Tom Fagan has done a very nice job of calling our attention to these exceptionally important and concordant sets of results supporting Robin Holliday's original proposal for a role for epigenetic modifications in long- term memory (Holliday, 1999). Robin emphasized methylations and demethylations of CpGs in his 1999 paper; less was known at that time about alterations in gene expression associated with chromatin modifications by histone acetylases and deacetylases.

The important phenotypic consequences of haploinsufficiency for the CREB binding protein provides a rationale for an investigation of potential roles of genetic polymorphisms, or better, of haplotype variations, in the modulation of long-term memory in human subjects.

PS: I also want to give special thanks to Tom Fagan for having highlighted the excellent accompanying commentary by Kelsey C. Martin and YE Sun. (Kelsey Martin is my daughter!)

View all comments by George M. Martin

I see that many of the signs of Rubenstein-Taybi syndrome are also reported in Down's syndrome.

The study by Branchi et al. (1) finding that overexpression of DYRK1A results in increased phosphorylation of FKHR, high levels of cyclin B1 and increased phosphorylation of CREB is of great interest.

They report increased brain weight associated with DYRK1A overexpression, yet reduced brain weight is reported in Down's syndrome.

Of further interest is the study by Daitoku et al. (2) finding that CREB-binding protein binds and acetylates FKHR and that Sir2 binds and deacetylates residues acetylated by CREB-binding protein.

Do the CBP mutations reported in RTS allow for FKHR binding?

Ironic that the CREB pathway required for learning and memory is also affected by the longevity gene, Sir2.

Is this one reason for the mental retardation and reduced lifespan reported in Down's syndrome?

References:
(1) Journal of Neuropathology and Experimental Neurology: Vol. 63, No. 5, pp. 429–440. Transgenic...  Read more

I see that many of the signs of Rubenstein-Taybi syndrome are also reported in Down's syndrome.

The study by Branchi et al. (1) finding that overexpression of DYRK1A results in increased phosphorylation of FKHR, high levels of cyclin B1 and increased phosphorylation of CREB is of great interest.

They report increased brain weight associated with DYRK1A overexpression, yet reduced brain weight is reported in Down's syndrome.

Of further interest is the study by Daitoku et al. (2) finding that CREB-binding protein binds and acetylates FKHR and that Sir2 binds and deacetylates residues acetylated by CREB-binding protein.

Do the CBP mutations reported in RTS allow for FKHR binding?

Ironic that the CREB pathway required for learning and memory is also affected by the longevity gene, Sir2.

Is this one reason for the mental retardation and reduced lifespan reported in Down's syndrome?

References:
(1) Journal of Neuropathology and Experimental Neurology: Vol. 63, No. 5, pp. 429–440. Transgenic Mouse In Vivo Library of Human Down Syndrome Critical Abstract

(2) Proc Natl Acad Sci U S A. 2004 Jun 25 [Epub ahead of print] Silent information regulator 2 potentiates Foxo1-mediated transcription through its deacetylase activity. Daitoku H, Hatta M, Matsuzaki H, Aratani S, Ohshima T, Miyagishi M, Nakajima T, Fukamizu A. Abstract

View all comments by Mary Reid

Which of the human sirtuins might target FKHR? Might we suspect SIRT2, as North et al. (1) find that it is a tubulin deacetylase.

Hempen et al. (2) report decreased acetylated alpha-tubulin in neurofibrillary tangle-bearing neurons in AD.

Does the overexpression of DYRK1A reported by Funakoshi et al. (3), which has resulted in chromosome missegregation, suggest that it may be a downstream effect on FKHR/SIRT2 and resultant deacetylated alpha-tubulin?

Might we suspect a SIRT1/FKHR association? Takata and Ishikawa (4) report that SIRT1 associates with HES1 and HEY2.

Does the fact that DYRK1A overexpression resulting in increased phosphorylated CREB also implicate this gene product in the increased presenilin-1 levels found in Down's syndrome?

Mitsuda et al. (5) report that CREB controls expression of presenilin-1.

