Missing ‘Lnc’? Long Noncoding RNAs Bind Tau, Tame Stress Granules

Mutations in the tau gene that cause frontotemporal dementia wreak all manner of neuronal havoc, from endolysosomal traffic jams to mitochondrial distress to a standstill in nucleocytoplasmic transport. How can a single point mutation inflict such a broad set of disasters? The answer may have to do with long noncoding RNAs, according to a paper published September 20 in Molecular Psychiatry.

  • In human neurons, FTLD-MAPT mutations change expression of long noncoding RNAs.
  • Downregulation of the lncRNA SNHG8 ups stress granules.
  • SNHG8 binds both tau and stress granule proteins.

Researchers led by Celeste Karch of Washington University in St. Louis report that in human neurons, pathological tau mutations skew the abundance of a cadre of lncRNAs, a still-mysterious species of RNA that can exert dramatically pleiotropic effects. One, called SNHG8, plummeted in neurons harboring a tau mutation, and also was abnormally low in postmortem brains of people with tauopathies. Lo and behold, this particular transcript was found to bind tau itself. It also binds to TIA1, a protein that forms stress granules. Tau mutations somehow thwarted SNHG8 expression, which led to a dramatic uptick in stress granule formation.

“This is is a very elegant study with very interesting results,” wrote Ben Wolozin, Boston University (full comment below.)

While details of the pathway remain to be ironed out, the study illuminates a nexus among stress granules, lncRNA, and tauopathy that may have implications for neurodegenerative disease.

Gone are the days when scientists viewed RNA as a mere intermediary between genes and proteins. They now appreciate that the vast majority of RNA species—lncRNAs among them—do not encode proteins at all. Around 100,000 distinct lncRNAs have been identified, and their expression varies from cell type to cell type. At 200 nucleotides or longer, these RNAs can contort into complex structures. This allows them to form specific partnerships with DNA, proteins, metabolites, or other RNAs, thus meddling in all manner of cellular processes (for review, see Oo et al., 2022). They also buddy up with RNA binding proteins, including those that drive the liquid-liquid phase separation of membraneless organelles such as stress granules (Khong et al., 2017; van Treek et al., 2018). These transient, gel-like organelles carry out essential functions in the cell, but may also serve as incubators for proteopathic aggregation in neurodegenerative diseases (Naskar et al., 2023). 

Might lncRNAs play a hand in the neuronal fallout from tau mutations? First author Reshma Bhagat and colleagues addressed this question in their new study. They generated induced pluripotent stem cell (iPSC)-derived neurons from three MAPT mutation carriers with FTD, along with an isogenic control line for each. Each of the three variants—IVS10+6, P301L, and R406W—fall into a distinct class of tau mutation. Bhagat then compared the abundance of lncRNAs in each mutant line with its isogenic control, identifying 766, 972, and 141 that were differentially expressed with each mutation, respectively.

Among them, the abundance of 15 lncRNAs was altered in the same direction across all three mutations. For eight of these 15, the scientists found a nearby protein-coding gene that changed expression in lockstep with the lncRNA in the mutant neurons. These genes were involved in neuronal pathways including neurotrophic factor signaling, lipoprotein lipase activity, and axonal guidance. This suggested that at least some of the lncRNAs imparted gene expression changes in response to mutated tau.

Because lncRNAs interact with RNA binding proteins, the researchers used a computer algorithm to investigate these liaisons among the 15 tau-associated lncRNAs. The lncRNAs were predicted to interact with 255 RNABPs. Strikingly to Karch, the RNA binding proteins predicted to interact most strongly with these lncRNAs were FUS, TDP-43, DDX3X, and TIA1. While FUS and TDP-43 are clearly implicated in FTLD, DDX3X and TIA1 play a role in tauopathies more broadly.

These proteins, along with many others predicted to buddy up with the lncRNAs, also had another thing in common: All mediate the formation of stress granules. Looking back at the tau mutant iPSC-derived neurons, the researchers observed an uptick in TIA1-positive stress granules in the mutant lines. Could the association between lncRNAs and stress granule proteins mediate this effect?

Cells Under Stress. Human neurons carrying the P301L-tau mutation (right) contained more stress granules (arrow heads, TIA1, red) than isogenic neurons expressing wild-type tau (left). [Courtesy of Bhagat et al., Molecular Psychiatry, 2023.]

