Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells

Makarev, Eugene; Fortney, Kristen; Litovchenko, Maria; Braunewell, Karl-Heinz; Zhavoronkov, Alex; Atala, Anthony

doi:10.18632/oncotarget.4673

Cited by 11 publications

(11 citation statements)

References 27 publications

(39 reference statements)

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“…It has been used to analyze parallels in pathway activation between pathological and chronological aging in Hutchinson-Gilford Progeria Syndrome fibroblasts, a disease-based model of aging [ 36 ]. It has also been used in evaluating the therapeutic viability of pluripotent stem cells [ 37 ] and in cross-species analysis [ 38 ], an important aspect of aging research [ 30 ]. Additionally it has helped determine common pathway signatures in lung and liver fibrosis [ 39 ] and evaluate pro-fibrotic pathway activation in trabecular meshwork and lamina cribrosa in glaucoma [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state

Aliper

Belikov

Garazha

et al. 2016

Aging

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Populations in developed nations throughout the world are rapidly aging, and the search for geroprotectors, or anti-aging interventions, has never been more important. Yet while hundreds of geroprotectors have extended lifespan in animal models, none have yet been approved for widespread use in humans. GeroScope is a computational tool that can aid prediction of novel geroprotectors from existing human gene expression data. GeroScope maps expression differences between samples from young and old subjects to aging-related signaling pathways, then profiles pathway activation strength (PAS) for each condition. Known substances are then screened and ranked for those most likely to target differential pathways and mimic the young signalome. Here we used GeroScope and shortlisted ten substances, all of which have lifespan-extending effects in animal models, and tested 6 of them for geroprotective effects in senescent human fibroblast cultures. PD-98059, a highly selective MEK1 inhibitor, showed both life-prolonging and rejuvenating effects. Natural compounds like N-acetyl-L-cysteine, Myricetin and Epigallocatechin gallate also improved several senescence-associated properties and were further investigated with pathway analysis. This work not only highlights several potential geroprotectors for further study, but also serves as a proof-of-concept for GeroScope, Oncofinder and other PAS-based methods in streamlining drug prediction, repurposing and personalized medicine.

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Section: Discussionmentioning

confidence: 99%

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state

Aliper

Belikov

Garazha

et al. 2016

Aging

Self Cite

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“… 19 It was shown to be efficient in finding new cancer biomarkers, more stable than individual gene expression patterns. 11 To date, OncoFinder was applied for many objects including induced pluripotent stem cells, 20 leukemia and solid cancers, 21,22,23 Hutchinson Gilford Disease, 24 and Age-Related Macular Degeneration Disease. 25 …”

Section: Introductionmentioning

confidence: 99%

MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways

Artcibasova

Korzinkin²,

Sorokin³

et al. 2016

Cell Cycle

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MicroRNAs (miRs) are short noncoding RNA molecules that regulate expression of target mRNAs. Many published sources provide information about miRs and their targets. However, bioinformatic tools elucidating higher level impact of the established total miR profiles, are still largely missing. Recently, we developed a method termed OncoFinder enabling quantification of the activities of intracellular molecular pathways basing on gene expression data. Here we propose a new technique, MiRImpact, which enables to link miR expression data with its estimated outcome on the regulation of molecular pathways, like signaling, metabolic, cytoskeleton rearrangement, and DNA repair pathways. MiRImpact uses OncoFinder rationale for pathway activity calculations, with the major distinctions that (i) it deals with the concentrations of miRs - known regulators of gene products participating in molecular pathways, and (ii) miRs are considered as negative regulators of target molecules, if other is not specified. MiRImpact operates with 2 types of databases: for molecular targets of miRs and for gene products participating in molecular pathways. We applied MiRImpact to compare regulation of human bladder cancer-specific signaling pathways at the levels of mRNA and miR expression. We took 2 most complete alternative databases of experimentally validated miR targets – miRTarBase and DianaTarBase, and an OncoFinder database featuring 2725 gene products and 271 signaling pathways. We showed that the impact of miRs is orthogonal to pathway regulation at the mRNA level, which stresses the importance of studying posttranscriptional regulation of gene expression. We also report characteristic set of miR and mRNA regulation features linked with bladder cancer.

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“…What could be the factors serving as roadblocks on the way immortalized cell being reprogrammed into iPSC? It is known that an abnormal cell signaling, for instance, activation of MAPK (p38) [ 46 – 48 ], TGFβ [ 49 , 50 ], or Hippo/LATS2 [ 51 ] pathways strongly suppress the iPSC generation. From the other side, it was shown that cell immortality is a crucial and rate-limiting step towards the establishment of a pluripotent state in somatic cells.…”

Section: Resultsmentioning

confidence: 99%

Immortalized murine fibroblast cell lines are refractory to reprogramming to pluripotent state

2018

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To date different cell types of various mammalian species have been reprogrammed to induced pluripotent stem cells (iPSCs) using Yamanaka's cocktail of transcription factors (Oct4, Klf4, Sox2, and cMyc). It has been shown that several primary human cancer cell lines could be reprogrammed to iPSCs. We sought if immortalized mouse fibroblast cell lines could also be reprogrammed to iPSCs. The approach of generating iPSCs from such cells should be valuable in different experimental settings as it allows clonally derive cell lines carrying mutations whose impact on reprogramming could be next evaluated. Therefore, we investigated reprogramming of widely used immortalized cell lines (NIH3T and STO), as well as of de novo immortalized fibroblast line (tKM) with the use of highly effective lentiviral polycistronic OKSM expression system. Our reprogramming experiments have shown that in contrast to mouse embryonic fibroblasts (MEFs), none of the immortalized cell lines can be reprogrammed to pluripotent state. Contrary to colonies derived from MEFs, those derived from the immortalized cells lines (1) developed much later, (2) contained large round cells, not typical for iPSCs, and (3) were negative for trusted markers of matured iPSCs, Nanog and SSEA1. Immortalized cell lines NIH3T and STO are known to be mostly aneuploid, whereas tKM population includes cells with normal karyotype, however, neither cell type can be reprogrammed. Thus our data argue that aneuploidy per se is not a reason for the observed refractoriness of mouse immortalized cells to reprogramming to pluripotent state.

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Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells

Cited by 11 publications

References 27 publications

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state

MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways

Immortalized murine fibroblast cell lines are refractory to reprogramming to pluripotent state

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