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Gene expression profiling of neural stem cells derived from iPS cells (iPSc) of Sanfilippo syndrome type B (MPSIIIB) patient versus control

ABSTRACT: We generated iPSc from skin fibroblasts of two MPSIIIB patients (P1 and P2). MPSIIIB-associated cell defects were prominent in undifferentiated iPSc, in neural stem cells and in their neuronal progeny. We explored alterations of metabolic pathways in MPSIIIB neural cells by performing gene expression profiling of patient versus control neural stem cells. Exon array transcriptome analysis showed 295 transcripts with increased expression level and 1275 transcripts with decreased expression level in patient versus control neural precursors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE23075 | GEO | 2010/07/24

SECONDARY ACCESSION(S): PRJNA131683

REPOSITORIES: GEO

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Gene expression profiling of neural stem cells derived from iPS cells (iPSc) of Sanfilippo syndrome type B (MPSIIIB) patient versus control

Project description:We generated iPSc from skin fibroblasts of two MPSIIIB patients (P1 and P2). MPSIIIB-associated cell defects were prominent in undifferentiated iPSc, in neural stem cells and in their neuronal progeny. We explored alterations of metabolic pathways in MPSIIIB neural cells by performing gene expression profiling of patient versus control neural stem cells. Exon array transcriptome analysis showed 295 transcripts with increased expression level and 1275 transcripts with decreased expression level in patient versus control neural precursors. Total RNA was extracted from proliferating neurosphere cultures derived from two control (C1 and C3) and three patient (P1.1, P1.3, and P2.3) iPSc clones. We considered a minimal fold change of 1.5 fold and a corrected P value lower than 0.05.

2010-07-24 | E-GEOD-23075 | biostudies-arrayexpress

A threshold level of NFATc1 activity is critical for thymocyte differentiation and to prevent leukemia development

Project description:NFATc1 plays a critical role in double-negative thymocyte survival and differentiation. However, the signals that regulate Nfatc1 expression are unknown. Here we show a developmental stage-specific differential expression pattern of Nfatc1 driven by the distal (P1) or proximal (P2) promoters in thymocytes. Whereas, preTCR-negative thymocytes exhibited only P2 promoter-derived Nfatc1b expression, preTCR-positive thymocytes expressed both Nfatc1b and P1 promoter-derived Nfatc1a transcripts. Inducing NFATc1a activity from P1 promoter in preTCR-negative thymocytes, in addition to the NFATc1a from P2 promoter impaired thymocyte development resulting in severe T cell lymphopenia. Additionally, we show that NFATc1 activity suppressed the B-lineage potential of immature thymocytes, and consolidated their differentiation to T cells. Further, in the pTCR-positive DN3 cells, a threshold level of NFATc1 activity was vital in facilitating T cell differentiation and to prevent T-acute lymphoblastic leukemia (T-ALL) development. Altogether, our results show NFATc1 activity is crucial in determining the T cell fate of thymocytes.

2016-04-20 | GSE80138 | GEO

ib101206 - proteome data analysis

Project description:P2 is a spontaneous mutant selected from P1, an entomopathogenic fungus Beauveria bassiana that hyper-produces extracellular protease(s), compared to P1. The major expressed serine protease, called SBP, is shown to be up-regulated at the transcriptional level in the P2 mutant strain. The insecticidal potential of P1 and P2 strains was evaluated against Tuta absoluta larvae under laboratory conditions. Both strains are effective but P2 showed stronger effect than P1. Median lethal concentration (LC50) of P2 is 26 fold lower than that of P1. Median lethal times (LT50) of P1 and P2 are 4.38 and 0.84 days using 105 conidia ml-1. Enzymatic assays analysis showed that extracellular enzymes are differently expressed by the two strains, especially proteases and chitinases. Two-dimensional gel electrophoresis and mass spectrometry analysis confirmed the overexpression by P2 strain of protease and chitinase and revealed further the over-expression of several protease isoforms. Here we show a direct link between fungal enzymatic profile and insect’s pathogenesis, giving a molecular explanation for the insecticidal potential of B. bassiana fungus.

2018-03-19 | PXD003287 | Pride

Developmentally regulated isoform of HNF4α reprograms the adult liver

Project description:Hepatocyte Nuclear Factor 4α (HNF4α), master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4α but not P2-HNF4α is expressed in normal adult liver in fed conditions. Both P1- and P2-HNF4α are expressed in fetal liver. P2-HNF4α expression is increased in fasted conditions, high fat diet, alcoholic liver and liver cancer. To determine the target genes of the P1- and P2-HNF4α isoforms, we compared P2-HNF4α-expressing exon swap mice (a7HMZ) to wildtype (WT) male mice. Liver ChIP-seq samples were taken at 10:30 AM (ZT 3.5)

2023-05-10 | GSE231538 | GEO

ISG15 in regulation of interferon responses

Project description:We assessed how lack of ISG15 influences the levels of transcripts after IFNa stimulation. Expression data from ISG15 deficient patients (P1, P2, P3) and control (C1, C6, C16) hTert fibroblasts

2014-12-01 | GSE60359 | GEO

Developmentally regulated isoform of HNF4α reprograms the adult liver

Project description:Hepatocyte Nuclear Factor 4α (HNF4α), master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4α but not P2-HNF4α is expressed in normal adult liver while both P1- and P2-HNF4α are expressed in fetal liver and liver cancer. To determine the physiological function of the HNF4α isoforms, we compared P2-HNF4α-expressing exon swap mice to wildtype (WT) using RNA-seq, ChIP-seq, proteomics, protein binding microarrays (PBMs) and metabolomics. P2-HNF4α orchestrates a distinct transcriptomic and metabolomic profile.