Next, the researchers zeroed in on one of the mutant-tau associated lncRNAs.  The SNHG8 transcript was downregulated by a full order of magnitude across the iPSC-derived mutant neurons, and it also dropped with age in the brains of P301L tauopathy mice. Most importantly, SNHG8 expression was reduced in human brain samples from carriers of FTLD-MAPT mutations, as well as in people with the sporadic primary tauopathy progressive supranuclear palsy, and in Alzheimer’s disease, a secondary tauopathy. In all, this cast SNHG8 as a commonly downregulated lncRNA across tauopathies.

Bhagat found that SNHG8 interacted directly with the tau protein, as well as with TIA1, an RNA binding protein that forms stress granules. Tau and TIA1 have their own history, as previous studies led by Benjamin Wolozin at Boston University have shown that TIA1 interacts with tau and pulls it into stress granules. There, it misfolds and oligomerizes, hastening neurodegeneration (May 2016 news; Nov 2017 news). Separately, tau has been reported to coalesce into droplets with RNA (Jul 2017 news; Aug 2017 news).

How would SNHG8 factor into these partnerships? The researchers conducted cell culture experiments to find out, reporting that this lncRNA discourages the formation of stress granules. Under normal conditions, SNHG8 interacts with tau, perhaps preventing it from binding TIA1. However, when tau is mutated, or in a stressful situation such as nutrient deprivation, SNHG8 levels drop, freeing up tau to join up with TIA1 and the stress granule gang.

LncRNA Connection. MAPT mutation or other stressors turn down expression of SNHG8, which frees tau to bind TIA1 and also leads to TIA1 upregulation. This promotes formation of stress granules. [Courtesy of Bhagat et al., Molecular Psychiatry, 2023.]

How do tau mutations lead to the downregulation of SNHG8? Karch would like to know the answer to this question. She speculated that stress signals triggered by the mutation could incite the downregulation of SNHG8, just as other stress signals do.

Notably, the scientists found that SNHG8 suppresses expression of TIA1. Therefore, a drop in SNHG8 could set off a double whammy, leading to a rise both in TIA1 and in tau’s availability to hook up with the stress granule protein. In support of this idea, the researchers found that overexpressing SNHG8 reduced the number of TIA1+ stress granules in P301L-tau expressing human neurons.

Because SNHG8 was downregulated in the brains of people who died with different tauopathies, Karch believes that this lncRNA and others may play a broad role in the pathogenesis of tauopathies and perhaps in other neurodegenerative proteopathies. Karch told Alzforum that her group is investigating the role of SNHG8 and other lncRNAs in mouse models of tauopathy.—Jessica Shugart

Comments

  1. This is is a very elegant study with very interesting results. First I want to note the elegant design of this study. Bhagat and colleagues examine lncRNAs among multiple iPSC lines harboring exon 10 mutations and identify a series of lncRNAs that show consistent changes (reduction) with mutations. They then extend the results to examine iPSC lines with other tau mutations and observe that the lncRNA SNHG8 is consistently reduced in all of the lines. They show that SNHG8 is also reduced in human tauopathies. Finally, increasing SNHG8 reduces stress granule levels. All of this data convincingly shows a strong bidirectional link between the pathophysiology of tau and SNHG8.

    This work is important for multiple reasons. First, it identifies a lncRNA that is directly regulated by tau. Second, it highlights involvement of a specific lncRNA in the pathophysiology of tauopathies, and suggests dysfunction of this pathway occurs early in the pathophysiology of tauopathies. This manuscript certainly feeds into the increasing interest in understanding the role of noncoding RNAs in the pathophysiology of ADRD. The manuscript also expands the literature suggesting that tau functions in part to regulate RNA metabolism, and in the case of SNHG8, a specific RNA species.

    Many studies now show that tau interacts, both directly and indirectly, with RNA.  In the 1990s, the Mandelkow laboratory showed that RNA promotes tau aggregation (Friedhoff et al., 1998). Multiple groups have now shown that RNA promotes tau liquid-liquid phase separation (Zhang et al., 2017; Wegmann et al., 2018; Ash et al, 2021). More recently, the Kraemer group has developed an antibody that recognizes tau-RNA complexes, and they observe that the antibody exhibits a distribution pattern similar to that of the TOMA series tau oligomer antibodies developed by the Kayed group (McMillan et al., 2023; Castillo-Carranza et al., 2014; Ruan et al., 2021; Sengupta et al., 2018). 

