Model Testing of PluriTest with Next-Generation Sequencing Data

Schulze, Markus; Hoja, S; Winner, Beate; Winkler, Jürgen; Edenhofer, Frank; Riemenschneider, Markus J.

doi:10.1089/scd.2015.0266

Cited by 6 publications

(16 citation statements)

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“…1b ). We then validated that all iPSCs corresponded to high quality pluripotent cells according to our recent PluriTest adaption for NGS [ 57 ] (Fig. 1c ).…”

Section: Resultsmentioning

confidence: 99%

“…1c ). This means that all cell preparations mapped at least within a calculated statistical cut-off, with most preparations also meeting the requirements of an empirical cut-off of high quality pluripotent cells (for further information see [ 57 ]). We checked for the expression of pluripotency marker genes (in the range of high quality pluripotent cells, Additional file 2 : Figure S1), ensured that cells showed viral transgene silencing (examined by direct mapping to the vector sequences used for reprogramming) and excluded that markers of insufficient viral transgene silencing were overexpressed [ 27 ] (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The neurons generated cluster well with dopaminergic neurons available in databases [ 34 ]. c PluriTest [ 40 ] adaption [ 57 ] showing high similarity between embryonic stem cells and induced pluripotent stem cells in our cohort. d CTRL and PD iPSCs are comparable in their viral transgene silencing as well as in the range of a published iPSC cohort [ 1 ].…”

Section: Resultsmentioning

confidence: 99%

“…Due to historical reasons, the mRNA data for quality control analyses of iPSCs were mapped to the human genome GRCh37 without mismatch. We included all samples that we analysed, as long as they met the following criteria: iPSCs had to show a marker expression of the pluripotency markers DNMT3B, SOX2, NANOG, OCT4 and REX1 within the range of a previously analysed high quality ESC cohort and to fall at least in the safety margin of a previously established database driven PluriTest adaption [ 57 ]. Furthermore, viral transgene silencing had to be comparable to a published cohort for which NGS raw data was freely available [ 1 ].…”

Section: Methodsmentioning

confidence: 99%

“…We analysed viral transgene silencing both by comparison of RPKM values of established markers of viral transgene silencing [ 27 ] as well as by direct mapping of the plasmids used for reprogramming counting multiple and unique hits when mapping against the vector sequence (excluding the coding regions of the pluripotency factors) normalized to the number of unique hits of the respective sequencing run when mapped to the genome. The upper-limit cut-offs shown in the supplementary material were calculated as described in [ 57 ]. SNPs were called within the Genomatix Genome analyser with a workflow based on samtools, with at least 4 x coverage per SNP and exclusion of indels.…”

Section: Methodsmentioning

confidence: 99%

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Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Schulze

Sommer

Plötz

et al. 2018

acta neuropathol commun

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Differentiated neurons established via iPSCs from patients that suffer from familial Parkinson’s disease (PD) have allowed insights into the mechanisms of neurodegeneration. In the larger cohort of patients with sporadic PD, iPSC based information on disease specific cellular phenotypes is rare. We asked whether differences may be present on genomic and epigenomic levels and performed a comprehensive transcriptomic and epigenomic analysis of fibroblasts, iPSCs and differentiated neuronal cells of sporadic PD-patients and controls. We found that on mRNA level, although fibroblasts and iPSCs are largely indistinguishable, differentiated neuronal cells of sporadic PD patients show significant alterations enriched in pathways known to be involved in disease aetiology, like the CREB-pathway and the pathway regulating PGC1α. Moreover, miRNAs and piRNAs/piRNA-like molecules are largely differentially regulated in cells and post-mortem tissue samples between control- and PD-patients. The most striking differences can be found in piRNAs/piRNA-like molecules, with SINE- and LINE-derived piRNAs highly downregulated in a disease specific manner. We conclude that neuronal cells derived from sporadic PD-patients help to elucidate novel disease mechanisms and provide relevant insight into the epigenetic landscape of sporadic Parkinson’s disease as particularly regulated by small RNAs.Electronic supplementary materialThe online version of this article (10.1186/s40478-018-0561-x) contains supplementary material, which is available to authorized users.

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“…1b ). We then validated that all iPSCs corresponded to high quality pluripotent cells according to our recent PluriTest adaption for NGS [ 57 ] (Fig. 1c ).…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Schulze

Sommer

Plötz

et al. 2018

acta neuropathol commun

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Induced neural progenitor cells and iPS-neurons from major depressive disorder patients show altered bioenergetics and electrophysiological properties

et al. 2022

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The molecular pathomechanisms of major depressive disorder (MDD) are still not completely understood. Here, we follow the hypothesis, that mitochondria dysfunction which is inevitably associated with bioenergetic disbalance is a risk factor that contributes to the susceptibility of an individual to develop MDD. Thus, we investigated molecular mechanisms related to mitochondrial function in induced neuronal progenitor cells (NPCs) which were reprogrammed from fibroblasts of eight MDD patients and eight non-depressed controls. We found significantly lower maximal respiration rates, altered cytosolic basal calcium levels, and smaller soma size in NPCs derived from MDD patients. These findings are partially consistent with our earlier observations in MDD patient-derived fibroblasts. Furthermore, we differentiated MDD and control NPCs into iPS-neurons and analyzed their passive biophysical and active electrophysiological properties to investigate whether neuronal function can be related to altered mitochondrial activity and bioenergetics. Interestingly, MDD patient-derived iPS-neurons showed significantly lower membrane capacitance, a less hyperpolarized membrane potential, increased Na+ current density and increased spontaneous electrical activity. Our findings indicate that functional differences evident in fibroblasts derived from MDD patients are partially present after reprogramming to induced-NPCs, could relate to altered function of iPS-neurons and thus might be associated with the aetiology of major depressive disorder.

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Human Induced Pluripotent Stem Cell-Derived Pericytes as Scalable and Editable Source to Study Direct Lineage Reprogramming Into Induced Neurons

Menon

Petrucci

Lohrer

et al. 2023

Cellular Reprogramming

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Model Testing of PluriTest with Next-Generation Sequencing Data

Cited by 6 publications

References 3 publications

Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Induced neural progenitor cells and iPS-neurons from major depressive disorder patients show altered bioenergetics and electrophysiological properties

Human Induced Pluripotent Stem Cell-Derived Pericytes as Scalable and Editable Source to Study Direct Lineage Reprogramming Into Induced Neurons

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