelium overlaid by complex human gut microbial communities within microfluidic Intestine Chips may enable investigations of host-microbiome interactions that were not possible previously, and serve as a discovery tool for development of new microbiome-related therapeutics, probiotics, and nutraceuticals.

bioengineering↗