    In parallel work, to explore physiological interactions between tau and RNA, my lab showed that tau regulates RNA metabolism by interacting with RNA binding proteins to form stress granules (Wolozin and Ivanov, 2019; Vanderweyde et al., 2016; Jiang et al., 2021). TIA1 has been one of the RNA binding proteins exhibiting strong colocalization with pathologically phosphorylated as well as oligomerized tau. The work by Bhagat and colleagues fits nicely with this work, showing the colocalization of tau, TIA1 and SNHG8 in stress granules.

    More recently, we used optogenetics and an unbiased proteomic screen to show that oligomeric tau interacts most abundantly with the RNA binding protein HNRNPA2B1, stimulating the translational stress response (Jiang et al., 2021). The Abisambra group has shown that phosphorylated tau interacts directly with ribosomes to regulate protein synthesis (Koren et al., 2020; Koren et al., 2019). Conversely, Wang and Jurgasia’s groups recently showed that G3BP2 interacts selectively with monomeric tau and acts as a break on aggregation and tau-mediated stress granule formation (Wang et al., 2023). All of this data suggests that hyperphosphorylated tau has a normal biological function that is independent of microtubule stabilization. This function is to regulate RNA metabolism. Finally, tau likely has other biological functions. For instance, the Parker group has shown that tau acts in the nucleus interacting with nuclear speckles (Lester et al., 2021). 

    Pathological phosphorylation of tau was probably not designed by nature with the goal of giving neuropathologists a biomarker to investigate. It seems more likely that the phosphorylation of tau that we consider pathological actually has a normal biological function, but perhaps this function goes awry in tauopathies. The research described above suggests that one important biological function of pathologically phosphorylated tau is to regulate the translational stress response. Since phosphorylated tau oligomerizes rapidly we can extend this idea to assume that the phosphorylated tau involved in the translational stress response is also oligomeric. Chronic stress goes in tandem with chronic disease. Thus, it is easy to imagine that persistent activation of this pathway is deleterious, much like high blood pressure is necessary for exertion, but chronic high blood causes disease.

    Our understanding of the biology of these pathways, though, continues to evolve. The current manuscript by Bhagat et al. now extends the Tau, TIA1, stress granule pathway to include the lncRNA, SNHG8.  The exact function of SNHG8, though, remains to be determined. Since many lncRNAs also function in the nucleus, interacting with nuclear speckles, this fascinating lncRNA pathway might integrate cytoplasmic and nuclear functions of tau, and also integrate all of this with the pathophysiology of tauopathies.

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    View all comments by Benjamin Wolozin

  2. This is a really thorough write-up of an exciting finding.

    View all comments by Kumar Sambamurti

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References

News Citations

  1. Stress Granule Protein Entwines and Misfolds Tau
  2. Stress Granule Protein Stabilizes Tau Oligomers, Hastens Neurodegeneration
  3. Tau Hooks Up with RNA to Form Droplets
  4. More Droplets of Tau

Paper Citations

  1. Oo JA, Brandes RP, Leisegang MS. Long non-coding RNAs: novel regulators of cellular physiology and function. Pflugers Arch. 2022 Feb;474(2):191-204. Epub 2021 Nov 18 PubMed.
  2. Khong A, Matheny T, Jain S, Mitchell SF, Wheeler JR, Parker R. The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules. Mol Cell. 2017 Nov 16;68(4):808-820.e5. Epub 2017 Nov 9 PubMed.
  3. Van Treeck B, Protter DS, Matheny T, Khong A, Link CD, Parker R. RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome. Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2734-2739. Epub 2018 Feb 26 PubMed.
  4. Naskar A, Nayak A, Salaikumaran MR, Vishal SS, Gopal PP. Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders. Front Mol Neurosci. 2023;16:1242925. Epub 2023 Sep 1 PubMed.

Further Reading

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Primary Papers

  1. Bhagat R, Minaya MA, Renganathan A, Mehra M, Marsh J, Martinez R, Eteleeb AM, Nana AL, Spina S, Seeley WW, Grinberg LT, Karch CM. Long non-coding RNA SNHG8 drives stress granule formation in tauopathies. Mol Psychiatry. 2023 Nov;28(11):4889-4901. Epub 2023 Sep 21 PubMed.

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