Apr 122011

ResearchBlogging.orgThe classic neuropathological hallmarks of Alzheimer’s disease are the appearance of amyloid plaques composed primarily of amyloid beta (Aβ) peptides, and neurofibrillary tangles composed mainly of hyperphosphorylated tau protein. For many years, research into treatments for Alzheimer’s disease proceeded on the hypothesis that the plaques were toxic to the surrounding neurons. More recently, however, evidence has shown that soluble Aβ oligomers may be the primary toxic species. A recent paper in Proceedings of the National Academy of Sciences supports this hypothesis by showing that Aβ oligomers isolated from the brains of Alzheimer’s sufferers cause neuronal degradation and improper phosphorylation of tau (1). This paper is open access, so open it upand read along.

Jin et al. isolated dimers of Aβ from homogenates of human brains from Alzheimer’s patients. Dimers were separated from monomers and higher-order oligomers by size-exclusion chromatography in the presence of a strong detergent that typically breaks up folded proteins and repeating aggregates. This separates the dimers and higher oligomers from each other, and also dissociated weakly-interacting peptides (due to the effects of the detergent). As you can see from Fig. 1A, this produced fractions that contained either detergent-stable Aβ dimers (AD-TBS) or normal cortical proteins (cont-TBS) in identical solution conditions. They also created synthetic dimers by mutating Aβ to contain a cysteine that could form a covalent linkage between peptides (Aβ40S26C). They then used these various materials to treat primary cultures of neurons (that is, neurons that were obtained by directly harvesting them from an animal), with the dimers reaching a final concentration 0.5 nM in the growth medium.

Fig 1B establishes that, among the materials studied here, Aβ dimers are uniquely responsible for the appearance of tau “beads” along the neurites of the cultured cells after 3 days (the widespread dots in the final column of images). This effect is quantified in 1C, which shows that the dimer-containing fractions produced a dramatic increase in this clumping. According to the authors, these easily-visible clumps are only one symptom of widespread problems with the cells’ cytoskeletons. This sort of cytoskeletal trouble is expected because tau’s function is to stabilize and assist in the formation of microtubules from tubulin. The upshot of this figure is that continuous exposure to Aβ dimers (Fig 1D establishes that the dimers persist through the treatment period) appears to cause some sort of trouble with tau, which may reflect the incipient formation of the famous tangles.

The natural follow-up question is whether tau is necessary for this cytoskeletal derangement. The fact that the cultured neurons must mature, with a correlated increase in tau expression, for Aβ dimers to have an effect suggests that it must be. To check this, the authors used RNA inhibition to knock down tau levels. Fig 2A demonstrates that tau, but not tubulin, expression was altered using the tau-specific RNAi (but not the scrambled cont-RNAi). The cytoskeletal damage caused by both the natural dimer and the Aβ40S26C synthetic dimer were suppressed by tau-RNAi (Fig. 2B). At least at this timescale, it therefore appears that normal tau expression levels are necessary for this toxic effect of Aβ dimers. However, as tau in neurofibrillary tangles never breaks down, it seems like a longer exposure to Aβ under these conditions should produce similar toxic effects eventually.

The complementary experiment, is shown in Fig. 3, using a hybrid construct where human tau was fused to a fluorescent protein. As you can see from these images, under control conditions (columns labeled EGFP), cells treated with Aβ monomers and dimers have only subtle differences after two days, and beading is only evident after three days of treatment. When tau is overexpressed (columns labeled tau-EYFP), the cytoskeletal issues are obvious a day earlier. The tau-EYFP appears to be distributed in the same places as normal tau (fourth row), so the EYFP tag probably isn’t responsible for this effect, and the normal behavior of monomer-treated cells is reassuring. However, the EYFP tag may make tau more susceptible to some kind of dysregulation. Because this experiment both increases the total amount of tau and introduces the human protein, the reason for the enhanced susceptibility is difficult to determine. A control experiment in which rat tau-EYFP was expressed in the same construct would have been very helpful in clarifying this point.

As I mentioned above the formation of the tangles is associated with tau becoming highly phosphorylated. Jin et al. therefore made an effort to confirm that this was happening in their cultured cells, using antibodies that would recognize some specific sites in the tau protein that receive phosphate tags. Fig. 4 summarizes the results, indicating that human tau expressed in rat neurons becomes highly phosphorylated at serines 202, 205, and 262. For some reason, the endogenous rat tau did not become significantly phosphorylated at S262; this may have something to do with the apparently enhanced toxicity of Aβ dimers in the presence of human tau.

