Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS

Abstract

Algorithms designed to identify canonical yeast prions predict that around 250 human proteins, including several RNA-binding proteins associated with neurodegenerative disease, harbour a distinctive prion-like domain (PrLD) enriched in uncharged polar amino acids and glycine. PrLDs in RNA-binding proteins are essential for the assembly of ribonucleoprotein granules. However, the interplay between human PrLD function and disease is not understood. Here we define pathogenic mutations in PrLDs of heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1 in families with inherited degeneration affecting muscle, brain, motor neuron and bone, and in one case of familial amyotrophic lateral sclerosis. Wild-type hnRNPA2 (the most abundant isoform of hnRNPA2B1) and hnRNPA1 show an intrinsic tendency to assemble into self-seeding fibrils, which is exacerbated by the disease mutations. Indeed, the pathogenic mutations strengthen a ‘steric zipper’ motif in the PrLD, which accelerates the formation of self-seeding fibrils that cross-seed polymerization of wild-type hnRNP. Notably, the disease mutations promote excess incorporation of hnRNPA2 and hnRNPA1 into stress granules and drive the formation of cytoplasmic inclusions in animal models that recapitulate the human pathology. Thus, dysregulated polymerization caused by a potent mutant steric zipper motif in a PrLD can initiate degenerative disease. Related proteins with PrLDs should therefore be considered candidates for initiating and perhaps propagating proteinopathies of muscle, brain, motor neuron and bone.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Identification of previously unknown disease mutations in MSP and ALS.
Figure 2: Cytoplasmic pathology of hnRNPA2B1 and hnRNPA1.
Figure 3: The disease mutations affect a PrLD in hnRNPA2B1 and hnRNPA1.
Figure 4: Disease mutations accelerate hnRNPA2 and hnRNPA1 fibrillization.
Figure 5: hnRNPA2 recruitment to stress granules is accelerated by disease mutation.
Figure 6: Mutant hnRNPA2 forms cytoplasmic inclusions in Drosophila.

References

  1. 1

    Nalbandian, A. et al. The multiple faces of valosin-containing protein-associated diseases: inclusion body myopathy with Paget’s disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. J. Mol. Neurosci. 45, 522–531 (2011)

    CAS  Article  Google Scholar 

  2. 2

    Johnson, J. O. et al. Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 68, 857–864 (2010)

    CAS  Article  Google Scholar 

  3. 3

    Watts, G. D. et al. Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia is caused by mutant valosin-containing protein. Nature Genet. 36, 377–381 (2004)

    CAS  Article  Google Scholar 

  4. 4

    Neumann, M., Tolnay, M. & Mackenzie, I. R. The molecular basis of frontotemporal dementia. Expert Rev. Mol. Med. 11, e23 (2009)

    Article  Google Scholar 

  5. 5

    Shi, Z. et al. Characterization of the Asian myopathy patients with VCP mutations. Eur. J. Neurol. 19, 501–509 (2012)

    CAS  Article  Google Scholar 

  6. 6

    Chung, P. Y. et al. Indications for a genetic association of a VCP polymorphism with the pathogenesis of sporadic Paget’s disease of bone, but not for TNFSF11 (RANKL) and IL-6 polymorphisms. Mol. Genet. Metab. 103, 287–292 (2011)

    CAS  Article  Google Scholar 

  7. 7

    Kottlors, M. et al. Late-onset autosomal dominant limb girdle muscular dystrophy and Paget’s disease of bone unlinked to the VCP gene locus. J. Neurol. Sci. 291, 79–85 (2010)

    CAS  Article  Google Scholar 

  8. 8

    Buratti, E. et al. TDP-43 binds heterogeneous nuclear ribonucleoprotein A/B through its C-terminal tail: an important region for the inhibition of cystic fibrosis transmembrane conductance regulator exon 9 splicing. J. Biol. Chem. 280, 37572–37584 (2005)

    CAS  Article  Google Scholar 

  9. 9

    Ritson, G. P. et al. TDP-43 mediates degeneration in a novel Drosophila model of disease caused by mutations in VCP/p97. J. Neurosci. 30, 7729–7739 (2010)

