SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.

1. Autophagy. 2021 Aug;17(8):1889-1906. doi: 10.1080/15548627.2020.1796292. Epub 2020 Aug 7. SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation. Richard P(1)(2), Feng S, Tsai YL(1), Li W(3), Rinchetti P(4)(5), Muhith U(1), Irizarry-Cole J(1), Stolz K(1), Sanz LA(6), Hartono S(6), Hoque M(3), Tadesse S(7), Seitz H(8), Lotti F(4), Hirano M(7), Chédin F(6), Tian B(3)(9), Manley JL(1). Author information: (1)Department of Biological Sciences, Columbia University, New York, NY, USA. (2)Stellate Therapeutics, JLABS @ NYC, New York, NY, USA. (3)Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA. (4)Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA. (5)Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy. (6)Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA. (7)Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA. (8)Institut de Génétique Humaine, UMR 9002 CNRS and Université de Montpellier, Montpellier, France. (9)Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, USA. SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed the effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX-depleted cells. Importantly, we discovered a strong connection between SETX and the macroautophagy/autophagy pathway, reflecting a direct effect on transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2.Abbreviations: 3'READS: 3' region extraction and deep sequencing; ACTB: actin beta; ALS4: amyotrophic lateral sclerosis type 4; AOA2: ataxia with oculomotor apraxia type 2; APA: alternative polyadenylation; AS: alternative splicing; ATG7: autophagy-related 7; ATP6V0D2: ATPase H+ transporting V0 subunit D2; BAF: bafilomycin A1; BECN1: beclin 1; ChIP: chromatin IP; Chloro: chloroquine; CPT: camptothecin; DDR: DNA damage response; DNMT1: DNA methyltransferase 1; DRIP: DNA/RNA IP; DSBs: double strand breaks; EBs: embryoid bodies; FTD: frontotemporal dementia; GABARAP: GABA type A receptor-associated protein; GO: gene ontology; HR: homologous recombination; HTT: huntingtin; IF: immunofluorescence; IP: immunoprecipitation; iPSCs: induced pluripotent stem cells; KD: knockdown; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MN: motor neuron; MTORC1: mechanistic target of rapamycin kinase complex 1; PASS: PolyA Site Supporting; PFA: paraformaldehyde; RNAPII: RNA polymerase II; SCA: spinocerebellar ataxia; SETX: senataxin; SMA: spinal muscular atrophy; SMN1: survival of motor neuron 1, telomeric; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TSS: transcription start site; TTS: transcription termination site; ULK1: unc-51 like autophagy activating kinase 1; WB: western blot; WIPI2: WD repeat domain, phosphoinositide interacting 2; XRN2: 5'-3' exoribonuclease 2. DOI: 10.1080/15548627.2020.1796292 PMCID: PMC8386630 PMID: 32686621 [Indexed for MEDLINE] Conflict of interest statement: No potential conflict of interest was reported by the authors.