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!

SCAsourcelogo

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

 

 

 

The N6-furfuryladenine Hypothesis in HD

The summer of 2018 marks the third manuscript to come out of the lab defining the role of huntingtin in DNA damage repair, and a defective signaling pathway in HD caused by the proximity of expanded glutamine tracts to the kinase substrate site in huntingtin N17, the first 17 amino acids of huntingtin.

Since 2011, we have defined this site as hypo-phosphorylated in HD.  Since 2011, academic and industrial labs have reported that huntingtin is under-phosphorylated at many sites, and in all model and samples taken from humans.

Picture1

(Data from Hung et al., 2018, showing hypo-phosphorylation in human HD fibroblasts from clinic). Here’s Claudia:

claudia

 

With the help of a donor gift of a Nikon A1 confocal microscope, the CFI/OIT Leaders Opportunity Fund for a super-resolution SIM device, Laura Bowie set on to her PhD thesis work with CIHR doctoral Scholarship to set up an unbiased screening protocol in which a robotic stage took random shots around a  96 well plate well, with a library of natural compounds applied. This was supposed to be a pilot screen of only 130, to test out the microscopy acquisition and then use non-supervised machine sorting to sort the images, so from front-to-back, there is no possible investigator bias.

Here’s Laura:

Truant Bowie 2018 3 (002)

However, we got hits, most of them were anti-oxidants, which lead to our 2016 discovery that huntingtin was a ROS sensor via a single methionine at position eight, and this oxidation proceeded phosphorylation. The other hits affected the NFKb/ IKK kinase pathways, pathways we discovered in 2011. But we got one lone hit, distant and distinct in 3D prinicipal component analysis space: N6-furfuryladenine.

N6FFA

The rest, is now recent history.

The net results: YAC128 mice get better, and brain levels of huntingtin drop. Huntingtin hypo-phosphorylation is now restored to normal, with sub-micromolar levels required.

This was all outstanding mouse work from Melanie Alpaugh and Simonetta Sipione at the University of Alberta.

But what is N6-FFA? 

An astute eye will find an adenosine core, the same core of nature’s energy molecule, ATP, but count the positions around the rings from nitrogen 1, and at nitrogen 6 you will find a furfuryl ring -the 5 -sided ring with double carbon bonds and an oxygen. In DNA, this is what happens when you oxidize DNA, and this isn’t good. Instead of pairing with thymine (A-T), it can pair with guanine (A-G) -that’s not supposed to happen. So, the DNA gets fixed. In dividing cells, it get fixed by mismatch repair, which sees the N6-FFA:G mismatch and removes it. But in brains, neurons don’t divide, so they rely on Base Excision Repair or Nucleotide Excision Repair, in which a single nucleotide is removed and replaced, or a small patch of DNA. This is how oxidized guanines are removed and throw out of the body as garbage. We can even detect N6FFA in human pee.

N6FFA -Reduce, Reuse, Recycle

Neurons are weird cells. They don’t work like most other cells. They don’t divide, they are huge and spindly and they are energy hogs. Over half the energy in your body is used in the brain at rest, and it doesn’t really slow down or take a break. This means the brain takes huge amounts of fuel, and burns a lot of ATP. Neurons also rely heavily of recycling nucleotides, or salvaging, because at times, they run out of fuel and ATP is just not around. So the brain makes energy like other cells by oxidative phosphorylation and glycolysis (blow dust off the old biochemistry textbook). What happens if we don’t have the enzymes to salvage nucleotides? We get severe diseases, usually fatal in children. All this burning means pollution, in the form of reactive oxygen species, or ROS. Neurons need to get rid of ROS, or ROS will go nuts and react with everything around it, especially DNA.

Enter Nick Hertz

This is Nick.

Nick

In 2013, the Kevan Shokat lab at UCSF, with student Nick Hertz, did a screen to find molecules that could be used by a mutant form of Pink1 kinase, a form found in families with familial Parkinson’s disease.  (digression, Nick Hertz is the great Grandson of Gustav Hertz, who won the 1926 Nobel Prize with James Franck in Physics). What Nick discovered was that N6FFA can be salvaged to form weird triphosphate, with that adenosine core, and this triphosphate can be used by mutant Pink1 to restore it’s activity lost in Parkinson disease. We know this is also true to HD because a version of N6FFA that cannot be salvaged doesn’t work to fix mutant huntingtin hypo-phosphorylation. so, N6FFA is not the active molecule, it is a pro-drug, a compound that gets converted to an active form. This is a “neo-substrate” for a kinase, not ATP or GTP. This is an aspect of drug discovery called pharmacokinetics, or what the body does to the drug. Pharmacodynamics is what the drug does to the body. Both are essential to understand to make a lead like N6FFA into a drug. With David Litchfield, (another uncool biochemist) at  Western University, he could show that the huntingtin kinase, CK2, can also use this “neo-substrate”, while the Shokat lab thinks there are only two kinases that can do this: CK2 and Pink1. (digression #2, Litchfield was a graduate of McMaster Biochemistry Department).