    CAS  Article  Google Scholar 

  10. 10

    Iwahashi, C. K. et al. Protein composition of the intranuclear inclusions of FXTAS. Brain 129, 256–271 (2006)

    CAS  Article  Google Scholar 

  11. 11

    Sofola, O. A. et al. RNA-binding proteins hnRNP A2/B1 and CUGBP1 suppress fragile X CGG premutation repeat-induced neurodegeneration in a Drosophila model of FXTAS. Neuron 55, 565–571 (2007)

    CAS  Article  Google Scholar 

  12. 12

    Jin, P. et al. Pur α binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome. Neuron 55, 556–564 (2007)

    CAS  Article  Google Scholar 

  13. 13

    Salajegheh, M. et al. Sarcoplasmic redistribution of nuclear TDP-43 in inclusion body myositis. Muscle Nerve 40, 19–31 (2009)

    CAS  Article  Google Scholar 

  14. 14

    Alberti, S., Halfmann, R., King, O., Kapila, A. & Lindquist, S. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137, 146–158 (2009)

    CAS  Article  Google Scholar 

  15. 15

    Toombs, J. A., McCarty, B. R. & Ross, E. D. Compositional determinants of prion formation in yeast. Mol. Cell. Biol. 30, 319–332 (2010)

    CAS  Article  Google Scholar 

  16. 16

    Goldschmidt, L., Teng, P. K., Riek, R. & Eisenberg, D. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc. Natl Acad. Sci. USA 107, 3487–3492 (2010)

    ADS  CAS  Article  Google Scholar 

  17. 17

    Teng, P. K. & Eisenberg, D. Short protein segments can drive a non-fibrillizing protein into the amyloid state. Protein Eng. Des. Sel. 22, 531–536 (2009)

    CAS  Article  Google Scholar 

  18. 18

    Li, L. & Lindquist, S. Creating a protein-based element of inheritance. Science 287, 661–664 (2000)

    ADS  CAS  Article  Google Scholar 

  19. 19

    Kato, M. et al. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767 (2012)

    CAS  Article  Google Scholar 

  20. 20

    Wolozin, B. Regulated protein aggregation: stress granules and neurodegeneration. Mol. Neurodegener. 7, 56 (2012)

    CAS  Article  Google Scholar 

  21. 21

    Buchan, J. R. & Parker, R. Eukaryotic stress granules: the ins and outs of translation. Mol. Cell 36, 932–941 (2009)

    CAS  Article  Google Scholar 

  22. 22

    Weber, S. C. & Brangwynne, C. P. Getting RNA and protein in phase. Cell 149, 1188–1191 (2012)

    CAS  Article  Google Scholar 

  23. 23

    Neumann, M. et al. FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations. Brain 134, 2595–2609 (2011)

    Article  Google Scholar 

  24. 24

    King, O. D., Gitler, A. D. & Shorter, J. The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res. 1462, 61–80 (2012)

    CAS  Article  Google Scholar 

  25. 25

    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010)

    CAS  Article  Google Scholar 

  26. 26

    Katoh, K., Asimenos, G. & Toh, H. Multiple alignment of DNA sequences with MAFFT. Methods Mol. Biol. 537, 39–64 (2009)

    CAS  Article  Google Scholar 

  27. 27

    Goode, M. G. & Rodrigo, A. G. SQUINT: a multiple alignment program and editor. Bioinformatics 23, 1553–1555 (2007)

    CAS  Article  Google Scholar 

  28. 28

    Zwickl, D. J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. PhD thesis, Univ. Texas at Austin. (2006)

  29. 29

    Johnson, B. S., McCaffery, J. M., Lindquist, S. & Gitler, A. D. A yeast TDP-43 proteinopathy model: exploring the molecular determinants of TDP-43 aggregation and cellular toxicity. Proc. Natl Acad. Sci. USA 105, 6439–6444 (2008)

