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Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

ABSTRACT: Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

PROVIDER: PRJNA574945 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10202970.fastq.gz	Fastqsanger.gz
	SRR10202971.fastq.gz	Fastqsanger.gz
	SRR10202972.fastq.gz	Fastqsanger.gz
	SRR10202973.fastq.gz	Fastqsanger.gz
	SRR10202974.fastq.gz	Fastqsanger.gz

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Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

Project description:The PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) lines M98-WT and M98-E418K were obtained from a female, 18-y-old PROS patient by episomal reprogramming of a dermal fibroblast culture with 32% mosaicism for PIK3CA-E418K heterozygosity. All clones used for experimental studies were confirmed transgene-free and expressed high levels of pluripotent stem cell-specific markers, comparable to those of a reference hPSC line. Karyotyping on a single line from each genotype confirmed lack of microscopic genetic rearrangements. The original patient-derived dermal fibroblasts were obtained with full informed consent in accord with the Declaration of Helsinki. The study was approved by The Cambridge South Ethics.

2019-10-01 | GSE138161 | GEO

High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs

Project description:We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles of a wild-type induced pluripotent stem cell (iPSC) line (WTC11; Coriell # GM25256; P37-P38). Four cultures from each genotype (3 wild-type clones, 3 heterozygous clones, 2 homozygous clones) were subjected to paired-end mRNA sequencing (mean read length = 150 bp). The aim of this experiment was to confirm and expand upon previous transcriptomic results suggesting a near-binary transcriptional effect in homozygous versus heterozygous PIK3CA-H1047R iPSCs (publication doi: 10.1073/pnas.1821093116). According to the high-depth transcriptomic dataset, PIK3CA-H1047R/H1047R iPSCs exhibited altered expression of 5644 genes, whereas heterozygous hPSCs showed 492 differentially-expressed genes, supporting a nearly deterministic phenotypic effect of homozygosity for PIK3CA-H1047R. The differential gene expression analyses were performed based on the limma/voom/eBayes framework (doi: 10.1093/nar/gkv007), using customised scripts with FDR < 0.05 and absolute log2(fold-change) cut-off >= 1.3.

2019-10-01 | GSE134076 | GEO

Heterozygous and homozygous knock-in of PIK3CA-H1047R into human iPSCs

Project description:Heterozygous and homozygous knock-in of PIK3CA-H1047R into human iPSCs

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Heterozygous and homozygous knock-in of PIK3CA-H1047R into human iPSCs

Project description:We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles of a wild-type induced pluripotent stem cell (iPSC) line (WTC11; Coriell # GM25256; P37-P38). Three clones from each genotype (wild-type, heterozygous, homozygous) were subjected to single-end mRNA sequencing (mean read depth per sample: 20 million) to determine whether PIK3CA-H1047R exerts allele dose-dependent transcriptional effects. Multidimensional scaling demonstrated distinct transcriptomic signatures of wild-type, heterozygous and homozygous cells. The transcriptome of heterozygous cells was nearly identical to wild-type controls, with only 131 differentially-expressed transcripts (FDR = 0.05). In contrast, homozygosity for PIK3CA-H1047R led to differential expression of 1,914 genes. This indicates widespread transcriptional remodeling with a sharp allele dose-dependency, suggestive of a threshold effect.

2019-02-15 | GSE126562 | GEO

High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs

Project description:High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs

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High-dose oncogenic PIK3CA drives constitutive cellular stemness through increased NODAL/TGFb signaling

Project description:Oncogenic PIK3CA mutations activate phosphoinositide 3-kinase (PI3K) and are among the commonest somatic mutations in cancer and mosaic, developmental overgrowth disorders. We recently demonstrated that the ‘hotspot’ variant PIK3CAH1047R exerts striking allele dose-dependent effects on stemness in human induced pluripotent stem cells (iPSCs), and moreover demonstrated multiple oncogenic PIK3CA copies in a substantial subset of human cancers. To identify the molecular mechanism underpinning PIK3CAH1047R allele dose-dependent stemness, we profiled isogenic wild-type, PIK3CAWT/H1047R and PIK3CAH1047R/H1047R iPSCs by high-depth transcriptomics, proteomics and reverse-phase protein arrays (RPPA). PIK3CAH1047R/H1047R iPSCs exhibited altered expression of 5644 genes and 248 proteins, whereas heterozygous hPSCs showed 492 and 54 differentially-expressed genes and proteins, respectively, confirming a nearly deterministic phenotypic effect of homozygosity for PIK3CAH1047R. Pathway and network-based analyses predicted a strong association between self-sustained TGFb/NODAL signaling and the ‘locked’ stemness phenotype induced by homozygosity for PIK3CAH1047R. This stemness gene signature was maintained without exogenous NODAL in PIK3CAH1047R/H1047R iPSCs and was reversed by pharmacological inhibition of TGFb/NODAL signaling but not by PIK3CA-specific inhibition. Analysis of PIK3CA-associated human breast cancers revealed increased expression of the stemness markers NODAL and POU5F1 as a function of disease stage and PIK3CAH1047R allele dosage. Together with emerging realization of the link between NODAL re-expression and aggressive cancer behavior, our data suggest that TGFb/NODAL inhibitors warrant testing in advanced breast tumors with multiple oncogenic PIK3CA copies.

