A comparative study of endoderm differentiation in humans and chimpanzees

Blake, Lauren E.; Thomas, Samantha M.; Blischak, John; Hsiao, Chiaowen Joyce; Chavarria, Claudia; Myrthil, Marsha; Gilad, Yoav; Pavlovic, Bryan J.

doi:10.1101/135442

Cited by 4 publications

(4 citation statements)

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“…Comparisons of gene expression between iPSCs of different species have found them to be a useful tool for studying interspecific differences, including those between closely related primates [112][113][114], without confounding effects of cell type of origin on gene expression [115]. These cells can be made into different germ layer primordia [116], or differentiated into terminal cells types, such as heart muscle [112,117],endoderm [118], or neural cells [74]. An example of the workflow and the resulting cells from these transformations is shown in Figure 4, where iPSCs have been transformed into neural progenitor cells (Figure 4B-C), and those cells have then additionally been induced towards a fate of a neuron or astrocyte (Figure 4D-E Single cell RNA-Seq (scRNA-Seq) pairs well with stem cell methodologies by assessing genomic expression of single cells (either neurons or glia) of brain tissue and thus simplifying an inherently complex biological system [111,119].…”

Section: Emerging Opportunities To Understand Consequences Of Molecular Changes In Human Brain Evolutionmentioning

confidence: 99%

Metabolic changes in human brain evolution

Bauernfeind

Babbitt

2020

Evolutionary Anthropology

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Section: Emerging Opportunities To Understand Consequences Of Molecular Changes In Human Brain Evolutionmentioning

confidence: 99%

Metabolic changes in human brain evolution

Bauernfeind

Babbitt

2020

Evolutionary Anthropology

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“…To address this challenge, we previously established a 49 panel of iPSCs from human and chimpanzee fibroblasts (Gallego Romero et al 2015;Burrows et 50 al. 2016; Blake et al 2017). We can use this comparative iPSC panels to derive multiple cell types 51 representative of the three germ layers.…”

Section: Introduction 44mentioning

confidence: 99%

“…We can use this comparative iPSC panels to derive multiple cell types 51 representative of the three germ layers. For example, we recently differentiated the human and 52 chimpanzee iPSCs into definitive endoderm cells (Blake et al 2017) to study conservation in 53 gene expression trajectories during early development. Our hope is that employing iPSC-based 54 models from humans and chimpanzees will provide researchers with a dynamic and flexible 55 system for comparative functional genomic studies in a large number of cell types.…”

Section: Introduction 44mentioning

confidence: 99%

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A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

Pavlovic

Blake

Roux

et al. 2018

Preprint

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17Comparative genomic studies in primates have the potential to reveal the genetic and 18 mechanistic basis for human specific traits. These studies may also help us better understand 19inter-species phenotypic differences that are clinically relevant. Unfortunately, the obvious 20 limitation on sample collection and experimentation in humans and non-human apes severely 21 restrict our ability to perform dynamic comparative studies in primates. Induced pluripotent 22 stem cells (iPSCs), and their corresponding differentiated cells, may provide a suitable 23 alternative system for dynamic comparative studies. Yet, to effectively use iPSCs and 24 differentiated cells for comparative studies, one must characterize the extent to which these 25 systems faithfully represent biological processes in primary tissues. To do so, we compared 26 gene expression data from primary adult heart tissue and iPSC-derived cardiomyocytes from 27 multiple human and chimpanzee individuals. We determined that gene expression in cultured 28 cardiomyocytes from both human and chimpanzee is most similar to that of adult hearts 29 compared to other adult tissues. Using a comparative framework, we found that 50% of gene 30 regulatory differences between human and chimpanzee hearts are also observed between 31 species in cultured cardiomyocytes; conversely, inter-species regulatory differences seen in 32 cardiomyocytes are found significantly more often in hearts than in other primary tissues. Our 33 work provides a detailed description of the utility and limitation of differentiated 34 cardiomyocytes as a system for comparative functional genomic studies in primates. 35 36 Data availability and resource sharing 37 Gene expression (RNA-seq) data are available at GEO under accession number GSE110471. All 38 human and chimpanzee iPSCs are available upon request without restriction or limitation. 39 40 41 42 43

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A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

Pavlovic

Blake

Roux

et al. 2018

Sci Rep

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Comparative genomic studies in primates have the potential to reveal the genetic and mechanistic basis for human specific traits. These studies may also help us better understand inter-species phenotypic differences that are clinically relevant. Unfortunately, the obvious limitation on sample collection and experimentation in humans and non-human apes severely restrict our ability to perform dynamic comparative studies in primates. Induced pluripotent stem cells (iPSCs), and their corresponding differentiated cells, may provide a suitable alternative system for dynamic comparative studies. Yet, to effectively use iPSCs and differentiated cells for comparative studies, one must characterize the extent to which these systems faithfully represent biological processes in primary tissues. To do so, we compared gene expression data from primary adult heart tissue and iPSC-derived cardiomyocytes from multiple human and chimpanzee individuals. We determined that gene expression in cultured cardiomyocytes from both human and chimpanzee is most similar to that of adult hearts compared to other adult tissues. Using a comparative framework, we found that 50% of gene regulatory differences between human and chimpanzee hearts are also observed between species in cultured cardiomyocytes; conversely, inter-species regulatory differences seen in cardiomyocytes are found significantly more often in hearts than in other primary tissues. Our work provides a detailed description of the utility and limitation of differentiated cardiomyocytes as a system for comparative functional genomic studies in primates.

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A comparative study of endoderm differentiation in humans and chimpanzees

Abstract: Abstract

Cited by 4 publications

References 58 publications

Metabolic changes in human brain evolution

Metabolic changes in human brain evolution

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

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