    ADS  CAS  Article  Google Scholar 

  30. 30

    Johnson, B. S. et al. TDP-43 is intrinsically aggregation-prone, and amyotrophic lateral sclerosis-linked mutations accelerate aggregation and increase toxicity. J. Biol. Chem. 284, 20329–20339 (2009)

    CAS  Article  Google Scholar 

  31. 31

    Sun, Z. et al. Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. PLoS Biol. 9, e1000614 (2011)

    CAS  Article  Google Scholar 

  32. 32

    Alberti, S., Gitler, A. D. & Lindquist, S. A suite of Gateway® cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae . Yeast 24, 913–919 (2007)

    CAS  Article  Google Scholar 

  33. 33

    Ross, E. D., Edskes, H. K., Terry, M. J. & Wickner, R. B. Primary sequence independence for prion formation. Proc. Natl Acad. Sci. USA 102, 12825–12830 (2005)

    ADS  CAS  Article  Google Scholar 

  34. 34

    Song, Y. et al. Role for Hsp70 chaperone in Saccharomyces cerevisiae prion seed replication. Eukaryot. Cell 4, 289–297 (2005)

    CAS  Article  Google Scholar 

  35. 35

    Ross, C. D., McCarty, B. M., Hamilton, M., Ben-Hur, A. & Ross, E. D. A promiscuous prion: efficient induction of [URE3] prion formation by heterologous prion domains. Genetics 183, 929–940 (2009)

    CAS  Article  Google Scholar 

  36. 36

    Guthrie, C. & Fink, G. R. Methods in Ezymology: Guide to Yeast Genetics and Molecular and Cell Biology 169 (Academic, 2002)

    Google Scholar 

  37. 37

    Ito, H., Fukuda, Y., Murata, K. & Kimura, A. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163–168 (1983)

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Ross, E. D., Edskes, H. K., Terry, M. J. & Wickner, R. B. Primary sequence independence for prion formation. Proc. Natl Acad. Sci. USA 102, 12825–12830 (2005)

    ADS  CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank the patients whose participation made this work possible. We thank the St Jude Pediatric Cancer Genome Project and J. Zhang in particular for providing access to control sequencing data. We thank C. Gellera, B. Baloh, M. Harms, S. Krause, G. Dreyfuss and T. Cundy for sharing reagents. We thank S. Donkervoort and S. Mumm for coordinating samples, and A. Taylor for editorial assistance. J.P.T. was supported by ALSAC, the Packard Foundation and the National Institutes of Health (NIH) (NS053825); J.P.T. and M.B. were supported by the ALS Association; J.Q.T. was supported by the NIH (AG032953); J.S. was supported by the NIH (DP2OD002177 and NS067354) and the Ellison Medical Foundation; E.D.R. was supported by the National Science Foundation (MCB-1023771). C.C.W. was supported by the NIH (AG031867).

Author information

Affiliations

Authors

Contributions

H.J.K., N.C.K., E.D.R., C.C.W., J.S. and J.P.T. designed experiments. H.J.K., N.C.K., E.A.S., J.Moore, Z.D., K.S.M., B.F., S.L., A.M., A.P.K., Y.R.L. and A.F.F. performed the experiments. K.B.B., A.M.W., R.R., J.L.P., S.A.G., J.Q.T., B.N.S., S.T., A.-S.G., J.Miller, C.E.S., M.K., J.K., A.P., M.B. and V.E.K. provided patient clinical material, clinical evaluation, or evaluation of patient clinical material. H.J.K., N.C.K., Y.-D.W., R.C., B.J.T., A.D.G., O.D.K., E.D.R., J.S. and J.P.T. contributed to data analysis. E.D.R., O.D.K. and C.C.W. contributed to manuscript preparation. H.J.K., J.S. and J.P.T. wrote the manuscript.

Corresponding authors

Correspondence to James Shorter or J. Paul Taylor.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-18, Supplementary Tables 1-3 and additional references. (PDF 14474 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kim, H., Kim, N., Wang, YD. et al. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 495, 467–473 (2013). https://doi.org/10.1038/nature11922

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing