Tissue- and cell-specific whole-transcriptome meta-analysis from brain and retina reveals differential expression of dystrophin complexes and new dystrophin spliced isoforms

Abstract

The large DMD gene encodes a group of dystrophin proteins in brain and retina, produced from multiple promoters and alternative splicing events. Dystrophins are core components of different scaffolding complexes in distinct cell types. Their absence may thus alter several cellular pathways, which might explain the heterogeneous genotype–phenotype relationships underlying central comorbidities in Duchenne muscular dystrophy (DMD). However, the cell-specific expression of dystrophins and associated proteins (DAPs) is still largely unknown. The present study provides a first RNA-Seq-based reference showing tissue and cell-specific differential expression of dystrophins, splice variants and DAPs in mouse brain and retina. We report that a cell type may express several dystrophin complexes, perhaps due to expression in separate cell subdomains and/or subpopulations, some of which with differential expression at different maturation stages. We also identified new splicing events in addition to the common exon-skipping events. These include a new exon within intron 51 (E51b) in frame with the flanking exons in retina, as well as inclusions of intronic sequences with stop codons leading to the presence of transcripts with elongated exons 40 and/or 41 (E40e, E41e) in both retina and brain. PCR validations revealed that the new exons may affect several dystrophins. Moreover, immunoblot experiments using a combination of specific antibodies and dystrophin-deficient mice unveiled that the transcripts with stop codons are translated into truncated proteins lacking their C-terminus, which we called N-Dp427 and N-Dp260. This study thus uncovers a range of new findings underlying the complex neurobiology of DMD.

Dmd mdx mice have defective oligodendrogenesis, delayed myelin compaction and persistent hypomyelination

“…However, since we observed fewer proliferating OPCs during increased expression of SOX2, additional molecular changes are probably involved, which lead to OPC alterations. One possibility is that loss of dystrophin affects the number of astrocytes, which also express dystrophin ( Nico et al, 2003 ; Garcia-Cruz et al, 2023 ). However, we did not observe changes in levels of GFAP, widely used a marker for astrocytes.…”

“…Previous studies have revealed dystrophin expression in multiple areas of the brain, including neurons, astrocytes and oligodendrocytes (OLs) ( Hoffman et al, 1988 ; Miike et al, 1989 ; Gorecki et al, 1991 ; Bies et al, 1992 ; Yoshioka et al, 1992 ; Lidov et al, 1993 ; Tokarz et al, 1998 ; Garcia-Cruz et al, 2023 ; Aranmolate et al, 2017 ), yet the cell and molecular mechanisms that contribute to neurological deficits in DMD remain largely unexplored. In addition, dystrophin expression in the brain appears to be highly complex, with different dystrophin gene products being regulated both spatially and temporally ( Garcia-Cruz et al, 2023 ; Romo-Yanez et al, 2020 ).…”

“…Previous studies have revealed dystrophin expression in multiple areas of the brain, including neurons, astrocytes and oligodendrocytes (OLs) ( Hoffman et al, 1988 ; Miike et al, 1989 ; Gorecki et al, 1991 ; Bies et al, 1992 ; Yoshioka et al, 1992 ; Lidov et al, 1993 ; Tokarz et al, 1998 ; Garcia-Cruz et al, 2023 ; Aranmolate et al, 2017 ), yet the cell and molecular mechanisms that contribute to neurological deficits in DMD remain largely unexplored. In addition, dystrophin expression in the brain appears to be highly complex, with different dystrophin gene products being regulated both spatially and temporally ( Garcia-Cruz et al, 2023 ; Romo-Yanez et al, 2020 ). Of particular note, dystrophin expression and function has been identified in neuronal inhibitory synapses ( Zarrouki et al, 2022 ; Vaillend and Chaussenot, 2017 ; Miranda et al, 2009 ) and in astrocytic terminal processes (also known as endfeet) of the blood-brain barrier ( Nico et al, 2003 , 2004 ), implicating these cells in DMD neuropathology.…”

Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology

“…The production of precursor messenger RNA and alternative RNA splicing play a crucial part in the post-transcriptional regulation of gene expression. For example, the sarcoplasmic reticulum Ca 2+ -ATPase exists in the form of several protein Some genes that contain protein-coding sequences for the production of musclespecific components, such as the extremely large X-chromosomal DMD gene that encodes the Dp427-M isoform of the membrane cytoskeletal protein named dystrophin, have more than one promoter [282] (Figure 9). Thus, several protein products with tissuespecific expression patterns can derive from the sequence information that is stored in one individual gene.…”

Nuclear Small Dystrophin Isoforms during Muscle Differentiation

“…The resulting dystrophin proteins (Dp) have been named according to their molecular mass. So far, the described proteins include Dp427 (full-length dystrophin), Dp260, Dp140, Dp116, Dp71, and Dp40, which are found in different tissues, such as the brain, muscle, retina, kidney, peripheral nerves, liver and lung [ 1 , 4 ].…”