Huntingtin chromatin retention in PARP knockout cells

Blog post by Dr. Tamara Maiuri

Another quick report on some year-old data that missed the boat on Zenodo deposits.

How to measure huntingtin chromatin retention

The method for measuring huntingtin chromatin retention upon oxidative stress makes use of a fluorescent huntingtin-specific intrabody, so we can follow the movement of endogenous huntingtin.

The method is described in this Zenodo post, including all the necessary controls to make sure the huntingtin chromatin retention is specific to huntingtin, and specific to oxidative stress conditions. Briefly, the YFP-tagged huntingtin-specific intrabody is co-transfected with H2B-mCherry (transfection control and marker of chromatin). After treatment, soluble proteins are extracted and cells are fixed and imaged. CellProfiler [1] is used to identify nuclei by the H2B-mCherry signal, and the nuclear YFP signal remaining bound to chromatin is quantified for several hundred cells.

Is PARP activity required for huntingtin chromatin retention?

Once these conditions were established, I was able to apply them to ask a biological question: is PARP activity required for huntingtin chromatin retention?

The Keith Caldecott lab at University of Sussex kindly provided us with a panel of PARP knock out cell lines. These are RPE1 cells with either PARP1 or PARP2 or both PARP1/PARP2 deleted by CRISPR/Cas9 [2].

When I first did this experiment, I was somewhat confused by the results. Huntingtin chromatin retention was diminished in PARP1 knockout cells and in PARP2 knockout cells, suggesting a role for PAR in the recruitment of huntingtin to chromatin. This would be expected based on our previous results that huntingtin binds PAR and acts as a scaffold for DNA repair proteins [3].

Blog post 15 fig1 copy

 

However, the double knockout cells seemed to retain huntingtin at chromatin more efficiently than either single knockout cell line. This didn’t make sense until I noticed that the huntingtin intrabody expression pattern in the double knockout cells had very bright nuclear and cytoplasmic staining (almost like inclusions) compared to the diffuse nuclear staining seen in wild type cells. To take a closer look, I compared the expression patterns by high magnification microscopy.

Blog post 15 fig2

In wild type RPE1 cells, the intrabody is recruited to the chromatin in response to KBrO3 and displays diffuse nuclear localization. A small proportion of cells also have bright punctate staining in the nucleus and cytoplasm. In PARP1/2 double knockout cells, on the other hand, the intrabody forms large inclusions, some of which may be positioned over the nucleus. If so, in the quantification process, these inclusions would be scored as nuclear nucHCB2 intensity within the confines of the H2B-mCherry-delineated nucleus, skewing the results.

So I acquired a Z-stack to see whether the inclusions are within or above the nucleus:

Blog post 15 fig3

Sure enough, the bright inclusions are positioned above the nucleus. This means that huntingtin localization is somehow dysregulated in PARP1/2 double knock out cells. Cytoplasmic inclusion formation skews CellProfiler results when inclusions are positioned over the nucleus. Transient transfection of the huntingtin-specific intrabody is therefore not the method of choice for measuring huntingtin chromatin retention in these cells.

The experimental details and results of huntingtin chromatin retention for all three cell lines have now been deposited to Zenodo.

In the end, what we have are a few more clues. The fact that huntingtin chromatin retention is diminished in PARP1 KO cells and PARP2 KO cells is worth investigating further. The fact that huntingtin localization is dysregulated in the double KO cells is also worth pursuing, but it makes these cells unusable for further experiments of this type.

 

 

 

  1. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7: R100.
  2. Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic Acids Res. 2017;45: 2546–2557.
  3. Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet. 2017;26: 395–406.

Detecting poly ADP ribose

Blog post by Dr. Tamara Maiuri

As mentioned in the year-end review post, there were a few experiments I forgot to deposit to Zenodo.

Here is one: optimizing the method of detecting poly-ADP ribose (PAR) by immunofluorescence. Nothing ground-breaking in this report, but it was the key to detecting the increased PAR levels in HD patient fibroblasts.

Trying to detect PAR by immunofluorescence was very frustrating until I went to the CSHL meeting on The PARP Family and ADP-ribosylation last year. There I met Dr. Hana Hanzlikova, previously from Prof. Keith Caldecott’s lab at University of Sussex and now at the Institute of Molecular Genetics of the ASCR in Prague.

Dr. Hanzlikova gave me two important tips: you need to block the degradation of PAR using PARG inhibitors (because PAR turnover is too fast to catch it in action), and the best detection reagent is MABE1016, a macro domain fused to rabbit Fc tag.  Sure enough, these conditions allowed us to visualize PAR formation in response to oxidative stress. The conditions and results have now been deposited to Zenodo.

The Year in Review

Blog post by Dr. Tamara Maiuri

Most researchers would agree, it feels like we just can’t get enough experiments done, and those, not fast enough. But it’s useful to pause the benchwork from time to time and review a project–what worked, what didn’t, and what we may have missed in our rush to move on to the next thing.

That’s what I’ve done at the end of Year 2 of the HDSA Berman-Topper Fellowship. One of the requirements of the fellowship is that you summarize your work in a report at the end of each year–a daunting task, but well worth the time. It certainly put things in perspective. In a nutshell, what the report says is:

The major finding of the first year of the Berman-Topper fellowship was that many proteins that interact with the huntingtin protein bear a molecule involved in the DNA repair process: poly ADP ribose (PAR). This led us to investigate a connection between huntingtin and PAR signaling in the second year of the fellowship. Methods for detecting PAR were optimized, and a hyper-PAR phenotype was identified in HD patient fibroblasts and in HD mouse striatal precursor cells. The huntingtin-PAR interaction was confirmed in cells and in vitro.

Elevated PAR levels may arise from unrepaired DNA damage and lead to cellular energy deficits, both of which have been observed in many HD models and tissues. Our results introduce the exciting possibility that inhibitors of poly ADP ribose polymerase (PARP), drugs that have already been through clinical trials for a number of cancers, can be explored as a therapeutic option for HD. This is an avenue that has not been considered in the past, and shows promise for other neurodegenerative diseases including Parkinson’s, Alzheimer’s, and ALS.

What is needed at this point is rigorous pre-clinical testing of

  • Whether PARP inhibitors affect HD model phenotypes
  • Safety profiles of PARP inhibitor drugs that would make promising therapeutic leads

Preliminary experiments suggest that PARP inhibitors, which trap PARP at DNA, are co-trapping huntingtin at DNA. This is not likely to be beneficial as it may interfere with huntingtin function. As such, PARP lowering strategies will also be considered in the final year of the fellowship. Complete characterization of the mechanism and function of huntingtin PAR binding is also underway.

 

The full report, with links to all the raw data, is available on Zenodo. I have also deposited last year’s year-end report and the shorter quarterly reports for 2017-2018.

In reviewing the year’s data, I realized that I failed to deposit a few experiments to Zenodo. I’m doing so now, and I’ll post about them in the coming weeks.

Why the heck does huntingtin bind PAR?

Blog post by Dr. Tamara Maiuri

I’ve previously described our hypothesis that huntingtin binds poly ADP ribose and our preliminary evidence that it does so. I now have a few more pieces of data to add to that story.

