An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion

Abstract

Kiselev (2016) An integrative analysis of reprogramming in human isogenic system identified a clone selection criterion, Cell Cycle, 15:7, 986-997, DOI: 10.1080/15384101.2016 ABSTRACTThe pluripotency of newly developed human induced pluripotent stem cells (iPSCs) is usually characterized by physiological parameters; i.e., by their ability to maintain the undifferentiated state and to differentiate into derivatives of the 3 germ layers. Nevertheless, a molecular comparison of physiologically normal iPSCs to the "gold standard" of pluripotency, embryonic stem cells (ESCs), often reveals a set of genes with different expression and/or methylation patterns in iPSCs and ESCs. To evaluate the contribution of the reprogramming process, parental cell type, and fortuity in the signature of human iPSCs, we developed a complete isogenic reprogramming system. We performed a genome-wide comparison of the transcriptome and the methylome of human isogenic ESCs, 3 types of ESC-derived somatic cells (fibroblasts, retinal pigment epithelium and neural cells), and 3 pairs of iPSC lines derived from these somatic cells. Our analysis revealed a high input of stochasticity in the iPSC signature that does not retain specific traces of the parental cell type and reprogramming process. We showed that 5 iPSC clones are sufficient to find with 95% confidence at least one iPSC clone indistinguishable from their hypothetical isogenic ESC line. Additionally, on the basis of a small set of genes that are characteristic of all iPSC lines and isogenic ESCs, we formulated an approach of "the best iPSC line" selection and confirmed it on an independent dataset.

Differentiation of Human Pluripotent Stem Cells into Mesodermal and Ectodermal Derivatives Is Independent of the Type of Isogenic Reprogrammed Somatic Cells

“…should be used for reprogramming remains open. According to our results and other studies, isogenic iPSCs derived from different somatic cell types are functionally similar [5, 7]. However, taking into account the fact that they should be further differentiated into specialized types of cells in vitro , it is necessary to know how their ability to differentiate would vary.…”

“…We used the cell lines hESM01, hESM01n5 (hereinafter n5), fibroblasts, neurons, retinal pigment epithelial cells differentiated from hESM01n5 (F, N, R, respectively), and the iPSC lines iF, iN, iR obtained by genetic reprogramming of the lines F, N, R, respectively [5]. …”

“…The isogenic system of cell lines has allowed us to show that iPSC clones do not leave traces of their tissue-specific origin upon complete functional reprogramming. However, the reprogrammed cells acquired individual epigenetic marks specific to each iPSC clone, indicating that the establishment of pluripotency did not occur in the usual way but through mechanisms different from germline pathways [5]. The appearance of these individual features not related to the reprogramming can be caused by technical manipulations in vitro such as cloning, cell sorting, etc..…”

Bestrophin 1 and retinal disease

“…While initially there were concerns that iPSCs may be different than embryonic stem cells and less suitable for transplantation (Rohani et al, 2014), more recent work has demonstrated that iPSCs and embryonic stem cells are highly analogous if not completely identical (Shutova et al, 2016). Autologous stem cell transplantation is commonly performed with mesenchymal stem cells and numerous strategies have been devised to enhance their therapeutic efficacy.…”

The prospect of pluripotent stem cells for diabetes mellitus treatment

“…Для более точного отбора линий ИПСК, соответствую-щих ранее существовавшим ЭСК, нами была определена панель из 280 генов, экспрессия которых позволяет мини-мум из 5 независимо отобранных клонов выбрать наиболее «совершенную» линию [33]. Помимо существенного изме-нения транскрипционного паттерна, репрограммирова-ние сопровождается глобальными изменениями на уровне эпигенома, гистонового кода и метилирования ДНК.…”