Belur NR, Bustos BI, Lubbe SJ, Mazzulli JR. Nuclear aggregates of NONO/SFPQ and A-to-I-edited RNA in Parkinson's disease and dementia with Lewy bodies. Neuron. 2024 Aug 7;112(15):2558-2580.e13. Epub 2024 May 17 PubMed.
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Columbia University
This is a well-done and surprising study, indicating a new form of protein inclusion in PD and synucleinopathy patients, namely, nuclear aggregates consisting of RNA-editing proteins and/or two RNA-binding proteins. The formation of these impressively large, and apparently common, nuclear structures appears to be downstream of a step in α-synuclein handling, and while misfolded synuclein has been shown to bind hundreds of proteins, the presence of these newly discovered aggregates in genuine disease is dramatic. It should encourage more research into consequences of the localization of synuclein with the nucleus, which has long been noted, but remains poorly understood.
The functional consequences of the aggregates are not yet clear, and while the authors have done an excellent job of determining that their function in editing RNA could potentially play a role in neuronal stress, there are additional possibilities, including effects on trafficking and/or the cytoskeleton, which could be required for the aggregate formation.
Given their abundance, the aggregates may also be a source of neoantigens. Alternatively, it is possible that these nuclear structures, as suspected for cytosolic Lewy body inclusions, may be a stress response that plays a protective role. In any case, this report spawns exciting new questions, the mark of a good discovery, and may hold an important piece of the puzzle as to what causes these disorders.
View all comments by David SulzerNational Institute on Aging
Belur et al. report a novel consequence of nuclear synuclein oligomers, namely the accumulation of NONO and SFPQ, leading to aberrant editing of Alu elements and the formation of novel inclusions in SNCA p.A53T ISPC lines. There is prior evidence that nuclear synuclein may affect RNA processing, notably work from the Khurana lab (Hallacli et al., 2022), showing in triplication iPSC lines that non-membrane bound synuclein can interact with P-bodies, which are involved in mRNA storage and turnover.
Put together, these studies suggest that dysregulation of mRNA processing may be a relatively major consequence of synuclein mutations. That a consistent shift in solubility is now reported in brains from donors who had dementia with Lewy bodies suggests that a similar process may occur in vivo.
One area that I found particularly interesting was the change in proteins that are related to other neurodegenerative diseases, notably FUS, a gene mutated in ALS-FTD (reviewed in Abramzon et al., 2020). Given that PD and ALS-FTD are clinically and pathologically distinctive, I wonder if RNA dysregulation is a relatively later common pathway for neuronal death and therefore downstream of initiating events such as a gene mutation.
If correct, one might expect to see converging events related to RNA processing and editing across different disease groups. In this context, it is worth noting that we have generated multiple iPSC lines in a consistent genetic background including SNCA p.A53T and multiple FUS variants. It would be of great interest to examine RNA processing, editing, and translation across multiple lines to confirm the reported phenotypes and evaluate when convergence begins to emerge.
References:
Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell. 2022 Jun 9;185(12):2035-2056.e33. PubMed.
Abramzon YA, Fratta P, Traynor BJ, Chia R. The Overlapping Genetics of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Front Neurosci. 2020;14:42. Epub 2020 Feb 5 PubMed.
View all comments by Mark CooksonBrigham and Women's Hospital, Harvard Medical School; Broad Institute of Harvard and MIT; Harvard Stem Cell Institute
I very much enjoyed reading this important paper from Belur, Mazzulli, and colleagues. It reinforces the emerging function of α-synuclein in gene regulation and RNA metabolism, and a potentially important role of dysregulation of these pathways in the pathogenesis of synucleinopathies. More generally, it draws attention to how complex and widespread the consequences of protein misfolding and mislocalization are in the cell. This phenomenon was well documented by Haenig and colleagues some years ago when they showed that protein-protein interaction mapping could reveal proteins that co-aggregate in degenerative proteinopathies (Haening et al., 2020). Among such proteins, RNA-binding proteins (RBPs) are ideal candidates to undergo co-aggregation. These proteins are rich in prion domains and primed to undergo phase separation. Interestingly, Brunet, Jarosz, and colleagues very recently showed that RBPs comprise the major class of proteins that become progressively insoluble in the aging vertebrate brain (Harel et al., 2024). Like the current paper, these others powerfully exploited the growing toolbox of systems cell biology to gain a more global view of how protein misfolding perturbs the cellular proteome.