How does huntingtin bind PAR?

Full length huntingtin, as well as a fragment spanning amino acids 78-426, can bind PAR in vitro in a PAR overlay assay. In an attempt to narrow down which part of the huntingtin protein might bind PAR, I looked at the huntingtin sequence to identify potential PAR-binding motifs (PBMs). Peptides representing four of the most promising PAR-binding motifs (PBMs) were tested for their ability to bind PAR in vitro. PBM3 peptide, which corresponds to amino acids 1782-1804 of the huntingtin sequence (with the PBM at 1790-1798), was the only peptide to bind PAR. The experiment required optimization to maintain peptides on the nitrocellulose membrane. These optimization steps and the results have been deposited to Zenodo.

I was somewhat surprised to find that PBM1 did not bind PAR. That was the only PBM that I could find within the 78-426 fragment, which can bind PAR. It could be that the 78-426 fragment is binding PAR non-specifically, or it could bind PAR through a different motif.

What’s the point of huntingtin PAR-binding?

Current efforts are focused on figuring out the physiological relevance of huntingtin PAR binding. So far, no dice. We asked the following questions:

Is it to stick to chromatin in response to oxidative stress?

Nope.

Truant lab student Carlos Barba tested endogenous huntingtin chromatin recruitment upon enzymatic inhibition of PARP by veliparib. The amount of endogenous huntingtin bound to chromatin after a Triton X-100 wash, which increases upon KBrO3 treatment, was not reduced by inhibition of PARP with veliparib:

 

2019-04-01 Endogenous huntingtin CRA veliparib copy

 

Similarly, the amount of transfected huntingtin 1-586 fragment bound to chromatin after a Triton X-100 wash, which increases upon KBrO3 treatment, was not reduced by inhibition of PARP with veliparib (data deposited to Zenodo).

We also found that endogenous huntingtin was still recruited to chromatin in PARP1/PARP2 knockout cells [1] upon oxidative stress. The knockout cells were highly susceptible to stress, so it’s not clear whether huntingtin was bound to chromatin as part of the DNA repair process (which would lead to recovery) or as part of a cell death process. Enzymatic inhibition of PARP3 in the PARP1/PARP2 knockout cells was toxic.

An unexpected result

When I reported to Ray my lack of success in determining why the heck huntingtin binds PAR, he suggested I try looking at the dynamics of huntingtin chromatin retention using Fluorescence Recovery After Photobleaching (FRAP) of the YFP-tagged intrabody that recognizes endogenous huntingtin [2]. I found that KBrO3 slows huntingtin mobility, as would be expected upon huntingtin chromatin binding. If huntingtin uses PAR binding as a mechanism of chromatin retention, then inhibition of PAR formation should restore huntingtin mobility. In contrast, veliparib significantly reduced huntingtin mobility beyond the degree caused by KBrO3 alone. PARP inhibitors are known to “trap” PARP at chromatin, so it’s possible that huntingtin is also being trapped. I will repeat these experiments using PARP knock down strategies to try and clarify what’s happening, and deposit everything to Zenodo.

2019-04-01 FRAP copy

 

Is it to get to huntingtin stress bodies (HSBs)?

Nope.

HSBs are spots in the cytoplasm where huntingtin accumulates upon cell stress [3]. There are many types of stress bodies in cells, and some of them use PAR in their formation [4]. I tested whether HSBs could still form in the presence of a PARP inhibitor and found it had no effect on HSB formation.

 

Is it to interact with PARylated proteins?

The plot thickens…

We set out on this PAR journey because we found that a large proportion of the huntingtin interacting proteins we identified are also part of PARylated protein databases. To make sure that huntingtin does indeed physically interact with PARylated proteins, I performed co-immunoprecipitation experiments. Not surprisingly, huntingtin pulls down many PARylated proteins (experiments deposited to Zenodo). One of those proteins is the PARP enzyme itself, although the conditions promoting huntingtin-PARP interaction were variable (see Zenodo entry). What came as a surprise was that inhibition of PARP with veliparib actually increased the interaction between huntingtin and PARylated proteins, including PARP. It’s possible that this is related to the slowed huntingtin mobility observed in FRAP experiments upon veliparib treatment.

Is it to get into or out of nuclear speckles?

Not sure yet.

Nuclear speckles, or SC35 domains, are sub-nuclear regions of low DNA and high protein where huntingtin lives [5]. We have found PAR at these sites [2], where it is thought to nucleate liquid-liquid phase transition of proteins into this “membraneless organelle” [6]. I am currently conducting experiments to find out whether huntingtin binds PAR to localize to these sites.

Any other ideas?

If anyone has other suggestions for figuring out why the heck huntingtin binds PAR, I am all ears!

 

  1. Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic Acids Res. 2017;45: 2546–2557.
  2. Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet. 2017;26: 395–406.
  3. Nath S, Munsie LN, Truant R. A huntingtin-mediated fast stress response halting endosomal trafficking is defective in Huntington’s disease. Hum Mol Genet. 2015;24: 450–462.
  4. Leung AKL, Vyas S, Rood JE, Bhutkar A, Sharp PA, Chang P. Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm. Mol Cell. 2011;42: 489–499.
  5. Hung CL-K, Maiuri T, Bowie LE, Gotesman R, Son S, Falcone M, et al. A Patient-Derived Cellular Model for Huntington’s Disease Reveals Phenotypes at Clinically Relevant CAG Lengths. Mol Biol Cell. 2018; mbcE18090590.
  6. Leung AKL. Poly(ADP-ribose): an organizer of cellular architecture. J Cell Biol. 2014;205: 613–619.

Could cancer drugs help with HD?

Blog post by Dr. Tamara Maiuri

I would like to start this post by saying that the ideas below are PURELY SPECULATIVE at this point. But I’m excited about them and feel they definitely warrant further investigation.

So here’s the deal: In a study funded by the HDSA Berman/Topper fellowship, we have found that the huntingtin protein interacts with proteins modified by poly ADP ribose (PAR), and that PAR levels are elevated in cells from HD patients.

 

What is PAR?

PAR is a branched chain-like molecule that acts as a recruitment scaffold for DNA repair proteins. It’s made by an enzyme called poly ADP ribose polymerase (PARP) upon DNA damage (we and others also see elevated levels of DNA damage in HD patient cells [1–3]).

 

What is PARP?

There are several PARP enzymes, but let’s concentrate on PARP1 for now. PARP1 is a major player in the DNA damage response.

PARP1 uses a building material called NAD+ to generate the branched PAR chains that recruit DNA repair factors. The problem is, NAD+ is needed for other things in the cell, especially for converting food into energy. So PARP1 activity is great for a quick response to clear up some DNA damage, but if the damage is too great (or if it’s prolonged), then energy levels in the cell get depleted.