The paper’s final figure tests whether antibodies directed against specific sites in Aβ can prevent the observed cytoskeletal degradation. They found that two antibodies that bound to the N-terminus of Aβ significantly suppressed the effect of the dimers over the three-day timespan (fourth and fifth columns of A). However, an antibody directed towards the C-terminus of Aβ42 did not have much effect. Fig. 5C suggests that this is because this antibody simply didn’t bind to much of the Aβ in solution, either because most of the isoforms are shorter or because the C-terminus is protected in some way.

These results clearly link cytoskeletal disruptions caused by tau to the presence of soluble Aβ dimers, linking the two well-known pathological hallmarks of Alzheimer’s disease. That soluble oligomers, rather than fibrils, were responsible for the effect does not necessarily prove that the plaques aren’t important, for two reasons. The first is that, while these results clearly demonstrate dysregulation and aggregation of tau, true neurofibrillary tangles did not appear, and until we can assemble a full chain of events leading from beads to tangles the case, though strong, is still unproven. Secondly, as I’ve discussed previously, research has shown that the plaques can release soluble oligomers into the surrounding neural tissue and will therefore serve as reservoirs of toxic protein even if the fibrils themselves are completely inert.

That Aβ dimers can derange tau regulation in cultured neurons is not a new finding; similar results were reported last year using synthetic dimers (2). Zempel et al.‘s experiments used Aβ concentrations up to 5 μM, but Jin et al. show that naturally-obtained dimers have toxic effects at much, much lower concentrations. As the Zempel et al. paper suggests (consistent with much previous work), dysregulation of calcium levels caused by Aβ oligomers may be how they cause these effects. It is not presently clear why natural oligomers should be four orders of magnitude more potent than the various kinds of synthetic dimers at causing the effect; an understanding of this difference may be crucial in developing a suite of effective treatments for the disease.

1) Jin, M., Shepardson, N., Yang, T., Chen, G., Walsh, D., & Selkoe, D. (2011). Soluble amyloid β-protein dimers isolated from Alzheimer cortex directly induce Tau hyperphosphorylation and neuritic degeneration. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1017033108 OPEN ACCESS

2) Zempel, H., Thies, E., Mandelkow, E., & Mandelkow, E. (2010). Aβ Oligomers Cause Localized Ca2+ Elevation, Missorting of Endogenous Tau into Dendrites, Tau Phosphorylation, and Destruction of Microtubules and Spines. Journal of Neuroscience, 30 (36), 11938-11950 DOI: 10.1523/JNEUROSCI.2357-10.2010

Apr 142010
ResearchBlogging.orgAlthough we are most familiar with the circadian rhythm from its effects on our physiological state, the roots of the phenomenon lie in the molecular biology of individual cells. The circadian rhythm is the result of a transcriptional control system that regulates the levels of many different proteins in the cell with the passing of time. Not all of the proteins subject to this control have yet been catalogued, and as a result some surprising effects are still being discovered. A recent article in Proceedings of the National Academy of Sciences from the Sancar lab at UNC suggests that circadian control of a DNA repair factor may be a way to enhance the effectiveness of a chemotherapeutic agent. The article is open access, so I encourage you to open it up and read along.

Previously, the Sancar group has shown that the circadian rhythm affects DNA repair in brain cells. In that case, DNA had been damaged by UV irradiation, a lesion that had to be replaced by the excision repair mechanism. Because one of the critical factors for this kind of repair, the Xeroderma Pigmentosum A protein (XPA), undergoes a circadian oscillation, the efficiency of repair depends on the time of day at which the damage occurred. Kang et al. hypothesized that this circadian dependence could also be true for other forms of DNA damage that undergo excision repair.

This led them to cisplatin, a drug used as primary chemotherapy or part of a combinatorial regimen for several kinds of cancer. Cisplatin creates covalent bonds crosslinking DNA bases in an intra-strand or inter-strand manner. These covalent linkages make replication (and therefore mitosis) impossible, and elicit a DNA repair response. If the cell cannot clear the crosslink, it will either die by apoptosis, or if the apoptotic response is suppressed, fail to produce viable daughter cells. Either way, the growth of the tumor is suppressed. The excision-repair pathway is the only mechanism of clearing this kind of DNA damage, so Kang et al. thought that there might be a robust circadian dependence. In order to test this idea, they carried out experiments using extracts from mouse liver and testis.

