TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage.

Marta Giannini,Andrés Aguilera,Cristina Cereda,Aleix Bayona-Feliu,Sonia I Barroso,Daisy Sproviero,Dmitry A Gordenin

doi:10.1371/journal.pgen.1009260

Abstract

TDP-43 is a DNA and RNA binding protein involved in RNA processing and with structural resemblance to heterogeneous ribonucleoproteins (hnRNPs), whose depletion sensitizes neurons to double strand DNA breaks (DSBs). Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder, in which 97% of patients are familial and sporadic cases associated with TDP-43 proteinopathies and conditions clearing TDP-43 from the nucleus, but we know little about the molecular basis of the disease. After showing with the non-neuronal model of HeLa cells that TDP-43 depletion increases R loops and associated genome instability, we prove that mislocalization of mutated TDP-43 (A382T) in transfected neuronal SH-SY5Y and lymphoblastoid cell lines (LCLs) from an ALS patient cause R-loop accumulation, R loop-dependent increased DSBs and Fanconi Anemia repair centers. These results uncover a new role of TDP-43 in the control of co-transcriptional R loops and the maintenance of genome integrity by preventing harmful R-loop accumulation. Our findings thus link TDP-43 pathology to increased R loops and R loop-mediated DNA damage opening the possibility that R-loop modulation in TDP-43-defective cells might help develop ALS therapies.

Highlights

TDP-43 is a nuclear RNA binding protein (RBP) with a repressor role of HIV-1 transcription
The nuclear TDP-43 RNA binding protein, is encoded by a major gene for Amyotrophic Lateral Sclerosis (ALS) susceptibility whose mutations are found in 3% of familial and 2% of sporadic ALS cases
Thanks to its ability to recognize DNA and RNA, TDP-43 is involved in different steps of mRNA metabolism and in several mechanisms of genome integrity

Summary

Introduction

TDP-43 is a nuclear RNA binding protein (RBP) with a repressor role of HIV-1 transcription. It binds to the trans-active response element DNA sequence of the viral genome [1, 2]. A382T TDP-43 accumulation in the cytoplasm can reduce its physiological nuclear function, such as transcription regulation, mRNA splicing and transport [13,14,15] and miRNAs biogenesis [5, 9]. TDP-43 aggregates are identified as a major component of the ubiquitinated neuronal cytoplasmic inclusions deposited in spinal motor neurons both in familiar and sporadic ALS patients [18]

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