Abstract
Fragile X syndrome (FXS) patients carry the expansion of over 200 CGG repeats at the promoter of fragile X mental retardation 1 (FMR1), leading to decreased or absent expression of its encoded fragile X mental retardation protein (FMRP). However, the global transcriptional alteration by FMRP deficiency has not been well characterized at single nucleotide resolution, i.e., RNA-seq. Here, we performed in-vitro neuronal differentiation of human induced pluripotent stem (iPS) cells that were derived from fibroblasts of a FXS patient (FXS-iPSC). We then performed RNA-seq and examined the transcriptional misregulation at each intermediate stage during in-vitro differentiation of FXS-iPSC into neurons. After thoroughly analyzing the transcriptomic data and integrating them with those from other platforms, we found up-regulation of many genes encoding TFs for neuronal differentiation (WNT1, BMP4, POU3F4, TFAP2C, and PAX3), down-regulation of potassium channels (KCNA1, KCNC3, KCNG2, KCNIP4, KCNJ3, KCNK9, and KCNT1) and altered temporal regulation of SHANK1 and NNAT in FXS-iPSC derived neurons, indicating impaired neuronal differentiation and function in FXS patients. In conclusion, we demonstrated that the FMRP deficiency in FXS patients has significant impact on the gene expression patterns during development, which will help to discover potential targeting candidates for the cure of FXS symptoms.
Highlights
Fragile X syndrome (FXS) is a common hereditary disorder associated with an array of intellectual limitations and emotional disabilities, and is referred to as the most frequent monogenic cause of autism
Some microarray-based gene expression profiling data were generated from Fmr1 null mice (D’Agata et al, 2002), FXS patients’ lymphoblastoid cells (Bittel et al, 2007), and FXS patient derived induced pluripotent stem (iPS) cells (Halevy et al, 2015), RNA-seq with higher throughput and resolution is urgently needed to dissect the transcriptional perturbation evoked by Fragile X mental retardation protein (FMRP) deficiency
Investigators are pursuing the question of whether and how the transcription machinery is altered in the FXS patients (Bittel et al, 2007; D’Agata et al, 2002; Halevy et al, 2015), the disturbed translation has been widely accepted as molecular mechanism underlying FXS (Darnell and Klann, 2013)
Summary
Fragile X syndrome (FXS) is a common hereditary disorder associated with an array of intellectual limitations and emotional disabilities, and is referred to as the most frequent monogenic cause of autism. In FXS patients, the CGG repeats at the 5′ untranslated region (5′ UTR) of fragile X mental retardation 1 (FMR1) are dramatically increased (>200) compared to the healthy individuals. This trinucleotide expansion results in many epigenetic alterations including DNA hypermethylation and histone modifications, which silences the expression of FMR1 (Bagni et al, 2012). FMRP comprises the nuclear export signal (NES) and nuclear localization signal (NLS) domains and shuttles between the nucleus and cytoplasm (Eberhart et al, 1996; Feng et al, 1997; Sittler et al, 1996) Since it functions as a chromatin-binding protein responding to the DNA damage (Alpatov et al, 2014), it is very likely that FMRP may directly modulate the transcription in the nucleus. Some microarray-based gene expression profiling data were generated from Fmr null mice (D’Agata et al, 2002), FXS patients’ lymphoblastoid cells (Bittel et al, 2007), and FXS patient derived iPS cells (Halevy et al, 2015), RNA-seq with higher throughput and resolution is urgently needed to dissect the transcriptional perturbation evoked by FMRP deficiency
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