Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS - PubMed (original) (raw)

. 2014 Sep 3;83(5):1043-50.

doi: 10.1016/j.neuron.2014.07.041. Epub 2014 Aug 14.

Yongjie Zhang 2, Tania F Gendron 2, Peter O Bauer 2, Jeannie Chew 2, Wang-Yong Yang 1, Erik Fostvedt 1, Karen Jansen-West 2, Veronique V Belzil 2, Pamela Desaro 3, Amelia Johnston 3, Karen Overstreet 3, Seok-Yoon Oh 4, Peter K Todd 4, James D Berry 5, Merit E Cudkowicz 5, Bradley F Boeve 6, Dennis Dickson 2, Mary Kay Floeter 7, Bryan J Traynor 8, Claudia Morelli 9, Antonia Ratti [ 10](#full-view-affiliation-10 "Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi, 18, 20095 Cusano Milanino (Milan), Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via Sforza, 35, 20122, Milan, Italy."), Vincenzo Silani [ 11](#full-view-affiliation-11 "Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via Sforza, 35, 20122, Milan, Italy; Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA."), Rosa Rademakers 2, Robert H Brown 12, Jeffrey D Rothstein 13, Kevin B Boylan 3, Leonard Petrucelli 14, Matthew D Disney 15

Affiliations

Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS

Zhaoming Su et al. Neuron. 2014.

Erratum in

Abstract

A repeat expansion in C9ORF72 causes frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). RNA of the expanded repeat (r(GGGGCC)exp) forms nuclear foci or undergoes repeat-associated non-ATG (RAN) translation, producing "c9RAN proteins." Since neutralizing r(GGGGCC)exp could inhibit these potentially toxic events, we sought to identify small-molecule binders of r(GGGGCC)exp. Chemical and enzymatic probing of r(GGGGCC)8 indicate that it adopts a hairpin structure in equilibrium with a quadruplex structure. Using this model, bioactive small molecules targeting r(GGGGCC)exp were designed and found to significantly inhibit RAN translation and foci formation in cultured cells expressing r(GGGGCC)66 and neurons transdifferentiated from fibroblasts of repeat expansion carriers. Finally, we show that poly(GP) c9RAN proteins are specifically detected in c9ALS patient cerebrospinal fluid. Our findings highlight r(GGGGCC)exp-binding small molecules as a possible c9FTD/ALS therapeutic and suggest that c9RAN proteins could potentially serve as a pharmacodynamic biomarker to assess efficacy of therapies that target r(GGGGCC)exp.

Copyright © 2014 Elsevier Inc. All rights reserved.

PubMed Disclaimer

Figures

Fig. 1

Fig. 1. Probing r(GGGGCC)n secondary structures

A) CD spectra of r(GGGGCC)4,6,8 and r(CGG)12 in the presence of various monovalent cations. B) Optical melting curves for r(GGGGCC)4,6,8 and r(CGG)12 monitored at 295 nm. RNA samples (4 μM) were folded prior to recording CD spectra (20°C) and optical melting curves. C) DMS mapping data (left), enzymatic mapping data (middle) and predicted hairpin structure of r(GGGGCC)8 using mapping restraints (right). DMS mapping lanes: 1, untreated RNA; 2, alkaline hydrolysis; 3, T1 digestion under denaturing conditions; 4, DMS modification in the presence of 185 mM Li+; 5, DMS modification in the presence of 185 mM K+. Enzymatic mapping lanes: 1, untreated RNA; 2, T1 digestion under denaturing conditions; 3, T1 digestion under native conditions; 4, V1 digestion in which base paired nucleotides are cleaved; 5, S1 digestion in which all single-stranded nucleotides are cleaved. D) 1D 1H NMR spectra of r(GGGGCC)8 in the presence of 100 mM K+ annealed at 37°C, 60°C, or 95°C. Blue circles are imino proton resonances from G residues present as base pairs and red squares are imino proton resonances from non-canonically paired G residues. E) Structures of lead compounds 1a, 2, and 3 that bind to r(GGGGCC)8. See also Figure S1.

Fig. 2

Fig. 2. Small molecules targeting r(GGGGCC) inhibit RAN translation and foci formation in (GGGGCC)66-expressing cells

