@article{sen_voulgaropoulos_keung_2021, title={Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids}, volume={21}, ISSN={["1472-6750"]}, url={https://doi.org/10.1186/s12896-021-00718-2}, DOI={10.1186/s12896-021-00718-2}, abstractNote={Abstract
                Background
                Human cerebral organoids (hCO) are attractive systems due to their ability to model important brain regions and transcriptomics of early in vivo brain development. To date, they have been used to understand the effects of genetics and soluble factors on neurodevelopment. Interestingly, one of the main advantages of hCOs are that they provide three dimensionality that better mimics the in vivo environment; yet, despite this central feature it remains unclear how spatial and mechanical properties regulate hCO and neurodevelopment. While biophysical factors such as shape and mechanical forces are known to play crucial roles in stem cell differentiation, embryogenesis and neurodevelopment, much of this work investigated two dimensional systems or relied on correlative observations of native developing tissues in three dimensions. Using hCOs to establish links between spatial factors and neurodevelopment will require the use of new approaches and could reveal fundamental principles of brain organogenesis as well as improve hCOs as an experimental model.
              
                Results
                Here, we investigated the effects of early geometric confinements on transcriptomic changes during hCO differentiation. Using a custom and tunable agarose microwell platform we generated embryoid bodies (EB) of diverse shapes mimicking several structures from embryogenesis and neurodevelopment and then further differentiated those EBs to whole brain hCOs. Our results showed that the microwells did not have negative gross impacts on the ability of the hCOs to differentiate towards neural fates, and there were clear shape dependent effects on neural lineage specification. In particular we observed that non-spherical shapes showed signs of altered neurodevelopmental kinetics and favored the development of medial ganglionic eminence-associated brain regions and cell types over cortical regions. Transcriptomic analysis suggests these mechanotransducive effects may be mediated by integrin and Wnt signaling.
              
                Conclusions
                The findings presented here suggest a role for spatial factors in brain region specification during hCO development. Understanding these spatial patterning factors will not only improve understanding of in vivo development and differentiation, but also provide important handles with which to advance and improve control over human model systems for in vitro applications.
              }, number={1}, journal={BMC BIOTECHNOLOGY}, author={Sen, Dilara and Voulgaropoulos, Alexis and Keung, Albert J.}, year={2021}, month={Oct} }
 @article{sen_drobna_keung_2021, title={Evaluation of UBE3A antibodies in mice and human cerebral organoids}, volume={11}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-021-85923-x}, abstractNote={AbstractUBE3A is an E3 ubiquitin ligase encoded by the neurally imprinted UBE3A gene. The abundance and subcellular distribution of UBE3A has been the topic of many previous studies as its dosage and localization has been linked to neurodevelopmental disorders including Autism, Dup15q syndrome, and Angelman syndrome. While commercially available antibodies have been widely employed to determine UBE3A localization, an extensive analysis and comparison of the performance of different UBE3A antibodies has not been conducted. Here we evaluated the specificities of seven commercial UBE3A antibodies in two of the major experimental models used in UBE3A research, mouse and human pluripotent stem cell-derived neural cells and tissues. We tested these antibodies in their two most common assays, immunofluorescence and western blot. In addition, we also assessed the ability of these antibodies to capture dynamic spatiotemporal changes of UBE3A by utilizing human cerebral organoid models. Our results reveal that among the seven antibodies tested, three antibodies demonstrated substantial nonspecific immunoreactivity. While four antibodies show specific localization patterns in both mouse brain sections and human cerebral organoids, these antibodies varied significantly in background signals and staining patterns in undifferentiated human pluripotent stem cells.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Sen, Dilara and Drobna, Zuzana and Keung, Albert J.}, year={2021}, month={Mar} }
 @misc{sen_keung_2020, title={Capturing complex epigenetic phenomena through human multicellular systems}, volume={16}, ISSN={["2468-4511"]}, DOI={10.1016/j.cobme.2020.05.008}, abstractNote={Epigenetic states inherently define a wide range of complex biological phenotypes and processes in development and disease. Accurate cellular modeling would ideally capture the epigenetic complexity of these processes as well as the accompanying molecular changes in chromatin biochemistry including in DNA and histone modifications. Here we highlight recent work that demonstrate how multicellular systems provide a natural approach to capture complex epigenetic phenomena. They accomplish this through more closely matching the in vivo environment and through the intrinsic nature of multicellular systems being able to generate and model multiple distinct cellular states, all within one system. We also discuss challenges and limitations of such systems, efforts to tune and modulate epigenetics directly in multicellular systems, and how molecular interventional approaches could advance and improve the utility of these models.}, journal={CURRENT OPINION IN BIOMEDICAL ENGINEERING}, author={Sen, Dilara and Keung, Albert J.}, year={2020}, month={Dec}, pages={34–41} }
 @article{sen_voulgaropoulos_drobna_keung_2020, title={Human Cerebral Organoids Reveal Early Spatiotemporal Dynamics and Pharmacological Responses of UBE3A}, volume={15}, ISSN={["2213-6711"]}, url={https://doi.org/10.1016/j.stemcr.2020.08.006}, DOI={10.1016/j.stemcr.2020.08.006}, abstractNote={Angelman syndrome is a complex neurodevelopmental disorder characterized by delayed development, intellectual disability, speech impairment, and ataxia. It results from the loss of UBE3A protein, an E3 ubiquitin ligase, in neurons of the brain. Despite the dynamic spatiotemporal expression of UBE3A observed in rodents and the potential clinical importance of when and where it is expressed, its expression pattern in humans remains unknown. This reflects a common challenge of studying human neurodevelopment: prenatal periods are hard to access experimentally. In this work, human cerebral organoids reveal a change from weak to strong UBE3A in neuronal nuclei within 3 weeks of culture. Angelman syndrome human induced pluripotent stem cell-derived organoids also exhibit early silencing of paternal UBE3A, with topoisomerase inhibitors partially rescuing UBE3A levels and calcium transient phenotypes. This work establishes human cerebral organoids as an important model for studying UBE3A and motivates their broader use in understanding complex neurodevelopmental disorders.}, number={4}, journal={STEM CELL REPORTS}, author={Sen, Dilara and Voulgaropoulos, Alexis and Drobna, Zuzana and Keung, Albert J.}, year={2020}, month={Oct}, pages={845–854} }