2018-08-31 | GSE117972 | GEO

From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells. Exon-level analysis

Project description:TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres to detect specific transcription isoforms associated to cancer stem cell. TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres. Exon-level transcription profiling was done using Affimetrix GeneChip Exon 1.0 ST. Exon-level analysis is more complex than gene-level analysis. The number of probesets to be investigated is at least 10 times larger in number than gene-level probesets. Thus results, upon statistical analysis, are massively contaminated by type I statistical errors, i.e. false positive [Della Beffa et al. 2008]. Furthermore, exon-level probesets are based only on four probes, which makes exon-level signal summarization more noisy than gene-level, where signal summarization is based on the overall probes encompassed by all exons of a gene. To moderate these issues we have expanded the number of experimental replications: six for TuBo and passage 1 mammosphere, four for passage 3 mammosphere and three for passage 2 mammosphere. Furthermore, after data summarization with RMA and normalization with sketch quantile method, alternative splicing detection between epithelial and mammospheres passages, was assessed using MiDAS, a two way anova developed by Affymetrix for the detection of alternative splicing events. We considered suitable for further investigations the splicing events in common between the sets of exons detected as spliced in each of the following comparisons: E vs P1, E vs P2 and E vs P3.

2013-11-30 | E-GEOD-21475 | biostudies-arrayexpress

Characterization of human sperm protamine proteoforms through a combination of top-down and bottom-up mass spectrometry approaches

Project description:Protamine 1 (P1) and protamine 2 family (P2) are the most abundant nuclear basic spermspecific proteins, packing 85-95% of the paternal DNA. P1 is synthesized as a mature form, whereas P2 components (HP2, HP3 and HP4) arise from the proteolysis of the precursor (pre-P2). Due to the particular protamine physical-chemical properties, their identification by standardized bottom-up mass spectrometry (MS) strategies are not straightforward. Therefore, the aim of this study was to identify the sperm protamine proteoforms profile including P1 and P2 members and their post-translational modifications in normozoospermic individuals using two complementary strategies, a top-down MS approach and a proteinase K-digestion based bottom-up MS approach. By top-down MS approach, both described and new truncated P1 and pre-P2 proteoforms were identified. Likewise, intact P1, pre-P2, and P2 mature forms and their phosphorylation pattern were detected, as well as a +61 Da modification in different proteoforms. Additionally, the bottom-up MS approach revealed phosphorylated residues for pre-P2 and the new P2 isoform 2, which is not annotated at UniProtKB database. Implementing these strategies in comparative studies of different infertile phenotypes would permit to determine alterations in the protamine proteoforms pattern and elucidate the role of phosphorylation/dephosphorylation dynamics in male fertility.

2019-11-11 | PXD014618 | Pride

Lin28R192G mutation in Parkinsons's disease

Project description:mRNA-seq analyses for the differentially expressed genes (DEGs) between Parkinsons's disease patient (holding Lin28 R192G hetero mutation)-iPSC (Pt-iPSC) derived neural stem cell vs Lin28 R192G hetero mutation corrected-iPSC (Corrected Pt-iPSC) derived neural stem cell. To gain further molecular insight into the observed Lin28R192G mutation in Parkinsons's disease (PD) patient iPSC-derived neural stem cell (NSC) functions, we performed mRNA-sequencing (RNA-seq) analysis of the PD patient (holding Lin28 R192G hetero mutation)-iPSC (Pt-iPSC) derived NSC and Lin28 R192G hetero mutation corrected-iPSC (Corrected Pt-iPSC) derived NSC.

2019-08-20 | GSE135995 | GEO

RNAseq for subpopulations of adipose tissue stromal cells from mouse inguinal adipose tissue

Project description:We performed bulk RNA sequencing of several subpopulations of adipose tissue stromal cells to better understand the function of preadipocyte subpopulation (P1 and P2) in mouse inguinal adipose tissue. P1 and P2 cells isolated from inguinal adipose tissue from male and female C57/B6 mice, collected by FACS. P1 cells are CD31-CD45-TER119-SCA1+CD55+VAP1-CD142- cell population, and P2 cells are CD31-CD45-TER119-SCA1+CD55-VAP1+CD142- cell population. 50,000 cells were collected for each populations.

2021-12-07 | E-MTAB-9827 | biostudies-arrayexpress

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