Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

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Lotus-root-shaped cell-encapsulated construct as a retrieval graft for long-term transplantation of human iPSC-derived β-cells

iScience ◽

10.1016/j.isci.2021.102309 ◽

2021 ◽

Vol 24 (4) ◽

pp. 102309

Author(s):

Fumisato Ozawa ◽

Shogo Nagata ◽

Haruka Oda ◽

Shigeharu G. Yabe ◽

Hitoshi Okochi ◽

...

Keyword(s):

Β Cells ◽

Lotus Root ◽

Shaped Cell ◽

Human Ipsc

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Maturation of Human iPSC-cardiomyocytes in Long-term Culture for Cardiotoxicity Testing

Journal of Pharmacological and Toxicological Methods ◽

10.1016/j.vascn.2017.09.227 ◽

2017 ◽

Vol 88 ◽

pp. 237-238

Author(s):

Liang Guo ◽

Michael Furniss ◽

Jodie Mussio ◽

John Hamre ◽

Sandy Eldridge ◽

...

Keyword(s):

Long Term Culture ◽

Human Ipsc

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DYRK1A Kinase Inhibitors Promote β-Cell Survival and Insulin Homeostasis

Cells ◽

10.3390/cells10092263 ◽

2021 ◽

Vol 10 (9) ◽

pp. 2263

Author(s):

Agata Barzowska ◽

Barbara Pucelik ◽

Katarzyna Pustelny ◽

Alex Matsuda ◽

Alicja Martyniak ◽

...

Keyword(s):

Cell Proliferation ◽

Small Molecule ◽

Kinase Inhibitors ◽

Human Islets ◽

Β Cell ◽

Insulin Homeostasis ◽

Current Therapies ◽

Comparable Activity ◽

Human Ipsc

The rising prevalence of diabetes is threatening global health. It is known not only for the occurrence of severe complications but also for the SARS-Cov-2 pandemic, which shows that it exacerbates susceptibility to infections. Current therapies focus on artificially maintaining insulin homeostasis, and a durable cure has not yet been achieved. We demonstrate that our set of small molecule inhibitors of DYRK1A kinase potently promotes β-cell proliferation, enhances long-term insulin secretion, and balances glucagon level in the organoid model of the human islets. Comparable activity is seen in INS-1E and MIN6 cells, in isolated mice islets, and human iPSC-derived β-cells. Our compounds exert a significantly more pronounced effect compared to harmine, the best-documented molecule enhancing β-cell proliferation. Using a body-like environment of the organoid, we provide a proof-of-concept that small–molecule–induced human β-cell proliferation via DYRK1A inhibition is achievable, which lends a considerable promise for regenerative medicine in T1DM and T2DM treatment.

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SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients

10.1101/2020.08.25.265561 ◽

2020 ◽

Cited By ~ 13

Author(s):

Juan A. Pérez-Bermejo ◽

Serah Kang ◽

Sarah J. Rockwood ◽

Camille R. Simoneau ◽

David A. Joy ◽

...

Keyword(s):

Nuclear Dna ◽

Distinct Pattern ◽

Cardiac Cells ◽

Productive Infection ◽

Heart Cells ◽

Cardiac Damage ◽

Autopsy Specimens ◽

Human Ipsc ◽

Human Autopsy

ABSTRACTAlthough COVID-19 causes cardiac dysfunction in up to 25% of patients, its pathogenesis remains unclear. Exposure of human iPSC-derived heart cells to SARS-CoV-2 revealed productive infection and robust transcriptomic and morphological signatures of damage, particularly in cardiomyocytes. Transcriptomic disruption of structural proteins corroborated adverse morphologic features, which included a distinct pattern of myofibrillar fragmentation and numerous iPSC-cardiomyocytes lacking nuclear DNA. Human autopsy specimens from COVID-19 patients displayed similar sarcomeric disruption, as well as cardiomyocytes without DNA staining. These striking cytopathic features provide new insights into SARS-CoV-2 induced cardiac damage, offer a platform for discovery of potential therapeutics, and raise serious concerns about the long-term consequences of COVID-19.