 

PARP hyper-activation

There are several negative consequences if PARP activity goes on too long. Let’s compare a list of these negative consequences to what is seen in HD models and patients (NB: these phenotypes are very much interrelated):

PARP hyper-activation phenotypes

HD phenotypes

ATP depletion [4–7] ATP depletion [8–13]
Mitochondrial dysfunction [14–17] Mitochondrial dysfunction (reviewed in [18])
Energy crisis [19,20] Energy crisis (reviewed in [21])
Cell death (through parthanatos) [22,23] Cell death through apoptosis, necrosis (parthanatos not yet tested) (reviewed in [24])
Neuroinflammation [25–29] Neuroinflammation [30–32]
Transcriptional and chromatin changes (reviewed in [33]) Transcriptional and chromatin changes (reviewed in [34,35])
Autophagy and protein clearance (reviewed in [36,37]) Autophagy and protein clearance (reviewed in [38,39])

Just looking at this list, even if we had no indication that PAR is dysregulated in HD, I would say it’s worth looking into! Turns out, PARP hyper-activation has been linked to other neurodegenerative diseases (reviewed in [40]), most recently Parkinson’s [41].

 

The good news

The cancer field has done decades of work to understand how to inhibit PARPs. I didn’t think this would be much use to us in the HD field, since the point of cancer drugs is to KILL TUMOUR CELLS, while we are looking for drugs to KEEP NEURONS ALIVE.

I was disabused of this notion when I read a very nice review article called Opportunities for the repurposing of PARP inhibitors for the therapy of non-oncological diseases [42]. The article recommends that for chronic, non-oncological indications where there is a significant unmet need, we should consider taking PARP inhibitors to trial.

 

Criteria for deciding whether to try PARP inhibitors for a non-oncological indication

Q: Is there preclinical data demonstrating the efficacy of PARP inhibition in clinically relevant preclinical models?
A: Not yet, but:
  • PARP inhibition is beneficial in R6/2 mice [43,44]
  • Truant lab student Carlos Barba is currently testing PARP inhibition in TruHD cells (and STHdh cells, although not as clinically relevant)
  • We have also asked Chris Ross’s lab to test PARP inhibition in neurons expressing the huntingtin 1-586 fragment (this is an overexpression system, but at least it is in neurons)

 

Q: Is there human data confirming activation of PARP in the target organ?
A: Not yet, but:

 

Q: Would the duration of treatment be short, to limit potential side effects?
A: Unfortunately, no. But intermittent administration (“drug holidays”) could be an option.

 

Q: Are existing therapeutic alternatives insufficient?
A: Yes.

 

Q: Is HD severe enough to justify an attempt for novel therapies, especially in light of the potential “genotoxic baggage” that comes with PARP inhibition?
A: Hell yes.

 

Q: Would a trial be logistically feasible?
A: The HD community has proven that they are very capable of designing, recruiting, and running clinical trials.

Preclinical studies should:

  • Use the drug that will eventually be trialed
  • Use the most clinically relevant models
  • Document the drug effects on DNA and chromosomal integrity (for ideas about safety)

The Truant lab works with preclinical systems. We are doing our best to make sure these preclinical studies are done properly so they can be most informative going forward. All of my results will be shared openly through this blog and our Zenodo Community. I welcome any comments or suggestions about how we might test PARP and PAR in HD systems. And now, back to the bench!

 