The current paper specifically identifies proteins that become insoluble in aging iPSC-derived dopaminergic neurons as α-synuclein misfolds. As noted in the Alzforum news piece, foremost among the many proteins recovered were the RBP proteins NONO and SFPQ. Importantly, these proteins themselves then mislocalize and aggregate in the nucleus, and are sequestered away from their normal functions, leading to alteration of RNA-specific adenosine deaminase (ADAR) function. Altered RNA editing and mRNA translation ensues, which correlates with dysregulation of key neuronal proteins.
In prior papers, we have adopted different systems-cell-biology approaches yet hit strikingly similar findings. NONO and SFPQ are among many RBPs that physically interact with a-synuclein, alter their localization when α-synuclein accumulates, and impact its toxicity when genetically manipulated (Chung et al., 2017; Khurana et al., 2017; Hallacli et al., 2022; Lam et al., 2022; Feb 2017 news; Jun 2022 news). While our own focus was drawn to mRNA stability and mRNA translation, the current paper elegantly extends this to RNA editing. I am struck by the strong overlap among specific proteins and protein classes recovered by these very different unbiased systems cell biology assays, conserved across species and cell types, all, in my mind, strengthening conviction in the biological connections.
How important are RBP perturbations for disease risk and progression? This will need further investigation. In the current paper, strong data tied altered base editing to alterations in levels of key neuronal proteins. The impact of these perturbations on neuronal health and viability can now be more directly tested with genetic manipulation in neurons and targeted human genetic studies. As we have previously reported, cumulative mutations in RBP pathways may give rise to stronger genetic signals than individual gene variation. Finding these signals may require new statistical genetic methods. If specific mRNA targets are repeatedly implicated, these may prove to be disease-relevant targets. In his comment, Mark Cookson raises the important question of how specific these changes in RNA metabolism are in different proteinopathies, and whether these are early or late. My own hunch is that these are early and specific effects. To give one example, we have shown previously that the effects of Ataxin-2 manipulation on TDP-43 and α-synuclein toxicities are strong but diametrically opposed (Khurana et al., 2017), and the risk signal we saw for P-body genes in synucleinopathies was absent in ALS. But more needs to be done to address his important question.
Finally, the paper nicely reminds us that our tidy view that many neurodegenerative diseases equate to the misfolding of one or a handful of proteins may be overly simplistic. Proteins fold, function, and traffic in an astonishingly crowded and harsh environment. As one protein misfolds and mislocalizes, there are corresponding shifts in many other proteins that can mislocalize, themselves misfold, or become destabilized. And, of course, these effects can extend to RNA, lipids, and other metabolites, etc. “Mixed pathologies” thus turn out to be far more extensive than in the standard neuropathological lens through which we view it! And this complexity may in turn be critical for understanding the vexing heterogeneity among patients with neurodegenerative disease.
References:
Haenig C, Atias N, Taylor AK, Mazza A, Schaefer MH, Russ J, Riechers SP, Jain S, Coughlin M, Fontaine JF, Freibaum BD, Brusendorf L, Zenkner M, Porras P, Stroedicke M, Schnoegl S, Arnsburg K, Boeddrich A, Pigazzini L, Heutink P, Taylor JP, Kirstein J, Andrade-Navarro MA, Sharan R, Wanker EE. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell Rep. 2020 Aug 18;32(7):108050. PubMed.
Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A. Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties. Cell Rep. 2024 Jun 25;43(6):112787. Epub 2024 May 28 PubMed.
Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Syst. 2017 Feb 22;4(2):242-250.e4. Epub 2017 Jan 25 PubMed.
Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. Cell Syst. 2017 Feb 22;4(2):157-170.e14. Epub 2017 Jan 25 PubMed.
Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell. 2022 Jun 9;185(12):2035-2056.e33. PubMed.
Lam I, Ndayisaba A, Lewis AJ, Fu Y, Sagredo GT, Zaccagnini L, Sandoe J, Sanz RL, Vahdatshoar A, Martin TD, Morshed N, Ichihashi T, Tripathi A, Ramalingam N, Oettgen-Suazo C, Bartels T, Schabinger M, Hallacli E, Jiang X, Verma A, Tea C, Wang Z, Hakozaki H, Yu X, Hyles K, Park C, Theunissen TW, Wang H, Jaenisch R, Lindquist S, Stevens B, Stefanova N, Wenning G, Luk KC, SanchezPernaute R, Gomez-Esteban JC, Felsky D, Kiyota Y, Sahni N, Yi SS, Chung C-Y, Stahlberg H, Ferrer I, Schoneberg J, Ell. Rapid iPSC inclusionopathy models shed light on formation, consequence and molecular subtype of alpha-synuclein inclusions. 2022 Nov 09 10.1101/2022.11.08.515615 (version 1) bioRxiv.
Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. Cell Syst. 2017 Feb 22;4(2):157-170.e14. Epub 2017 Jan 25 PubMed.
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