Biology subjects

Fernandes, T. G.

Publications and source records attributed to Fernandes, T. G..

3 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↗

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↗