References

  1. Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet. 2017;26: 395–406.
  2. Askeland G, Dosoudilova Z, Rodinova M, Klempir J, Liskova I, Kuśnierczyk A, et al. Increased nuclear DNA damage precedes mitochondrial dysfunction in peripheral blood mononuclear cells from Huntington’s disease patients. Sci Rep. 2018;8: 9817.
  3. Castaldo I, De Rosa M, Romano A, Zuchegna C, Squitieri F, Mechelli R, et al. DNA damage signatures in peripheral blood cells as biomarkers in prodromal huntington disease. Ann Neurol. 2019;85: 296–301.
  4. Sims JL, Berger SJ, Berger NA. Poly(ADP-ribose) Polymerase inhibitors preserve nicotinamide adenine dinucleotide and adenosine 5’-triphosphate pools in DNA-damaged cells: mechanism of stimulation of unscheduled DNA synthesis. Biochemistry. 1983;22: 5188–5194.
  5. Berger NA, Sims JL, Catino DM, Berger SJ. Poly (ADP-ribose) polymerase mediates the suicide response to massive DNA damage: studies in normal and DNA-repair defective cells. Princess Takamatsu Symp. 1983. pp. 219–226.
  6. Alano CC, Garnier P, Ying W, Higashi Y, Kauppinen TM, Swanson RA. NAD+ depletion is necessary and sufficient for poly(ADP-ribose) polymerase-1-mediated neuronal death. J Neurosci. 2010;30: 2967–2978.
  7. Ha HC, Snyder SH. Poly(ADP-ribose) polymerase is a mediator of necrotic cell death by ATP depletion. Proc Natl Acad Sci U S A. 1999;96: 13978–13982.
  8. Mochel F, Durant B, Meng X, O’Callaghan J, Yu H, Brouillet E, et al. Early alterations of brain cellular energy homeostasis in Huntington disease models. J Biol Chem. 2012;287: 1361–1370.
  9. Hung CL-K, Maiuri T, Bowie LE, Gotesman R, Son S, Falcone M, et al. A Patient-Derived Cellular Model for Huntington’s Disease Reveals Phenotypes at Clinically Relevant CAG Lengths. Mol Biol Cell. 2018; mbcE18090590.
  10. Milakovic T, Johnson GVW. Mitochondrial respiration and ATP production are significantly impaired in striatal cells expressing mutant huntingtin. J Biol Chem. ASBMB; 2005; Available: http://www.jbc.org/content/280/35/30773.short
  11. Trettel F, Rigamonti D, Hilditch-Maguire P, Wheeler VC, Sharp AH, Persichetti F, et al. Dominant phenotypes produced by the HD mutation in STHdh(Q111) striatal cells. Hum Mol Genet. 2000;9: 2799–2809.
  12. Seong IS, Ivanova E, Lee J-M, Choo YS, Fossale E, Anderson M, et al. HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism. Hum Mol Genet. 2005;14: 2871–2880.
  13. Jędrak P, Mozolewski P, Węgrzyn G, Więckowski MR. Mitochondrial alterations accompanied by oxidative stress conditions in skin fibroblasts of Huntington’s disease patients. Metab Brain Dis. 2018; doi:10.1007/s11011-018-0308-1
  14. Lai Y-C, Baker JS, Donti T, Graham BH, Craigen WJ, Anderson AE. Mitochondrial Dysfunction Mediated by Poly(ADP-Ribose) Polymerase-1 Activation Contributes to Hippocampal Neuronal Damage Following Status Epilepticus. Int J Mol Sci. 2017;18. doi:10.3390/ijms18071502
  15. Lehmann S, Costa AC, Celardo I, Loh SHY, Martins LM. Parp mutations protect against mitochondrial dysfunction and neurodegeneration in a PARKIN model of Parkinson’s disease. Cell Death Dis. 2016;7: e2166.
  16. Wen JJ, Yin YW, Garg NJ. PARP1 depletion improves mitochondrial and heart function in Chagas disease: Effects on POLG dependent mtDNA maintenance. PLoS Pathog. 2018;14: e1007065.
  17. Bai P. Biology of Poly(ADP-Ribose) Polymerases: The Factotums of Cell Maintenance. Mol Cell. 2015;58: 947–958.
  18. Carmo C, Naia L, Lopes C, Rego AC. Mitochondrial Dysfunction in Huntington’s Disease. Adv Exp Med Biol. 2018;1049: 59–83.
  19. Morales J, Li L, Fattah FJ, Dong Y, Bey EA, Patel M, et al. Review of poly (ADP-ribose) polymerase (PARP) mechanisms of action and rationale for targeting in cancer and other diseases. Crit Rev Eukaryot Gene Expr. 2014;24: 15–28.
  20. Buranasudja V, Doskey CM, Wagner BA, Du J, Gordon DJ, Koppenhafer S, et al. 236 – DNA Damage and Energy Crisis are Central in the Mechanism for the Cytotoxicity of Pharmacological Ascorbate in Cancer Treatment. Free Radical Biology and Medicine. 2017;112: 162.
  21. Mochel F, Haller RG. Energy deficit in Huntington disease: why it matters. J Clin Invest. 2011;121: 493–499.
  22. Fatokun AA, Dawson VL, Dawson TM. Parthanatos: mitochondrial-linked mechanisms and therapeutic opportunities. Br J Pharmacol. 2014;171: 2000–2016.
  23. David KK, Andrabi SA, Dawson TM, Dawson VL. Parthanatos, a messenger of death. Front Biosci . 2009;14: 1116–1128.
  24. Bano D, Zanetti F, Mende Y, Nicotera P. Neurodegenerative processes in Huntington’s disease. Cell Death Dis. 2011;2: e228.
  25. Martínez-Zamudio RI, Ha HC. PARP1 enhances inflammatory cytokine expression by alteration of promoter chromatin structure in microglia. Brain Behav. 2014;4: 552–565.
  26. Xu J-C, Fan J, Wang X, Eacker SM, Kam T-I, Chen L, et al. Cultured networks of excitatory projection neurons and inhibitory interneurons for studying human cortical neurotoxicity. Sci Transl Med. 2016;8: 333ra48.
  27. Rom S, Zuluaga-Ramirez V, Reichenbach NL, Dykstra H, Gajghate S, Pacher P, et al. PARP inhibition in leukocytes diminishes inflammation via effects on integrins/cytoskeleton and protects the blood-brain barrier. J Neuroinflammation. 2016;13: 254.
  28. Komirishetty P, Areti A, Yerra VG, Ruby PK, Sharma SS, Gogoi R, et al. PARP inhibition attenuates neuroinflammation and oxidative stress in chronic constriction injury induced peripheral neuropathy. Life Sci. 2016;150: 50–60.
  29. d’Avila JC, Lam TI, Bingham D, Shi J, Won SJ, Kauppinen TM, et al. Microglial activation induced by brain trauma is suppressed by post-injury treatment with a PARP inhibitor. J Neuroinflammation. 2012;9: 31.
  30. Lois C, González I, Izquierdo-García D, Zürcher NR, Wilkens P, Loggia ML, et al. Neuroinflammation in Huntington’s Disease: New Insights with 11C-PBR28 PET/MRI. ACS Chem Neurosci. 2018;9: 2563–2571.
  31. Crotti A, Glass CK. The choreography of neuroinflammation in Huntington’s disease. Trends Immunol. 2015;36: 364–373.
  32. Rocha NP, Ribeiro FM, Furr-Stimming E, Teixeira AL. Neuroimmunology of Huntington’s Disease: Revisiting Evidence from Human Studies. Mediators Inflamm. 2016;2016: 8653132.
  33. Posavec Marjanović M, Crawford K, Ahel I. PARP, transcription and chromatin modeling. Semin Cell Dev Biol. 2017;63: 102–113.
  34. Lee J, Hwang YJ, Kim KY, Kowall NW, Ryu H. Epigenetic mechanisms of neurodegeneration in Huntington’s disease. Neurotherapeutics. 2013;10: 664–676.
  35. Moumné L, Betuing S, Caboche J. Multiple Aspects of Gene Dysregulation in Huntington’s Disease. Front Neurol. 2013;4: 127.
  36. Fan J, Dawson TM, Dawson VL. Cell Death Mechanisms of Neurodegeneration. Adv Neurobiol. 2017;15: 403–425.
  37. Zhang D-X, Zhang J-P, Hu J-Y, Huang Y-S. The potential regulatory roles of NAD(+) and its metabolism in autophagy. Metabolism. 2016;65: 454–462.
  38. Boland B, Yu WH, Corti O, Mollereau B, Henriques A, Bezard E, et al. Promoting the clearance of neurotoxic proteins in neurodegenerative disorders of ageing. Nat Rev Drug Discov. 2018;17: 660–688.
  39. Harding RJ, Tong Y-F. Proteostasis in Huntington’s disease: disease mechanisms and therapeutic opportunities. Acta Pharmacol Sin. 2018;39: 754–769.
  40. Narne P, Pandey V, Simhadri PK, Phanithi PB. Poly(ADP-ribose)polymerase-1 hyperactivation in neurodegenerative diseases: The death knell tolls for neurons. Semin Cell Dev Biol. 2017;63: 154–166.
  41. Kam T-I, Mao X, Park H, Chou S-C, Karuppagounder SS, Umanah GE, et al. Poly(ADP-ribose) drives pathologic α-synuclein neurodegeneration in Parkinson’s disease. Science. 2018;362. doi:10.1126/science.aat8407
  42. Berger NA, Besson VC, Boulares AH, Bürkle A, Chiarugi A, Clark RS, et al. Opportunities for the repurposing of PARP inhibitors for the therapy of non-oncological diseases. Br J Pharmacol. Wiley Online Library; 2018;175: 192–222.
  43. Cardinale A, Paldino E, Giampà C, Bernardi G, Fusco FR. PARP-1 Inhibition Is Neuroprotective in the R6/2 Mouse Model of Huntington’s Disease. PLoS One. 2015;10: e0134482.
  44. Paldino E, Cardinale A, D’Angelo V, Sauve I, Giampà C, Fusco FR. Selective Sparing of Striatal Interneurons after Poly (ADP-Ribose) Polymerase 1 Inhibition in the R6/2 Mouse Model of Huntington’s Disease. Front Neuroanat. 2017;11: 61.

 

PNAS https://doi.org/10.1073/pnas.1801772115 Erratum

In July 2018 we published a manuscript in PNAS,

N6-Furfuryladenine is protective in Huntington’s disease models by signaling huntingtin phosphorylation

After publication, we were made aware of an error in a structure cartoon in Figure 3.

The compound was correct, the representation was wrong. The control compound is 9-deaza-kinetin. This compound is similar to N6FFA, but cannot be salvaged. The correct structure is below, within the corrected figure.

9DK

The Editors at PNAS were informed, but they decided a published erratum was not necessary.

