C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

Mila Mirceta; Monika H.M. Schmidt; Natalie Shum; Tanya K. Prasolava; Bryanna Meikle; Stella Lanni; Mohiuddin Mohiuddin; Paul M. McKeever; Ming Zhang; Minggao Liang; Ilse van der Werf; Stefaan Scheers; Patrick A. Dion; Peixiang Wang; Michael D. Wilson; Theresa Abell; Elliot A. Philips; Łukasz J. Sznajder; Maurice S. Swanson; Mustafa Hussain Mehkary; Mahreen Khan; Katsuyuki Yokoi; Christine J. Jung; Pieter J. de Jong; Catherine H. Freudenreich; Philip McGoldrick; Ryan K. C. Yuen; Agessandro Abrahão; Julia Lee Keith; Lorne H. Zinman

doi:10.1101/2024.10.26.620312

GeneticsbioRxivOct 26, 2024

Preprint

C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

Mila Mirceta, Monika H.M. Schmidt iD, Natalie Shum, Tanya K. Prasolava, Bryanna Meikle, Stella Lanni iD, Mohiuddin Mohiuddin iD, Paul M. McKeever iD, Ming Zhang iD, Minggao Liang iD, Ilse van der Werf iD, Stefaan Scheers, Patrick A. Dion iD, Peixiang Wang iD, Michael D. Wilson iD, Theresa Abell, Elliot A. Philips iD, Łukasz J. Sznajder iD, Maurice S. Swanson iD, Mustafa Hussain Mehkary iD, Mahreen Khan iD, Katsuyuki Yokoi iD, Christine J. Jung, Pieter J. de Jong iD, Catherine H. Freudenreich iD, , Christopher E. Pearson iD

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Abstract

The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. Here, we show C9orf72Exp in pre-symptomatic and ALS-FTD patient cells and brains cause the folate- sensitive chromosomal fragile site, FRA9A. FRA9A centers on >33kb of C9orf72 as highly-compacted chromatin embedded in an 8.2Mb fragility zone spanning 9p21, encompassing 46 genes, making FRA9A one of the largest fragile sites. C9orf72Exp cells show chromosomal instability, heightened global- and Chr9p-enriched sister-chromatid exchanges, truncated-Chr9s, acentric-Chr9s and Chr9-containing micronuclei, providing endogenous sources of damaged and immunostimulatory DNA. Cells from one C9orf72Exp patient contained highly-rearranged FRA9A-expressing Chr9 with Chr9-wide dysregulated gene expression. Somatic C9orf72Exp repeat instability and chromosomal fragility are sensitive to folate-deficiency. Age-dependent repeat instability, chromosomal fragility, and chromosomal instability can be transferred to CNS and peripheral tissues of transgenic C9orf72Exp mice, implicating C9orf72Exp as the source. Our results highlight unappreciated effects of C9orf72 expansions that trigger vitamin-sensitive chromosome fragility, adding structural variations to the disease-enriched 9p21 locus, and likely elsewhere. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/620312v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@154b23borg.highwire.dtl.DTLVardef@1814a6dorg.highwire.dtl.DTLVardef@13d713eorg.highwire.dtl.DTLVardef@d5d994_HPS_FORMAT_FIGEXP M_FIG C_FIG