Figure 1 shows the results of their experiment using liver extract. Panel C summarizes the key results (data shown in panels A and B) that XPA mRNA, XPA protein, and excision repair efficiency are correlated with the dark/light cycle the mice are experiencing, with the highest levels of protein and repair occurring in the late afternoon, and the lowest levels in the very early morning (around 5 AM). Panel E shows a comparison of excision repair between normal mice and ones that have been genetically modified to lack cryptochrome, a critical circadian clock protein. In these CryDKO mice the time of day has no effect on the efficiency of repair, and as panel F shows, they also do not have the daily fluctuation in XPA mRNA and protein levels. These results suggest that circadian control of XPA expression levels dictates repair efficiency in liver tissues — as panel D shows, addition of exogenous XPA protein can recover the excision repair activity. However, there was no detectable circadian dependence for excision repair activity in testis, as Figure 2 shows using similar experiments.

Circadian control of XPA activity is possible because the protein doesn’t last very long in the cell. Figure 3 shows experiments using two inhibitors: cycloheximide (CHX), which prevents protein synthesis, and MG132, which prevents protein degradation by the proteasome. The gel in panel A shows that in two different types of cells, CHX treatment caused XPA protein to disappear over a period of three hours, in contrast to the control protein actin, which was unaffected. Addition of MG132 caused XPA to accumulate with time, although actin levels were again constant. The fairly rapid degradation of XPA protein means that the overall quantity of that protein in a cell will be highly dependent on the concentration of its mRNA transcript. That is, you can only have high XPA levels if there’s a lot of mRNA so ribosomes can continue to produce it. Circadian control of transcription is therefore able to regulate protein concentration. The authors hypothesize that this tight circadian control may have developed to prevent deleterious effects of non-specific DNA repair activity during times when there is no chance of UV insult, although there is no specific evidence to support this conjecture presently.

The MG132 experiment indicates that XPA is degraded by ubiquitin ligation and subsequent destruction in the proteasome. Figures 4 and 5 show a variety of evidence indicating that this process is mediated by the ubiquitin ligase HERC2. The experiments in figure 4 establish that HERC2 binds to XPA (panels A and B) and colocalizes with it in the cell (panels C and D). The gels in Figure 5 show that when HERC2 levels in the cell are knocked down by RNA inhibition using siRNA specific for that protein, CHX treatment does not cause XPA to degrade. These facts indicate that HERC2 is the ubiquitin ligase for XPA. The direct effect of HERC2 activity on the repair of cisplatin DNA damage is shown by figure 6. Here, cells were treated with cisplatin and HERC2 siRNA. The left side of panel A shows the clearance of cisplatin adducts from A549 cells over time (the right side shows the total DNA). As you can see, addition of HERC2 siRNA allows for more rapid clearance of the adduct, with a particularly dramatic effect at low dosage.

Unfortunately, due to its extreme toxicity, treating cancer cells with CHX is not a viable strategy for chemotherapy. However, knowing that the level of XPA protein in some target cells varies in a predictable way with the time of day can help doctors optimize treatments for maximum effectiveness. In particular, for cancers originating in tissues that have a strong circadian rhythm and intact XPA, early-morning treatment with cisplatin may be more effective than treatment at other times of the day. More experiments are needed before this can be formally recommended — in particular, whole-animal studies and human trials will be necessary to definitively establish the effect. If these results hold up in whole organisms, however, the circadian effect on DNA repair may become a valuable tool for optimizing some chemotherapy regimens.

Kang, T., Lindsey-Boltz, L., Reardon, J., & Sancar, A. (2010). “Circadian control of XPA and excision repair of cisplatin-DNA damage by cryptochrome and HERC2 ubiquitin ligase”. Proceedings of the National Academy of Sciences, 107 (11), 4890-4895 DOI: 10.1073/pnas.0915085107

Full Disclosure: I have previously collaborated with Aziz and his group on a research project on eukaryotic cryptochromes.