Hypothesis: Poly ADP ribose signaling is dysregulated in Huntington’s disease

Blog post by Dr. Tamara Maiuri

In a previous post, I described two new hypotheses generated by the findings of the HDSA-funded project looking for DNA repair-relevant huntingtin interacting proteins: that huntingtin binds poly ADP ribose (PAR), and that PAR signaling is dysregulated in HD. Last time, I reported our preliminary results supporting the first hypothesis. In the current post, I’ll report our first solid clue that PAR signaling may be dysregulated in HD: cells from HD patients have higher levels of PAR.

Let’s take a step back and look at the bigger picture for a moment. We know that suboptimal DNA repair plays a role in many neurodegenerative diseases [1–3], and DNA repair genes are implicated in HD symptom onset [4–6]. PAR synthesis is one of the first steps of DNA repair: PARP proteins recognize breaks in DNA and string together chains of PAR to help recruit the DNA repair machinery. If all goes well, the damage is repaired, the PAR is broken down for recycling, and the cell can go about its business as usual.

If the DNA is not repaired properly, then PARPs keep trying to bring in the recruits–they keep generating PAR. This wouldn’t be a huge problem, except that it seriously messes with the cell’s energy factories, aka mitochondria, in a number of ways. First off, the raw material that PARPs use to make PAR (called NAD+) is also needed by mitochondria to convert food into energy. If PARPs use up all the NAD+ stores, then cells undergo “energetic collapse” and die [7]. Bad news for high-energy-burning neurons. To make matters worse, the PAR produced in the nucleus also travels out to mitochondria and signals them to carry out a form of programmed cell death called Parthanatos [8]. Additional “nucleus-to-mitochondria death signaling” is thought to contribute to neuronal death in a number of neurodegenerative diseases [9,10]. In fact, many of the phenotypes we see in HD models and tissues could be explained by energy-draining hyper-PARylation, including protein aggregation [11–13], ATP depletion [14], and mitochondrial dysfunction [15].

We know that the expanded huntingtin protein is the cause of HD. We also know that huntingtin physically locates to sites of DNA damage and scaffolds DNA repair proteins [16], and that neurons are exposed to more and more DNA-damaging reactive oxygen species (ROS) as we age [17]. So, it makes sense to hypothesize that

Suboptimal mutant huntingtin function in the repair of nuclear DNA leads to hyper-PARylation in the high-ROS-load neurons of the striatum.

Suboptimal DNA repair by expanded huntingtin would have some observable consequences. For one, there would be more damaged DNA accumulating in HD tissues. This is been seen in patient cells by us [16] and others [18]. Secondly, we would expect hyper-PARylation if PARPs are constantly recognizing DNA breaks and generating PAR. That’s what Truant lab member Carlos Barba Bazan tested in these experiments deposited to Zenodo. Carlos found that PAR levels are elevated in two different HD patient cell lines compared to control.

We’re pretty excited about this finding and what it might mean. Is hyper-PARylation the culprit behind neuronal death in HD brains? We have more experiments to do before we know the answer to that. But one important clue is that a PARP inhibitor was beneficial in an HD mouse model [19,20]. PARP inhibitors are commonly used drugs in the cancer field, which means there’s a tonne of information about them, and many have already been tested for safety. We have a ways to go before we know whether any of these drugs might be suitable to treat HD. We will share all of our results about how important PAR signaling might be to HD as soon as we get them!

keep-calm-and-test-your-hypothesis-3
Image credit

 

1. Maynard S, Fang EF, Scheibye-Knudsen M, Croteau DL, Bohr VA. DNA Damage, DNA Repair, Aging, and Neurodegeneration. Cold Spring Harb Perspect Med. 2015;5. doi:10.1101/cshperspect.a025130
2. Leandro GS, Sykora P, Bohr VA. The impact of base excision DNA repair in age-related neurodegenerative diseases. Mutat Res. 2015;776: 31–39.
3. Jeppesen DK, Bohr VA, Stevnsner T. DNA repair deficiency in neurodegeneration. Prog Neurobiol. 2011;94: 166–200.
4. Genetic Modifiers of Huntington’s Disease (GeM-HD) Consortium. Identification of Genetic Factors that Modify Clinical Onset of Huntington’s Disease. Cell. 2015;162: 516–526.
5. Bettencourt C, Hensman-Moss D, Flower M, Wiethoff S, Brice A, Goizet C, et al. DNA repair pathways underlie a common genetic mechanism modulating onset in polyglutamine diseases. Ann Neurol. 2016;79: 983–990.
6. Moss DJH, Pardiñas AF, Langbehn D, Lo K, Leavitt BR, Roos R, et al. Identification of genetic variants associated with Huntington’s disease progression: a genome-wide association study. Lancet Neurol. 2017;16: 701–711.
7. Cantó C, Menzies KJ, Auwerx J. NAD(+) Metabolism and the Control of Energy Homeostasis: A Balancing Act between Mitochondria and the Nucleus. Cell Metab. 2015;22: 31–53.
8. David KK, Andrabi SA, Dawson TM, Dawson VL. Parthanatos, a messenger of death. Front Biosci . 2009;14: 1116–1128.
9. Narne P, Pandey V, Simhadri PK, Phanithi PB. Poly(ADP-ribose)polymerase-1 hyperactivation in neurodegenerative diseases: The death knell tolls for neurons. Semin Cell Dev Biol. 2017;63: 154–166.
10. Fang EF, Scheibye-Knudsen M, Chua KF, Mattson MP, Croteau DL, Bohr VA. Nuclear DNA damage signalling to mitochondria in ageing. Nat Rev Mol Cell Biol. 2016;17: 308–321.
11. Dahl J-U, Gray MJ, Jakob U. Protein quality control under oxidative stress conditions. J Mol Biol. 2015;427: 1549–1563.
12. Squier TC. Oxidative stress and protein aggregation during biological aging. Exp Gerontol. 2001;36: 1539–1550.
13. Weids AJ, Ibstedt S, Tamás MJ, Grant CM. Distinct stress conditions result in aggregation of proteins with similar properties. Sci Rep. 2016;6: 24554.
14. Mochel F, Haller RG. Energy deficit in Huntington disease: why it matters. J Clin Invest. 2011;121: 493–499.
15. Carmo C, Naia L, Lopes C, Rego AC. Mitochondrial Dysfunction in Huntington’s Disease. Adv Exp Med Biol. 2018;1049: 59–83.
16. Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet. 2017;26: 395–406.
17. Mattson MP, Magnus T. Ageing and neuronal vulnerability. Nat Rev Neurosci. 2006;7: 278–294.
18. Askeland G, Dosoudilova Z, Rodinova M, Klempir J, Liskova I, Kuśnierczyk A, et al. Increased nuclear DNA damage precedes mitochondrial dysfunction in peripheral blood mononuclear cells from Huntington’s disease patients. Sci Rep. 2018;8: 9817.
19. Cardinale A, Paldino E, Giampà C, Bernardi G, Fusco FR. PARP-1 Inhibition Is Neuroprotective in the R6/2 Mouse Model of Huntington’s Disease. PLoS One. 2015;10: e0134482.
20. Paldino E, Cardinale A, D’Angelo V, Sauve I, Giampà C, Fusco FR. Selective Sparing of Striatal Interneurons after Poly (ADP-Ribose) Polymerase 1 Inhibition in the R6/2 Mouse Model of Huntington’s Disease. Front Neuroanat. 2017;11: 61.