I see that the Sambamurti group (6) find a CREB binding site on BACE.

References:
(1) North BJ, Marshall BL, Borra MT, Denu JM, Verdin E. The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Mol Cell. 2003...  Read more

Which of the human sirtuins might target FKHR? Might we suspect SIRT2, as North et al. (1) find that it is a tubulin deacetylase.

Hempen et al. (2) report decreased acetylated alpha-tubulin in neurofibrillary tangle-bearing neurons in AD.

Does the overexpression of DYRK1A reported by Funakoshi et al. (3), which has resulted in chromosome missegregation, suggest that it may be a downstream effect on FKHR/SIRT2 and resultant deacetylated alpha-tubulin?

Might we suspect a SIRT1/FKHR association? Takata and Ishikawa (4) report that SIRT1 associates with HES1 and HEY2.

Does the fact that DYRK1A overexpression resulting in increased phosphorylated CREB also implicate this gene product in the increased presenilin-1 levels found in Down's syndrome?

Mitsuda et al. (5) report that CREB controls expression of presenilin-1.

I see that the Sambamurti group (6) find a CREB binding site on BACE.

References:
(1) North BJ, Marshall BL, Borra MT, Denu JM, Verdin E. The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Mol Cell. 2003 Feb;11(2):437-44. Abstract

(2) J Neuropathol Exp Neurol. 1996 Sep;55(9):964-72. Reduction of acetylated alpha-tubulin immunoreactivity in neurofibrillary tangle-bearing neurons in Alzheimer's disease. Hempen B, Brion JP. Abstract

(3) BMC Cell Biol. 2003 Sep 10;4(1):12. Overexpression of the human MNB/DYRK1A gene induces formation of multinucleate cells through overduplication of the centrosome. Funakoshi E, Hori T, Haraguchi T, Hiraoka Y, Kudoh J, Shimizu N, Ito F. Abstract

(4) Biochem Biophys Res Commun. 2003 Jan 31;301(1):250-7. Human Sir2-related protein SIRT1 associates with the bHLH repressors HES1 and HEY2 and is involved in HES1- and HEY2-mediated transcriptional repression. Takata T, Ishikawa F. Abstract

(5) J Biol Chem. 2001 Mar 30;276(13):9688-98. Epub 2000 Dec 14. Activated cAMP-response element-binding protein regulates neuronal expression of presenilin-1. Mitsuda N, Ohkubo N, Tamatani M, Lee YD, Taniguchi M, Namikawa K, Kiyama H, Yamaguchi A, Sato N, Sakata K, Ogihara T, Vitek MP, Tohyama M. Abstract

(6) FASEB J. 2004 Jun;18(9):1034-6. Epub 2004 Apr 01. Gene structure and organization of the human beta-secretase (BACE) promoter. Sambamurti K, Kinsey R, Maloney B, Ge YW, Lahiri DK. Abstract

View all comments by Mary Reid

Homocysteine and AD: More Than Meets the Eye
Hyoung-gon Lee, Mark A. Smith, Barney Dwyer, Aki Nunomura, George Perry, Xiongwei Zhu Increased levels of plasma homocysteine (HC), a key metabolic intermediate in sulfur amino acid metabolism, have been associated with several disorders including Alzheimer disease (AD). While HC is toxic in cell culture models including primary cortical neurons, the mechanism of HC toxicity and the role of HC in disease pathogenesis remain unclear. Hasegawa and colleagues hypothesized that homocysteic acid (HA), an oxidant product of HC, might play an important role in the pathogenesis of AD by regulating amyloid-β (Aβ) production. They demonstrate that HA dramatically decreases the extracellular level of Aβ42 but increases the intracellular level of Aβ42 in primary cortical neurons and APP-overexpressing CHO cells, and they suggest that this is associated with HA toxicity. This finding led them to show that a γ-secretase inhibitor prevents HA toxicity. While the level of HC is increased both in plasma and CSF in...  Read more