2021-03-03 | PXD014719 | Pride

Transcriptomic profileing of iPSC-derived engineered cardiac tissue in which cMyBP-C have been ablated in the heterozygous and homozygous states on an isogenic background

Project description:Truncation mutations in cardiac myosin binding protein C (cMyBP-C), are common causes of hypertrophic cardiomyopathy (HCM). Heterozygous carriers present with classical HCM, while homozygous carriers present with early onset HCM that rapidly progress to heart failure. We used CRISPR-Cas9 to introduce heterozygous (cMyBP-C+/-) and homozygous (cMyBP-C-/-) frame-shift mutations into MYBPC3 in human iPSCs. Cardiomyocytes derived from these isogenic lines were used to generate engineered cardiac tissue constructs (ECTs). RNAseq analysis on 14 day old ECTs revealed enrichment of differentially expressed hypertrophic, sarcomeric, Ca2+-handling and metabolic genes in cMyBP-C+/- and cMyBP-C-/- ECTs.

2023-02-23 | GSE224129 | GEO

Comparison of gene expression profile of SMEI patient iPSCs and control human Embryonic stem cells

Project description:SMEI patient induced pluripotent stem cells (iPSCs) were derived from patient fibroblasts. In order to test the similarity between patient iPSCs and human embryonic stem (hES) cells, microarry analysis was carried out on SMEI patient iPSCs and human embryonic stem cells. SMEI patient iPSCs were derived from patient fibroblasts. Human embryonic stem cells were derived from human blastocyst.And we use the microarray method to compare the global expression of patient iPSCs and embryonic stem cells.

2013-10-01 | E-GEOD-46472 | biostudies-arrayexpress

Phosphoproteomic analysis of breast epithelial cells with isogenic knockin of PIK3CA mutations

Project description:The PIK3CA gene is frequently mutated in human cancers. To study the signaling mechanisms responsible for cell growth and invasion phenotypes induced by mutant PIK3CA molecules, we carried out a SILAC-based quantitative phosphoproteomic analysis of MCF10A, a spontaneously immortalized normal mammary epithelial cell line, and two MCF10A knockin cell lines containing different activating mutations of the PIK3CA gene. MCF10A and PIK3CA mutation knock in cells were propagated in DMEM/F12 SILAC media deficient in both L-lysine and L-arginine and supplemented with light lysine (K) and arginine (R) for light, 2H4-K and 13C6-R for medium state and 13C615N2-K and 13C615N4-R for heavy state labeling. Cell lysates were prepared in urea lysis buffer containing 20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, 1 mM ß-glycerophosphate and 5mM sodium fluoride. The lysates were reduced, alkylated and digested by trypsin. Tryptic peptides were desalted by C18 reverse phase column and followed by strong cation exchange (SCX) fractionation. Fractionated peptides were subjected to TiO2-based phosphopeptide enrichment. LC-MS/MS analysis of enriched phosphopeptides was carried out using a reverse-phase liquid chromatography system interfaced with an LTQ-Orbitrap Velos mass spectrometer. Proteome Discoverer (v 1.3) suite was used for quantitation and database searches. The tandem mass spectrometry data were searched using Mascot (2.2.0) and SEQUEST search algorithms against a Human RefSeq database supplemented with frequently observed contaminants.

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HBV-KMT2B integrated human induced pluripotent stem cells (KMT2B-Int iPSCs) vs heterozygous mutated KMT2B iPSCs (KMT2B-HT iPSCs) vs homozygous mutated KMT2B iPSCs (KMT2B-KO iPSCs) vs their original iPSCs (KMT2B-WT iPSCs)

Project description:HBV-KMT2B integrated human induced pluripotent stem cells (KMT2B-Int iPSCs) vs heterozygous mutated KMT2B iPSCs (KMT2B-HT iPSCs) vs homozygous mutated KMT2B iPSCs (KMT2B-KO iPSCs) vs their original iPSCs (KMT2B-WT iPSCs)

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