SCASource is alive!

It’s alive!

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SCAsource.net is based on the HDbuzz.net model of distilling primary research manuscripts to lay language that ataxia patients and familes can understand.

Why do this?

A few reasons:

  1. Science in the media is overall pretty poorly done.
  2. In the internet age, news is about clicks and hype, with a short attention span and no real emphasis on accuracy.
  3. Good knowledge is hard to get, but can empower those with disease to understand their disease and hopefully upcoming options.
  4. SCA families need a reliable source of information, they don’t need hype, so they can understand when it is time to get really excited about breakthroughs. We also need to share the process to show these families people are working very hard, dedicated, day and night to try and get a therapy for these diseases.

How did this Happen?

This was born at lunch tables at the National Ataxia Foundation bi-annual Ataxia Investigators Meeting. This was driven by young scientists, post-Doctoral Fellows and graduate students who got together and decided this was needed and a great idea to get the impact of their efforts beyond just other scientists.

The catalyst was Celeste Suart, who coordinated efforts and physically set up the site, the themes, logos, Twitter accounts…etc.

SCAsource

What Next?

Content! We are a work in progress and are open to any helpful input.

Follow us on Twitter!

Is huntingtin a PAR-binding protein?

Blog post by Dr. Tamara Maiuri

Previously I explained our rationale for hypothesizing that huntingtin may bind poly ADP-ribose (PAR). If so, this could be the way it gets to damaged DNA, and this might be dysregulated in HD. Since we know DNA repair genes impact whether HD patients get sick early or late in life, this is a good place to look for problems—then we can look for drugs that fix the problems.

But first things first: does huntingtin bind PAR? There are many “domains” or regions of proteins that are capable of binding PAR: PAR-binding motifs, macrodomains, and WWE domains to name a few. A quick scan of the huntingtin sequence revealed four potential PAR-binding motifs. We can look at the recently solved huntingtin structure to get some more clues:Blog Post 10

This is pure speculation at this point—many regions of the protein were left out of this structure so it’s too early to know for sure—but it’s fun to guess: the barrel of the huntingtin solenoid is the right size to accommodate DNA, as it is the same size as the DNA binding regions of other DNA repair proteins such as MSH2, MSH6, and PCNA (pictured above). Similar to MSH2, three of the potential PAR-binding motifs within huntingtin are exposed to the outer surface of the DNA binding region, suggesting a mechanism by which huntingtin is recruited by PAR, followed by direct binding to DNA. (Direct binding of purified full-length huntingtin to DNA has been shown by Dr. Rachel Harding and deposited to Zenodo: https://zenodo.org/record/801606#.Wr4eG5PwZ-V).

One way to get a clue about this is to immobilize huntingtin protein on a membrane, then overlay it with purified PAR polymer. If huntingtin binds PAR, it too will be stuck to the membrane. After washing away unbound PAR, you can detect whatever is left with an anti-PAR antibody. This is called a PAR overlay assay.

The first few experiments (deposited to Zenodo) look promising. Purified full length huntingtin (produced by Dr. Harding) reproducibly bound PAR in several experiments, as did a fragment made up of amino acids 78-426 (which conveniently contains one of the potential PAR binding motifs mentioned above). I also tried two preparations of expanded huntingtin (Q46 and Q54) in one experiment, with confusing results: huntingtin Q54 bound PAR while huntingtin Q46 did not. This could be because the Q46 prep was from an older stock—I’m currently repeating the experiment to find out what’s going on.

These are very early results, and I need to make mutations in the potential PAR-binding motifs to see whether they are specifically mediating the PAR interaction, or whether this is nonspecific binding. But we may be on to something here… in the next blog post I’ll share more preliminary data implicating PAR in huntingtin chromatin recruitment in cells.

A closer look at the hits generates 2 new hypotheses

Blog post by Dr. Tamara Maiuri

Forgive me readers for I have been busy, it has been 3 months since my last blog post. During this time, we published a very exciting story identifying a lead compound and how we think it works in HD. Also during this time, I have gone through the list of huntingtin interactors identified in my HDSA-funded project to find drug targets that are relevant to the process of DNA repair. We now have some interesting results!

As explained in my last post, the original aim to identify huntingtin interactors from human cells was not technically feasible and mouse cells were used instead. Several hundred protein-protein interactions were detected, then the list was further refined by only considering high and medium confidence hits. We now have a list of 314 proteins that interact with huntingtin reproducibly across biological replicates. See the end of this post for the lists of ROS-dependent interactors (Tables 1-3), proteins that interacted with huntingtin only in untreated cells (Table 4), and proteins found to be modified by poly ADP-ribose (PARylated proteins; Table 5). These tables have also been deposited to Zenodo.

Blog Post 9 fig

 

Indeed, the most notable finding of the ROS-dependent interactome analysis was the high degree of overlap with datasets of “PARylated” proteins. PAR is of interest to us because it is generated in response to DNA damage, and acts to recruit DNA repair proteins to damage sites.

This result led us to pursue two hypotheses with the aim of identifying drug targets relevant to DNA repair:

Huntingtin is a PAR-binding protein: Huntingtin may use PAR binding to interact with PARylated proteins. If so, this is likely to be the mechanism by which huntingtin interacts with chromatin and assembles DNA repair factors in its role as a scaffold, and this may be dysregulated in HD.

PAR signaling is dysregulated in HD: Regardless of whether huntingtin physically binds PAR, it is still possible that we have uncovered a previously unexplored aspect of HD pathology: there is strong genetic evidence that DNA repair genes influence disease [1-3], huntingtin participates in the process of DNA repair [4], and elevated levels of damaged DNA are common to HD tissues and models [4-8].

Old spider web. Shallow DOF.
© Bolotov | Stock Free Images

In response to DNA damage, PAR chains are the first scaffold generated for DNA repair factor assembly: a sticky web bound by proteins involved in DNA repair. So it’s possible that in HD, excess DNA damage accumulates due to sub-optimal huntingtin function in the repair process, leading to Poly ADP-Ribose Polymerase (PARP) hyperactivation and elevated PAR levels.

High PAR levels could not only interfere with huntingtin function if it binds PAR, but also cause an “energy crisis” in high-energy-consuming neurons [9-11]. In fact, energy deficits have been frequently observed across HD models and in HD patients [12]. Similarly, PARP hyperactivation is linked to cerebellar ataxia [13], and PARP inhibition has been reported to improve phenotypes in a HD mouse model, although by a different mechanism [14,15].

In the coming blog posts, I will share preliminary data that suggests huntingtin can bind PAR in a test tube, and that PAR is at least partially responsible for huntingtin recruitment to chromatin. We have also detected increased amounts of PAR and of chromatin-bound huntingtin in cells from an HD patient. Stay tuned!

