Prime time for primate functional genomics

Housman, Genevieve; Gilad, Yoav

doi:10.1016/j.gde.2020.04.007

Cited by 21 publications

(21 citation statements)

References 42 publications

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“…A third type of question with considerable potential has been explored much less, namely using iPSCs in a comparative framework to identify molecular or cellular properties that are conserved, i.e. functional across species (Enard, 2012(Enard, , 2016Housman and Gilad, 2020).This is similar to the comparative approach on the genotype level in which DNA or protein sequences are compared in orthologous regions among several species to identify conserved, i.e. functional elements (Alföldi and Lindblad-Toh, 2013).…”

Section: Implications For Generating Ipscs In Many Speciesmentioning

confidence: 99%

A non-invasive method to generate induced pluripotent stem cells from primate urine

Geuder

Ohnuki

Wange

et al. 2020

Preprint

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SummaryComparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that Sendai virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to generate iPSCs non-invasively from primate urine. This will allow to extend the zoo of species available for a comparative approach to molecular and cellular phenotypes.Graphical AbstractWorkflow overview for establishing iPSCs from primate urine(A) We established the protocol for human urine based on a previous description (Zhou 2012). We tested volume, storage and culture conditions for primary cells and compared reprogramming by overexpression of OCT3/4, SOX2, KLF4 and MYC (OSKM) via lipofection of episomal vectors and via transduction of a sendai virus derived vector (SeV). (B) We used the the protocol established in humans and adapted it for unsterile floor-collected samples from non-human primates by adding Normocure to the first passages of primary cell culture and reprogrammed visually healthy and uncontaminated cultures using SeV. (C) Pluripotency of established cultures was verified by marker expression, differentiation capacity and cell type classification using RNA sequencing.

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Section: Implications For Generating Ipscs In Many Speciesmentioning

confidence: 99%

A non-invasive method to generate induced pluripotent stem cells from primate urine

Geuder

Ohnuki

Wange

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…A third type of application with considerable potential has been explored much less, namely using iPSCs in a comparative framework to identify molecular or cellular properties that are conserved, i.e. functional across species 2,3,48 . This is similar to the comparative approach on the genotype level in which DNA or protein sequences are compared in orthologous regions among several species to identify conserved, i.e.…”

Section: Discussionmentioning

confidence: 99%

A non-invasive method to generate induced pluripotent stem cells from primate urine

Geuder

Wange

Janjic

et al. 2021

Sci Rep

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Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that suspension- Sendai Virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to non-invasively generate iPSCs from primate urine. This will extend the zoo of species available for a comparative approach to molecular and cellular phenotypes.

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“…This is because genetic variation between species is greater than genetic variation within species. Thus, regulatory differences that distinguish humans from other primates tend to have larger effect sizes than regulatory differences that distinguish between individual humans (Housman & Gilad 2020).…”

Section: Discussionmentioning

confidence: 99%

“…If these truncated isoforms are no longer targets of mRNA decay, this could cause some of these genes to appear up-regulated. We hypothesize that the within-species effects related to NSD were likely overshadowed by inter-species differences, which typically have much larger effect sizes than differences observed within a population (Housman & Gilad, 2020).…”

Section: Alternative Polyadenylation Is Associated With Gene Expression Divergencementioning

confidence: 99%

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

Mittleman

Pott

Warland

et al. 2021

eLife

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While comparative functional genomic studies have shown that inter-species differences in gene expression can be explained by corresponding inter-species differences in genetic and epigenetic regulatory mechanisms, co-transcriptional mechanisms, such as alternative polyadenylation (APA), have received little attention. We characterized APA in lymphoblastoid cell lines from six humans and six chimpanzees by identifying and estimating usage for 44,432 polyadenylation sites (PAS) in 9,518 genes. Although APA is largely conserved, 1,705 genes showed significantly different PAS usage (FDR 0.05) between species. Genes with divergent APA also tend to be differentially expressed, are enriched among genes showing differences in protein translation, and can explain a subset of observed inter-species protein expression differences that do not differ at the transcript level. Finally, we found that genes with a dominant PAS, which is used more often than other PAS, are particularly enriched for differentially expressed genes.

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Prime time for primate functional genomics

Cited by 21 publications

References 42 publications

A non-invasive method to generate induced pluripotent stem cells from primate urine

A non-invasive method to generate induced pluripotent stem cells from primate urine

A non-invasive method to generate induced pluripotent stem cells from primate urine

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees

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