“But why not just use ATP?!?” – several reviewers and pharma executives

Somehow in the last 40 years, biochemistry became uncool. We don’t teach it in the detail of the past because science is just moving too damn fast and we have more and more stuff to teach. It’s too bad, because biochemistry is what led to drugs that worked 40 years ago, and still work today.  It’s also complex, with steps and pathways and feedback loops and big wall charts no one looks at. The human neuron can undergo energy crisis, times where all the ATP is burned up, under periods of stress. Stress like high ROS levels due to human aging, which only increase as the brain gets older. DNA damage triggers an even called PARylation – PAR is poly-ADP-ribose, these are chains that grow out of sites of DNA damage that act like nets catching PAR-binding proteins, and when they form, they need to get removed or they will inhibit energy metabolism by draining NAD+, halting glycolysis, and ATP release from the energy plants of the neuron, the mitochondria. So, sorry “experts” but ATP is not universal and always abundant, and energy deficits is a long-standing observation in HD, which makes the comment from an HD expert rather bizarre.

There is defective DNA repair in HD (2017)

There is defective DNA repair in HD (2018)

The point is, there is defective DNA repair in HD.

To read more about PAR and PARylation, see the work in real-time with Dr. Maiuri.

What does this say about the Amyloid hypothesis in HD?

tombThe amyloid-like hypothesis in HD is fraught with problems. There is no explanation as to why aggregates of huntingtin can accumulate for decades, when neuronal protein half-lives don’t exceed 20 days.

Plus, the whole AD drug thing.

Regions with aggregates don’t map to regions of pathology in HD, and while there are phenotypes of disease in human cell from HD patients, we can’t find aggregates unless we force them to happen in tiny fragments overexpressed.  This is explained  by much hand -waving in the research community for 25 years, typically based around synthetic hyper-allele models of disease, that usually involves cutting off 97% of the protein.

ShySecretCoelacanth-max-1mb

The effect of N6FFA, and HD Genome-Wide Association Studies, suggests that aggregates are an effect, not cause in HD. DNA damage and energy crisis proceed protein misfolding. Misfolding is just a symptom of a sick neuron, particularly a sick ER. When we restored this signaling, mutant huntingtin inclusions disappear.

So, by unbiased microscopy screening, we hit the same answers as by unbiased GWAS in HD 2015. and again in 2017. Maybe hypothesis-driven research was not the best approach for HD.

 

So N6FFA is a drug? 

No. N6FFA is a lead. As a compound, it has very poor pharmacological properties for dosing in humans, but, derivatives are looking very promising to overcome these hurdles already, we just need to make sure we don’t gain any toxicity (N6FFA is a natural human metabolite). This is dull, pedantic work that needs to be done and tested in more animal models before we plan to trial in humans.

We also present the N6FFA hypothesis in a Youtube video abstract:

 

 

 

 

Next steps in the identification of ROS-related huntingtin protein-protein interactions

Blog post by Dr. Tamara Maiuri

In my last real-time report of the HDSA-funded project to identify of oxidation-related huntingtin protein-protein interactions, I was happy to report the successful purification of huntingtin and its interacting proteins from mouse cells. I was quite optimistic that the experiment would work using cells from an HD patient. This turned out not to be the case. Despite growing large amounts of cells, there was simply not enough starting material. Although we want to answer our questions about HD using human sources of information, it is just not technically possible with patient fibroblasts.

The good news is that I was able to generate two more replicates of the experiment in mouse cells. The total list of proteins identified by mass spectrometry can be found on Zenodo, and further refinement of the data was done by quantifying the intensity of each peptide (bit of protein) to give us a better sense of the most abundant hits. This has also been deposited on Zenodo.

Sifting through the data is taking some time—being a scaffold, huntingtin interacts with several hundred proteins. We are also in the final revision stages of a few manuscripts for which experiments have been prioritized (one manuscript describes how we turned HD patient skin cells into a tool for the HD research community—a pre-print can be read on Bioarchive). I will post a more detailed analysis in the coming weeks, but here are some general conclusions from the most reproducible results:

Stable interactions:

The proteins that interact with huntingtin in cells treated with DNA damaging agents also interact with huntingtin in untreated cells. This could be because

  • The treatment didn’t work, or the untreated cells are under an unintended form of stress
  • Huntingtin transiently “samples” interactions with many proteins in unstressed conditions, which it binds more tightly upon stress. In this case, the cross-linking step may cause us to capture weak interactions
  • Some of the interactions may be non-specific artifacts of the experimental set-up

These possibilities will be tested by following up on interesting hits in our human fibroblast system.

A connection to poly ADP ribose:

Many of the proteins that interact with huntingtin are also found in data sets of “PARylated” and “PAR-binding” proteins (see references below). Poly ADP ribose, or PAR, is a small biomolecule that plays a role in the process of DNA repair (among many other cellular processes). When the DNA repair protein “PARP1” notices some damaged DNA, it starts to attach chains of PAR to nearby proteins. This forms a sort of net to recruit other DNA repair factors. The overlap between our list of huntingtin interacting proteins and PARylated/PAR-binding proteins suggests that huntingtin may also bind PAR, just like many other DNA repair proteins. In fact, I have preliminary results suggesting it does just that. I will post them soon!

 

Data sets of PARylated and PAR-binding proteins:

Gagné J-P, Isabelle M, Lo KS, Bourassa S, Hendzel MJ, Dawson VL, et al. Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. Nucleic Acids Res. 2008;36: 6959–6976.

Jungmichel S, Rosenthal F, Altmeyer M, Lukas J, Hottiger MO, Nielsen ML. Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses. Mol Cell. 2013;52: 272–285.

Zhang Y, Wang J, Ding M, Yu Y. Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome. Nat Methods. 2013;10: 981–984.