References:

  1. Genetic Modifiers of Huntington’s Disease (GeM-HD) Consortium. Identification of Genetic Factors that Modify Clinical Onset of Huntington’s Disease. Cell. 2015;162: 516–526.
  2. Bettencourt C, Hensman-Moss D, Flower M, Wiethoff S, Brice A, Goizet C, et al. DNA repair pathways underlie a common genetic mechanism modulating onset in polyglutamine diseases. Ann Neurol. 2016;79: 983–990.
  3. Moss DJH, Pardiñas AF, Langbehn D, Lo K, Leavitt BR, Roos R, et al. Identification of genetic variants associated with Huntington’s disease progression: a genome-wide association study. Lancet Neurol. 2017;16: 701–711.
  4. Maiuri T, Mocle AJ, Hung CL, Xia J, van Roon-Mom WMC, Truant R. Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex. Hum Mol Genet. 2017;26: 395–406.
  5. Bogdanov MB, Andreassen OA, Dedeoglu A, Ferrante RJ, Beal MF. Increased oxidative damage to DNA in a transgenic mouse model of Huntington’s disease. J Neurochem. 2001;79: 1246–1249.
  6. Kovtun IV, Liu Y, Bjoras M, Klungland A, Wilson SH, McMurray CT. OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells. Nature. 2007;447: 447–452.
  7. Enokido Y, Tamura T, Ito H, Arumughan A, Komuro A, Shiwaku H, et al. Mutant huntingtin impairs Ku70-mediated DNA repair. J Cell Biol. 2010;189: 425–443.
  8. Askeland G, Dosoudilova Z, Rodinova M, Klempir J, Liskova I, Kuśnierczyk A, et al. Increased nuclear DNA damage precedes mitochondrial dysfunction in peripheral blood mononuclear cells from Huntington’s disease patients. Sci Rep. 2018;8: 9817.
  9. Morales J, Li L, Fattah FJ, Dong Y, Bey EA, Patel M, et al. Review of poly (ADP-ribose) polymerase (PARP) mechanisms of action and rationale for targeting in cancer and other diseases. Crit Rev Eukaryot Gene Expr. 2014;24: 15–28.
  10. Andrabi SA, Umanah GKE, Chang C, Stevens DA, Karuppagounder SS, Gagné J-P, et al. Poly(ADP-ribose) polymerase-dependent energy depletion occurs through inhibition of glycolysis. Proc Natl Acad Sci U S A. 2014;111: 10209–10214.
  11. Fouquerel E, Goellner EM, Yu Z, Gagné J-P, Barbi de Moura M, Feinstein T, et al. ARTD1/PARP1 negatively regulates glycolysis by inhibiting hexokinase 1 independent of NAD+ depletion. Cell Rep. 2014;8: 1819–1831.
  12. Dickey AS, La Spada AR. Therapy development in Huntington disease: From current strategies to emerging opportunities. Am J Med Genet A. 2017; doi:10.1002/ajmg.a.38494
  13. Hoch NC, Hanzlikova H, Rulten SL, Tétreault M, Komulainen E, Ju L, et al. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature. 2017;541: 87–91.
  14. Cardinale A, Paldino E, Giampà C, Bernardi G, Fusco FR. PARP-1 Inhibition Is Neuroprotective in the R6/2 Mouse Model of Huntington’s Disease. PLoS One. 2015;10: e0134482.
  15. Paldino E, Cardinale A, D’Angelo V, Sauve I, Giampà C, Fusco FR. Selective Sparing of Striatal Interneurons after Poly (ADP-Ribose) Polymerase 1 Inhibition in the R6/2 Mouse Model of Huntington’s Disease. Front Neuroanat. 2017;11: 61.

 

Table 1: Hit Proteins unique to H2O2-treated cells
Hit Protein (human homolog) Molecular Function Biological Function Interactions (UniprotKB, BioGrid) Disease Connections
TPT1 metal ion binding; protein binding; RNA binding

 

calcium binding and microtubule stabilization

 

TP53, XRCC5, XRCCC6, HSPB1, EF1D, PCH2, RHEB, EF1D-2, T22D1, AT1A1 Charcot Marie tooth, Distal hereditary motor neuropathy type II, several cancers
NDUFV1 metal ion binding; nucleotide binding; protein binding ATP synthesis
SLIRP RNA-binding RNA-binding protein that acts as a nuclear receptor corepressor PNMA1, C102B, MTUS2, K1C40, LPPRC Leigh Syndrome French Canadian Type
HINT2 nucleotide binding

 

steroid biosynthesis, apoptosis 33 interactors, including APP, TOP3A
ACAD9 nucleotide binding mitochondrial complex I assembly 79 interactors, including many mitochondrial proteins
PMPCB metal ion binding cleaves presequences (transit peptides) from mitochondrial protein precursors 77 interactors, including many mitochondrial proteins
IDH3G metal ion binding nucleotide binding tricarboxylic acid cycle 28 interactors, including KPNA2, HNRNPK, PQBP1
OAT protein binding amino acid biosynthesis 44 interactors, including SOD1, SOD2, PARK7, HDAC5, SIRT7, CDK2, FBXO6, FUS Parkinson’s disease
ACOT10 hydrolase activity acyl-CoA metabolic process
GCAT acetyltransferase activity amino acid metabolism 12 interactors, including ATXN3, MDM2, FBXO6 Spinocerebellar ataxia 3
DKC1 protein binding; RNA binding ribosome biogenesis, telomere maintenance RUVB1, HMBX1, NAF1 Hoyeraal Hreidaarsson syndrome
CHST2 nucleotide binding carbohydrate metabolism
HIBADH nucleotide binding amino acid catabolism 10 interactors, including BRCA1, SOD1
PPIF protein binding protein folding, mitochondrial permeability TP53, CKLF5, ABI2, BANP Li-Fraumeni syndrome, several cancers
MRPS33 mitochondrial translation 36 interactors, including several RNA-binding proteins
HAT1 histone acetyltransferase activity DNA packaging RBBP4, H4, VPR, REL, MEOX2, BACD2, ITF2 Pitt-Hopkins syndrome
PPM1G metal ion binding; protein binding; phosphatase activity cell cycle arrest TERF1, XRCC5, XRCC6, TAT, YBOX1
VAT1 metal ion binding negative regulation of mitochondrial fusion 25 interactors, including TP53, H2AFX, SOD1, PARK2, CDK2

 

Table 2: Hit Proteins unique to MMS-treated cells
Hit Protein (human homolog) Molecular Function Biological Function Interactions (UniprotKB, BioGrid) Disease Connections
TXNDC17 antioxidant activity redox reactions RUFY1, TINF2, EXOS8 Dyskeratosis congenita, Pontocerebellar hypoplasia
MRPS21 RNA binding structural molecule activity mitochondrial translation 38 interactors, including mitochondrial translation proteins, RNA-binding proteins
HMGA1 DNA binding; protein binding base excision repair, nucleosome disassembly ORC6, ANM6 Meier-Gorlin syndrome
MRPS26 RNA binding DNA damage response, mitochondrial translation 69 interactors, including mitochondrial translation proteins, RNA binding proteins
PEBP1 enzyme regulator activity;

nucleotide binding; protein binding;