A) Structure of 1a-CA-biotin; the chlorambucil moiety (CA) forms a covalent bond with the cellular target once the small molecule is bound. Biotin is used to isolate biomolecule-small molecule adducts from cells. B) Normalized enrichment of r(GGGGCC)66 from biomolecules isolated with streptavidin beads as compared to 18S rRNA determined by qRT-PCR. Cells were treated with 1a-CA-biotin alone or with 1a, 2 or 3 (competitive profiling). In competitive profiling experiments, the unreactive compound inhibits reaction of the target with 1a-CA-biotin and thus the target is depleted in pull-down fractions. Data presented as mean±SD (n=2). C) Cells overexpressing 66 (GGGGCC) repeats (C9-66R), but not 2 (C9-2R) or 20 (C9-20R), express poly(GP) and poly(GA) proteins. Asterisks demark non-specific bands. D) Western blot and densitometry of poly(GP) and poly(GA) proteins in (GGGGCC)66-expressing cells treated with DMSO or compounds 1a, 2 or 3 (100 μM, 24 h). Data represents mean+SEM (n=3). E) RNA foci (red) are detected in the nucleus (Hoechst; blue) of C9-66R cells. F) Evaluation of the percentage of foci-positive cells by RNA FISH post-treatment. Data represents mean+SEM in 10 fields. G-H) Compound 1a decreases RAN translation of poly(GP) proteins from sense (GGGGCC)66 repeats in C9-66R cells (G), but does not influence levels of poly(GP) or poly(PR) proteins RAN translated from antisense (CCCCGG)66 repeats in C9-AS-66R cells (H), as assessed by GP and PR immunoassays. Data represents mean+SEM (n=3 or 4). I) The percentage of r(CCCCGG)-containing foci in C9-AS-66R cells is not affected by 1a. J) 1a decreases RAN translation of poly(G) in cells expressing (CGG)88 upstream of GFP. Data presented as mean+SEM (n=3). *P<0.05, **P<0.01, ***P<0.001, as assessed by One-way ANOVA followed by Dunnett's Multiple Comparison Test. ##P<0.01, as assessed by t-test. See also Figure S2.

Fig. 3

Fig. 3. Small molecules targeting r(GGGGCC) inhibit RAN translation and foci formation in iNeurons with the C9ORF72 expansion

A) Immunofluorescence staining of fibroblasts transduced with non-silencing shRNA or shPTB1 for PTB1 and the neuronal marker, MAP2. Scale bar, 20 μm. B) PTB1 Western blot analysis of fibroblasts transduced or not with shPTB1. C) RNA foci accumulate in iNeurons with the C9ORF72 repeat expansion (C9ORF72+) but not in iNeurons lacking the expansion (C9ORF72-), as assessed by RNA FISH. Immunofluorescence staining with anti-GP or anti-PR illustrates the accumulation of c9RAN proteins specifically in C9ORF72+ iNeurons. Scale bars, 5 μm. D) Treatment of C9ORF72+ iNeurons with compound 1a (2 μM, 4 d) significantly decreased the percentage of cells with foci. For each iNeuron line, data reflects the average percentage of foci-positive cells+SEM in 3 separate fields. E-F) Compound 1a significantly decreased the percentage of cells with anti-GP, but not anti-PR, immunoreactive inclusions (magnification: 20x). For each line, data represent the average percentage of inclusion-positive cells+SEM counted in 9 wells of a 96-well plate. #P<0.05, ##P<0.01, as assessed by t test. See also Figure S3.

Fig. 4

Fig. 4. Poly(GP) proteins are detected in c9ALS cerebrospinal fluid

A) Poly(GP) expression in CSF from 5 healthy individuals, 25 ALS patients negative for the C9ORF72 repeat expansion, and 14 c9ALS patients were assessed by GP immunoassay. Response values correspond to the intensity of emitted light from which the background response was subtracted. Dashed line represents the limit of detection [LoD=LoB+1.645(SDblank); where LoB (limit of blank)=meanblank+1.645(SDblank)]. **P<0.001, ***P<0.001 as assessed by one-way ANOVA followed by Tukey's Multiple Comparison Test. B) Schematic representation of the effect of r(GGGGCC)exp-targeting small molecules on foci formation and RAN translation, and the potential use of extracellular c9RAN proteins as a pharmacodynamic marker of treatment efficacy. See also Figure S4.

Similar articles

Cited by

References

    1. Ash PE, Bieniek KF, Gendron TF, Caulfield T, Lin WL, Dejesus-Hernandez M, van Blitterswijk MM, Jansen-West K, Paul JW, 3rd, Rademakers R, et al. Unconventional translation of C9ORF72 GGGGCC expansion generates insoluble polypeptides specific to c9FTD/ALS. Neuron. 2013;77:639–646. - PMC - PubMed
    1. Bugaut A, Murat P, Balasubramanian S. An RNA hairpin to G-quadruplex conformational transition. J Am Chem Soc. 2012;134:19953–19956. - PMC - PubMed
    1. DeJesus-Hernandez M, Mackenzie IR, Boeve BF, Boxer AL, Baker M, Rutherford NJ, Nicholson AM, Finch NA, Flynn H, Adamson J, et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 2011;72:245–256. - PMC - PubMed
    1. Disney MD, Liu B, Yang WY, Sellier C, Tran T, Charlet-Berguerand N, Childs-Disney JL. A small molecule that targets r(CGG)(exp) and improves defects in fragile X-associated tremor ataxia syndrome. ACS Chem Biol. 2012;7:1711–1718. - PMC - PubMed
    1. Donnelly CJ, Zhang PW, Pham JT, Heusler AR, Mistry NA, Vidensky S, Daley EL, Poth EM, Hoover B, Fines DM, et al. RNA Toxicity from the ALS/FTD C9ORF72 Expansion Is Mitigated by Antisense Intervention. Neuron. 2013;80:415–428. - PMC - PubMed

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources