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Neuroscience. 2015 May 7;293:157-70. doi: 10.1016/j.neuroscience.2015.02.046. Epub 2015 Mar 2.

Proteomic analyses reveal that loss of TDP-43 affects RNA processing and intracellular transport.

Author information

1
Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, 1 Windsor Walk, London SE5 8AF, United Kingdom.
2
Cardiovascular Division, King's College London BHF Centre, 125 Coldharbour Lane, London SE5 9NU, United Kingdom.
3
Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
4
Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, 1 Windsor Walk, London SE5 8AF, United Kingdom.
5
Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Biomedical Research Institute BRIS, Puhova 10, SI-1000 Ljubljana, Slovenia. Electronic address: boris.rogelj@ijs.si.

Abstract

Transactive response DNA-binding protein 43 (TDP-43) is a predominantly nuclear, ubiquitously expressed RNA and DNA-binding protein. It recognizes and binds to UG repeats and is involved in pre-mRNA splicing, mRNA stability and microRNA metabolism. TDP-43 is essential in early embryonic development but accumulates in cytoplasmic aggregates in amyotrophic lateral sclerosis (ALS) and tau-negative frontotemporal lobar degeneration (FTLD). It is not known yet whether cytoplasmic aggregates of TDP-43 are toxic or protective but they are often associated with a loss of TDP-43 from the nucleus and neurodegeneration may be caused by a loss of normal TDP-43 function or a gain of toxic function. Here we present a proteomic study to analyze the effect of loss of TDP-43 on the proteome. MS data are available via ProteomeXchange with identifier PXD001668. Our results indicate that TDP-43 is an important regulator of RNA metabolism and intracellular transport. We show that Ran-binding protein 1 (RanBP1), DNA methyltransferase 3 alpha (Dnmt3a) and chromogranin B (CgB) are downregulated upon TDP-43 knockdown. Subsequently, transportin 1 level is increased as a result of RanBP1 depletion. Improper regulation of these proteins and the subsequent disruption of cellular processes may play a role in the pathogenesis of the TDP-43 proteinopathies ALS and FTLD.

KEYWORDS:

RanBP1; TDP-43; amyotrophic lateral sclerosis; comparative proteomics; frontotemporal lobar degeneration; intracellular transport

[Indexed for MEDLINE]

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