Cited by 91Genetics and Neurodevelopmental DisordersGenomics and Rare DiseasesNeuroscience and Neuropharmacology Research

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

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Pacheco, Natasha L., Heaven, Michael R., Holt, Leanne M., Crossman, David K., Boggio, Kristin J., Shaffer, Scott A., Flint, Daniel L., Olsen, Michelle L.·2017·Molecular Autism

Abstract

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by mutations in the transcriptional regulator MeCP2. Much of our understanding of MeCP2 function is derived from transcriptomic studies with the general assumption that alterations in the transcriptome correlate with proteomic changes. Advances in mass spectrometry-based proteomics have facilitated recent interest in the examination of global protein expression to better understand the biology between transcriptional and translational regulation. We therefore performed the first comprehensive transcriptome-proteome comparison in a RTT mouse model to elucidate RTT pathophysiology, identify potential therapeutic targets, and further our understanding of MeCP2 function. The whole cortex of wild-type and symptomatic RTT male littermates ( n = 4 per genotype) were analyzed using RNA-sequencing and data-independent acquisition liquid chromatography tandem mass spectrometry. Ingenuity® Pathway Analysis was used to identify significantly affected pathways in the transcriptomic and proteomic data sets. Our results indicate these two “omics” data sets supplement one another. In addition to confirming previous works regarding mRNA expression in Mecp2 -deficient animals, the current study identified hundreds of novel protein targets. Several selected protein targets were validated by Western blot analysis. These data indicate RNA metabolism, proteostasis, monoamine metabolism, and cholesterol synthesis are disrupted in the RTT proteome. Hits common to both data sets indicate disrupted cellular metabolism, calcium signaling, protein stability, DNA binding, and cytoskeletal cell structure. Finally, in addition to confirming disrupted pathways and identifying novel hits in neuronal structure and synaptic transmission, our data indicate aberrant myelination, inflammation, and vascular disruption. Intriguingly, there is no evidence of reactive gliosis, but instead, gene, protein, and pathway analysis suggest astrocytic maturation and morphological deficits. This comparative omics analysis supports previous works indicating widespread CNS dysfunction and may serve as a valuable resource for those interested in cellular dysfunction in RTT.

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  • Elimination of MeCP2 affects the expression of a profound number of pathways in the CNS, making it difficult to pinpoint which pathways play a key role in RTT pathology.

    “While Mecp2 mutant mice are an excellent model for RTT, elimination of MeCP2 affects the expression of a profound number of pathways in the CNS, making it difficult to pinpoint which ones play a key role in pathology [77,89,90].”

    From Rett syndrome: a neurological disorder with metabolic components (2018) · cites this paper as [90]

    The Results section (‘Pathway analysis in transcriptome and proteome implicate similar biological pathways’; page unavailable) reports diverse disrupted pathways in the cortex of Mecp2-deficient mice, supporting the claim that MeCP2 loss affects many pathways. The paper does not explicitly say that this makes it difficult to identify which pathways are key to RTT pathology, and its measurements are from cortex rather than the CNS as a whole. (LLM, conf=0.82)

    Experimental — accuracy not yet measured
  • MeCP2 may be defined as a transcriptional modulator.

    “Altogether, multiple studies suggest that genes can be activated or repressed by MeCP2, depending upon the cellular context [77,89,90], suggesting that MeCP2 may be defined as a transcriptional modulator.”

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Authors
Pacheco, N. L., Heaven, M. R., Holt, L. M., Crossman, D. K., Boggio, K. J., Shaffer, S. A., Flint, D. L., & Olsen, M. L.
Affiliations
  • University of Alabama at Birmingham (US)
  • University of Massachusetts Chan Medical School (US)
Corresponding author
Olsen, Michelle L.
Venue
Molecular Autism
Published
2017-10-24
Volume
8
Issue
1
Pages
56-56
ISSN
2040-2392 (ISSN-L)
OpenAlex
W2765768583
Cited by
90
References
157
Citations by year
2026: 5 · 2025: 6 · 2024: 10 · 2023: 10 · 2022: 9 · 2021: 14 · 2020: 15 · 2019: 13 · 2018: 8
FWCI
6.54
Type
journal article
Language
en
Open access
Locations
  • Molecular Autism (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • VTechWorks (Virginia Tech) (submittedVersion)
  • VTechWorks (Virginia Tech) (submittedVersion, public-domain)
Funders
  • National Institute of Neurological Disorders and Stroke (R01HL104101)
  • Civitan Emerging Research Scholar Award, University of Alabama at Birmingham (3116072)
  • Comprehensive Cancer Center, University of Alabama at Birmingham (CA13148)
  • Center for AIDS Research, University of Alabama at Birmingham (AI027767)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
Keywords
Rett syndrome, MeCP2, cerebral cortex, RNA metabolism, proteostasis, monoamine metabolism, cholesterol biosynthesis, calcium signaling, protein stability, astrocyte maturation, myelination, neuroinflammation, synaptic transmission, therapeutic target
MeSH terms
Animals, Cerebral Cortex, Chromatography, High Pressure Liquid, Disease Models, Animal, Female, Genotype, Male, Mice, Inbred C57BL, Neurons, Phenotype, RNA, Rett Syndrome, Sequence Analysis, RNA, Mice, Knockout, Proteome, Proteomics, Mice, Methyl-CpG-Binding Protein 2, Tandem Mass Spectrometry, Transcriptome

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