RNA binding

MAPK cascase 41 interactrs, including SOD1, SOD2, RAF1, LOX15, CFL1, PABPC3
CDC37 enzyme regulator activity;

protein binding

co-chaperone, mitophagy 246 interactions, including IKKA, IKKB, APOE, PSN1, LRKK2 Alzheimer’s disease, frontotemporal dementia, amyotrophic lateral sclerosis, Parkinson’s disease
TXNL1 antioxidant activity redox homeostasis 64 interactors, including proteasomal proteins
NARS nucleotide binding tRNA synthesis 67 interactors, including ATXN1, HDAC2, XRCC6, XRCC5 Spinocerebellar ataxia 1
FDPS metal ion binding;

RNA binding

cholesterol biosynthesis 50 interactors, including ATXN 1, G6PD, CREB3, PABPC1, PSME4 Spinocerebellar ataxia 1
PSME4 enzyme regulator activity;

protein binding

DNA repair, histone degradation 45 interactors, including proteasomal proteins, FDPS
Table 3: Hit Proteins common to H2O2- and MMS-treated cells
Hit Protein (human homolog) Molecular Function Biological Function Interactions (UniprotKB, BioGrid) Disease Connections
FAM135A hydrolase activity lipid metabolism 10 interactors, including EZR, RAB5A, RAB9A
CAVIN1 protein binding;

RNA binding

caveolae formation, transcription 115 interactors, including T10IP, CAV1, CAVN2, CAVN3, RCOR1, RAB5A, RAB7A, RAB5C Neurodegeneration syndrome
Table 4: Hit Proteins specific to untreated cells
Hit Protein (human homolog) Molecular Function Biological Function Interactions (UniprotKB, BioGrid) Disease Connections
TCEB1 protein binding translation 154 interactors, including APE1, FUS, SQSTM1, POU5F1, OTUB1, TOP2A, CENPC
RPS14 RNA binding;

structural molecule activity

translation 254 interactors, including MDM2 and many ribosomal proteins
BRK1 protein binding actin and microtubule organization 25 interactors, including BRAP, PFDN1 Hermansky-Pudlak syndrome
RPL24 protein binding;

RNA binding;

structural molecule activity

translation 165 interactors, including many ribosomal proteins
RPL15 protein binding;

RNA binding;

structural molecule activity

translation 197 interactors, including many ribosomal proteins
RAD23B DNA binding;

protein binding

DNA damage recognition, nucleotide excision repair 125 interactors, including HMGB1, MLH1, XPC, ATXN3, POU5F1, ERCC3, PUF60, G6PD, EWSR1, BRCA1 Xeroderma pigmentosum, Spinocerebellar ataxia 3, Verheij syndrome
NACA DNA binding;

protein binding

protein transport, transcription 55 interactors, including EWSR1, SOD1, BRCA1, PARK2, MDM2, H2AFX, APLP1 Parkinson’s disease
CAND1 protein binding ubiquitin conjugation 708 interactors, including many cullins X-linked syndromic mental retardation
PAICS nucleotide binding;

protein binding

purine biosynthesis 94 interactors, including BRCA1, FUS, 53BP1
EWSR1 metal ion binding;

protein binding;

RNA binding

transcription 650 interactors, including FUS, ATPF2, PABPN1, SOD1 Ewing sarcoma, Mitochondrial complex V deficiency nuclear 1, Amyotrophic lateral sclerosis, Frontotemporal dementia
TPM3 protein binding;

structural molecule activity

actin filament organization 133 interactors, including TP53, PARK7, PARK2, BRCA1 Dystonia, Parkinson’s disease
FHL1 metal ion binding;

protein binding

differentiation 35 interactors, including EWSR1 Emery-Dreifuss muscular dystrophy
HNRNPK DNA binding;

protein binding;

RNA binding

transcriptional regulation of TP53 DNA damage response 281 interactors, including TP53, MDM2, PABPC1, FUS, XRCC6, BRCA1, HMGB1, TOP1, PARK2 Amyotrophic lateral sclerosis, Li Fraumeni syndrome, Parkinson’s disease
RPL31 protein binding;

RNA binding;

structural molecule activity

translation 159 interactors, including BRCA1, EWSR1, APP, TP53 Diamond-Blackfan anemia
YBX1 DNA binding;

protein binding;

RNA binding

transcription, mRNA processing 290 interactors, including TP53, BRCA1, FUS, PCNA, H2AFX, APE1, EWSR1
LMNA protein binding;

structural molecule activity

nuclear assembly, chromatin organization 645 interactors, including FUS, PARP1, H2AFX Emery-Dreifuss muscular dystrophy, Charcot Marie tooth disease, Hutchinson-Gilford progeria syndrome, LMNA-related congenital muscular dystrophy
SNRPC metal ion binding;

protein binding;

RNA binding

mRNA splicing 90 interactors, including EWSR1, BARD1
FABP5 transporter activity fatty acid transport 40 interactors, including SOD1, POU5F1
RPL23A protein binding;

RNA binding;

structural molecule activity

translation 239 interactors, including TP53, BRCA1, MDM2, PARK2, many ribosomal proteins
UBA1 nucleotide binding;

protein binding;

RNA binding

 

ubiquitin conjugation, response to DNA damage 147 interactors, including FUS, BRCA1, SOD1, PABPC1 X-linked spinal muscular atrophy, Giant axonal neuropathy
RPL27 RNA binding;

structural molecule activity

translation 157 interactors, including TP53, BRCA1, PABPC1, many ribosomal proteins
RPL7 DNA binding;

protein binding;

RNA binding;

structural molecule activity

 

translation 230 interactors, including TP53, BRCA1, PABPC1, many ribosomal proteins
H3F3C DNA binding;

protein binding

nucleosome assembly 24 interactors, including FAN1, DNAJC11
RPL36 RNA binding;

structural molecule activity

translation 138 interactors, including BRCA1, many ribosomal proteins
Table 5: PARylated proteins
ABI1 DBD1 EWSR1 HMGA1 KRT1 PAICS RPL15 RPL6 RPS19 TUBA4A
ACTB DDX3X FLNA HMGB1 KRT10 PCBP1 RPL18 RPL7 RPS2 TUBB6
AHCY DEK FOXP1 HMGB2 LMNA PCBP2 RPL22 RPL7A RPS25 TUFM
ATP5A1 DKC1 FSCN1 HNRNPA1 LONP1 PCNA RPL23 RPLP0 RPS27A
CALR DNAJA1 FUS HNRNPAB MTHFD1L PIP5K1A RPL23A RPLP1 RPS3
CAND1 EEF1A1 GAPDH HNRNPD MYL12B PRTF RPL24 RPS10 RPS3A
CCT3 EEF1G GLUD1 HNRNPK MYL6 RAD23B RPL27 RPS11 RPS6
CCT4 EEF2 GSTP1 HSP90AA1 NACA RPL11 RPL27A RPS12 RPS8
CCT8 EIF2S1 HADHA HSPH1 NCKAP1 RPL 12 RPL3 RPS14 RPSA
CFL1 EIF4A1 HIST1H2A KPNA2 NCL RPL13 RPL31 RPS15A SFPQ
CYFIP1 ENO1 HIST4H4 KPNB1 PA2G4 RPL14 RPL4 RPS18 TCP1