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Long-term single-cell passaging of human iPSC fully supports pluripotency and high-efficient trilineage differentiation capacity

10.1101/663047 ◽

2019 ◽

Cited By ~ 1

Author(s):

Estela Cruvinel ◽

Isabella Ogusuku ◽

Rosanna Cerioni ◽

Jéssica Gonçalves ◽

Maria Elisa Góes ◽

...

Keyword(s):

Single Cell ◽

Disease Modeling ◽

Embryoid Body ◽

Population Doubling ◽

Population Doubling Time ◽

Differentiation Capacity ◽

Culture Cells ◽

High Efficient ◽

Human Ipsc

ABSTRACTObjectivesTo validate a straightforward single-cell passaging cultivation method that enables high-quality maintenance of hiPSC without the appearance of karyotypic abnormalities or loss of pluripotency.MethodsCells were kept in culture for over 50 passages, following a structured chronogram of passage and monitoring cell growth by population doubling time (PDT) calculation and cell confluence. Standard procedures for iPSC monitoring as embryonic body (EB) formation, karyotyping and pluripotency markers expression were evaluated in order to monitor the cellular state in the long-term culture. Cells that underwent these tests were then subjected to differentiation into keratinocytes and cardiomyocytes to evaluate its differentiation capacity.ResultshiPSC clones maintained its pluripotent capability as well as chromosomal integrity and were able to generate derivatives from the three germ layers at high passages by embryoid body formation and high-efficient direct differentiation into keratinocytes and cardiomyocytes.ConclusionOur findings support the routine of hiPSC single-cell passaging as a reliable procedure even after long-term cultivation, providing healthy PSCs to be used in drugs discovery, toxicity and disease modeling as well as for therapeutic approaches.

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Long-term development of human iPSC-derived pyramidal neurons quantified after transplantation into the neonatal mouse cortex

Developmental Biology ◽

10.1016/j.ydbio.2020.01.009 ◽

2020 ◽

Vol 461 (1) ◽

pp. 86-95 ◽

Cited By ~ 1

Author(s):

Rosa D’Alessio ◽

Fani Koukouli ◽

Stéphane Blanchard ◽

Julie Catteau ◽

Célia Raïs ◽

...

Keyword(s):

Pyramidal Neurons ◽

Neonatal Mouse ◽

Mouse Cortex ◽

Human Ipsc

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Improved modeling of human AD with an automated culturing platform for iPSC neurons, astrocytes and microglia

Nature Communications ◽

10.1038/s41467-021-25344-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Reina Bassil ◽

Kenneth Shields ◽

Kevin Granger ◽

Ivan Zein ◽

Shirley Ng ◽

...

Keyword(s):

Disease Modeling ◽

Neuronal Cell Death ◽

Neuronal Cell ◽

Induced Pluripotent Stem Cell ◽

Dystrophic Neurites ◽

Synapse Loss ◽

Induced Pluripotent ◽

Human Ipsc ◽

Dendrite Retraction

AbstractAdvancement in human induced pluripotent stem cell (iPSC) neuron and microglial differentiation protocols allow for disease modeling using physiologically relevant cells. However, iPSC differentiation and culturing protocols have posed challenges to maintaining consistency. Here, we generated an automated, consistent, and long-term culturing platform of human iPSC neurons, astrocytes, and microglia. Using this platform we generated a iPSC AD model using human derived cells, which showed signs of Aβ plaques, dystrophic neurites around plaques, synapse loss, dendrite retraction, axon fragmentation, phospho-Tau induction, and neuronal cell death in one model. We showed that the human iPSC microglia internalized and compacted Aβ to generate and surround the plaques, thereby conferring some neuroprotection. We investigated the mechanism of action of anti-Aβ antibodies protection and found that they protected neurons from these pathologies and were most effective before pTau induction. Taken together, these results suggest that this model can facilitate target discovery and drug development efforts.

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