title: SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage.
abstract: Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. TheSMN1protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as γ-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death.
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Mohini
authors.initials: M
authors.lastname: Jangi
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Christina
authors.initials: C
authors.lastname: Fleet
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Patrick
authors.initials: P
authors.lastname: Cullen
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Shipra V
authors.initials: SV
authors.lastname: Gupta
authors.affiliation: Stem Cell Research, Biogen, Cambridge, MA 02142.
authors.forename: Shila
authors.initials: S
authors.lastname: Mekhoubad
authors.affiliation: Stem Cell Research, Biogen, Cambridge, MA 02142.
authors.forename: Eric
authors.initials: E
authors.lastname: Chiao
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Norm
authors.initials: N
authors.lastname: Allaire
authors.affiliation: Neuroscience Drug Discovery, Ionis Pharmaceuticals, Carlsbad, CA 92008.
authors.forename: C Frank
authors.initials: CF
authors.lastname: Bennett
authors.affiliation: Neuroscience Drug Discovery, Ionis Pharmaceuticals, Carlsbad, CA 92008.
authors.forename: Frank
authors.initials: F
authors.lastname: Rigo
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Hurt
authors.affiliation: Computational Biology & Genomics, Biogen, Cambridge, MA 02142; john.carulli@biogen.com john.staropoli@biogen.com.
authors.forename: John P
authors.initials: JP
authors.lastname: Carulli
authors.affiliation: Rare Disease, Biogen, Cambridge, MA 02142 john.carulli@biogen.com john.staropoli@biogen.com.
authors.forename: John F
authors.initials: JF
authors.lastname: Staropoli
mesh_terms: D000818:Animals; D004249:DNA Damage; D004195:Disease Models, Animal; D006801:Humans; D007438:Introns; D051379:Mice; D009046:Motor Neurons / Q000378:metabolism; D009134:Muscular Atrophy, Spinal / Q000235:genetics / Q000378:metabolism*; D016376:Oligonucleotides, Antisense / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D055533:Survival of Motor Neuron 1 Protein / Q000235:genetics* / Q000378:metabolism*
chemical_list: D016376:Oligonucleotides, Antisense; D055533:Survival of Motor Neuron 1 Protein
keywords: DNA damage; SMA; SMN; neurodegeneration; splicing