Auto-qPCR: A Python-based web app for automated and reproducible analysis of qPCR data

Maussion, Gilles; Thomas, Rhalena A.; Demirova, Iveta; Gu, Gracia; Cai, Eddie; Chen, Carol X.-Q.; Abdian, Narges; Strauss, Theodore J. P.; Kelaï, Sabah; Javaudin, Angela Nauleau; Beitel, Lenore K.; Ramoz, Nicolás; Gorwood, Philip; Durcan, Thomas M.

doi:10.1101/2021.01.14.426748

Cited by 1 publication

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References 41 publications

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“…Two endogenous controls (beta-actin and GAPDH) were used for normalization. The normalized expression levels were determined according to the ΔCT method [28]. Data was analyzed with GraphPad Prism.…”

Section: Rna Extraction Cdna Synthesis and Quantitative Pcrmentioning

confidence: 99%

Transcriptional dysregulation and impaired neuronal activity inFMR1knock-out and Fragile X patients’ iPSC-derived models

Maussion,

Rocha,

Abdian

et al. 2023

Preprint

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The lack of fragile X mental retardation protein (FMRP) protein, due to a repression of the FMR1 gene, causes Fragile X syndrome (FXS), one of the most prevalent forms of syndromic autisms. The FMR1 gene codes for a RNA binding protein involved in the regulation of gene expression through RNA processing, control of local translation and protein-protein interactions; processes that are crucial for proper brain development. Taking advantage of induced pluripotent stem cells (iPSCs) and CRISPR-Cas9 genome editing technologies, we generated iPSC-derived cortical neural progenitors and cortical neurons from an FMR1 knock-out and patient cell line with the aim of identifying common phenotypes between the two cellular models. Using RNA sequencing, quantitative PCR and multielectrode array approaches, we assessed how the absence of the functional FMR1 gene affects the transcriptional profiles and the activities of iPSC-derived cortical neuronal progenitor cells (NPCs) and neurons with both models. We observed that FMR1 KO and FXS patient cells have a decrease in their mean firing rate; a cellular activity that can also be blocked by tetrodotoxin (TTX) application in wild type active neurons. Relative to wild type neurons, in FMR1 KO neurons, increased expression of presynaptic mRNA and transcription factors involved in the forebrain specification and decreased levels of mRNA coding AMPA and NMDA subunits was observed. Intriguingly, 40% of the differentially expressed genes were commonly deregulated between NPCs and differentiating neurons with significant enrichments in FMRP targets and Autism Related Genes found amongst downregulated genes. This implies that an absence of functional FMRP affects transcriptional profiles at the NPC stage, resulting in impaired activity and differentiation of the progenitors into mature neurons over time. These findings from the FMR1 KO lines were also shared with FXS patient's iPSC-derived cells that also present with an impairment in activity and neuronal differentiation, illustrating the critical role of FMRP protein in neuronal development.

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Section: Rna Extraction Cdna Synthesis and Quantitative Pcrmentioning

confidence: 99%