Jan 132009
ResearchBlogging.orgAlthough we still do not know the full breadth of our flavor-sensing capabilities, human beings are known to possess receptors for at least five basic tastes. Probably you have known about the sweet, sour, salty, and bitter flavors since you were in grade school, but the fifth, umami, was less widely accepted in the West until recently. Umami is a savory flavor element that is found in many foods, including tomatoes, parmesan cheese, truffles, and many kinds of meat and seafood. The umami taste primarily detects the amino acid glutamate (hence the popularity of the food additive monosodium glutamate, or MSG), but the effect is also intensified by the presence of the nucleotide inosine monophosphate (IMP). In a recent (open access) paper in PNAS, researchers from two corporations examined the umami taste receptor to understand how this happens.

The umami flavor is detected by a pair of G-protein coupled receptors (GPCRs) that have an external venus flytrap (VFT) domain in addition to their classic 7-helix trans-membrane domain (TMD). This complex is closely related to the sensor for the sweet flavor: in fact one of the receptors (called T1R3) is the same in both sensors. It is the second receptor (T1R1 for umami, T1R2 for sweet) that determines what taste is recognized. What we don’t know for sure is whether it is the TMD or the VFT of these receptors that identifies the flavor component.

In order to answer this question, the researchers performed an experiment known as a “domain swap”. Using recombinant DNA technology they assembled two chimeric proteins, one with the VFT of umami and the TMD of sweet, and one with the VFT of sweet and the TMD of umami. They then inserted these proteins into cultured cells that would fluoresce when the receptors were activated. The authors suspected that the VFT is primarily responsible for binding the ligand. As you can see from figures 1 & 2 (this is an open access paper, so go ahead and take a look), the experiment bears this out. The chimera with the VFT of sweet caused a fluorescent response in the presence of compounds such as sucrose and aspartame, while the umami-VFT chimera reacted to glutamate and aspartate. You can also see in figure 2C that the presence of IMP dramatically enhanced the activity of glutamate in this chimera. This indicates that the VFT is also responsible for IMP synergy in the umami receptor.

The hurdle in going further than this is that no structure of the umami VFT is available, which makes it difficult to figure out exactly how everything fits together. However, T1R1 has a close evolutionary relationship to the metabotropic glutamate receptors (mGluR), and a crystal structure of that VFT is available. Using conserved and homologous residues as a guide, the authors made a model of the T1R1 fold from the mGluR data. Based on this model they predicted certain amino acids that would be essential for glutamate binding in T1R1 and then mutated them in order to measure the effect. Residues that were predicted by the model to interact with the zwitterionic amino acid backbone proved to be essential for ligand recognition. Interestingly, the amino acids that contact the side-chain carboxylic acid of glutamate in mGluR are not conserved in T1R1, and mutations at the matching sites do not alter glutamate binding. However, these mutations eliminate the effect of IMP.

In order to understand this behavior, the authors modeled the binding cleft in the closed state, with IMP and glutamate in place. Glutamate binds at the bottom of the cleft, with its side chain pointed outwards. This conformation puts several positively-charged residues from the two lobes of the VFT close together higher up in the cleft. The authors propose, in keeping with previous models of VFT behavior, that the binding of the glutamate lowers the energy barrier between the open and closed states of the domain, but that glutamate alone is not sufficient to hold the domain closed. Their model places IMP higher up in the cleft, where its negatively-charged phosphate interacts with the positive residues. Thus, IMP stabilizes the closed conformation of the VFT domain.

Some more work here would be welcome, particularly in the form of experimental crystal structures of the T1R1 VFT that can confirm the homology model. The VFT is rather large, but using a perdeuterated sample in a high-field magnet it might be possible to confirm the population-shift mechanism using NMR experiments. Lower-resolution techniques such as FRET may also be able to catch this stabilization behavior. If the model proves to be accurate, it would serve as an interesting example of positive allostery from a population shift.

Although these experiments only concerned the umami taste receptor, this allosteric mechanism may be a more general feature of certain GPCRs. The authors indicate that they have unpublished data showing similar behavior in the sweet receptor, and it may be possible to design an allosteric stabilizer for any GPCR with a VFT domain. Because the related mGluR receptors are involved in many neurological and psychological diseases, successful design of such activators may have some therapeutic value.

F. Zhang, B. Klebansky, R. M. Fine, H. Xu, A. Pronin, H. Liu, C. Tachdjian, X. Li (2008). Molecular mechanism for the umami taste synergism Proceedings of the National Academy of Sciences, 105 (52), 20930-20934 DOI: 10.1073/pnas.0810174106 OPEN ACCESS

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