Homocysteine and AD: More Than Meets the Eye
Hyoung-gon Lee, Mark A. Smith, Barney Dwyer, Aki Nunomura, George Perry, Xiongwei Zhu Increased levels of plasma homocysteine (HC), a key metabolic intermediate in sulfur amino acid metabolism, have been associated with several disorders including Alzheimer disease (AD). While HC is toxic in cell culture models including primary cortical neurons, the mechanism of HC toxicity and the role of HC in disease pathogenesis remain unclear. Hasegawa and colleagues hypothesized that homocysteic acid (HA), an oxidant product of HC, might play an important role in the pathogenesis of AD by regulating amyloid-β (Aβ) production. They demonstrate that HA dramatically decreases the extracellular level of Aβ42 but increases the intracellular level of Aβ42 in primary cortical neurons and APP-overexpressing CHO cells, and they suggest that this is associated with HA toxicity. This finding led them to show that a γ-secretase inhibitor prevents HA toxicity. While the level of HC is increased both in plasma and CSF in AD, there is no change in HA levels. However, interestingly, increasing HC can effectively enhance HA toxicity manyfold, presumably also via the regulation of Aβ.

These interesting findings shed some new light on how increased levels of HC may contribute to the pathogenesis of AD—increased HC enhances HA toxicity, which results in intraneuronal accumulation of Aβ42 and subsequent neuronal death. However, such a conclusion warrants tempering. Indeed, it is ambiguous in this study whether intracellular Aβ42 actually leads to neuronal death, since there was a threefold increase of intracellular Aβ42 in ten μM HA-treated cells, yet no apparent neuronal death at this concentration. Nevertheless, it raises the question of how HA regulates Aβ42. As suggested by the authors, Aβ upregulation might involve oxidative stress, and this is consistent with in vivo and in vitro studies showing that oxidative stress precedes Aβ accumulation (Nunomura et al., 2001; Lee et al., 2004). Thus, it will be of interest to directly determine whether HA affects Aβ accumulation by oxidative stress and also the sequence of events regarding the elevation of HC and Aβ accumulation in AD patients. Recently we proposed that elevated HC may participate in a vicious cycle involving iron dysregulation, resulting in oxidative stress and other early events seen in AD (Dwyer et al., 2004). The increased vulnerability against HA by the elevated level of HC may also contribute to such a vicious cycle and enhance oxidative damage. This article provides a solid foundation for such studies.

References:
Dwyer BE, Raina AK, Perry G, Smith MA. Homocysteine and Alzheimer's disease: a modifiable risk? Free Radic Biol Med. 2004 Jun 1;36(11):1471-5. Abstract

Lee HG, Casadesus G, Zhu X, Takeda A, Perry G, Smith MA. Challenging the amyloid cascade hypothesis: senile plaques and amyloid-beta as protective adaptations to Alzheimer disease. Ann N Y Acad Sci. 2004 Jun;1019:1-4. Review. Abstract

Nunomura A, Perry G, Aliev G, Hirai K, Takeda A, Balraj EK, Jones PK, Ghanbari H, Wataya T, Shimohama S, Chiba S, Atwood CS, Petersen RB, Smith MA. Oxidative damage is the earliest event in Alzheimer disease. J Neuropathol Exp Neurol. 2001 Aug;60(8):759-67. Abstract

View all comments by Barney Dwyer
View all comments by Hyoung-gon Lee
View all comments by Akihiko Nunomura
View all comments by George Perry
View all comments by Mark A. Smith
View all comments by Xiongwei Zhu

Homocysteine, oxidative stress, and AD: An even more vicious cycle!
Commenting on Hasegawa et al., Dwyer and collaborators note that elevated homocysteine may participate in a vicious cycle involving iron dysregulation, resulting in oxidative stress seen in AD (Dwyer et al., 2004). Their proposed mechanism suggests that localized heme deficiency in AD brain could result in loss of cystathionine β-synthase redox responsiveness and incur increased homocysteine during periods of oxidative stress.

It is also important to note that the other major route of homocysteine metabolism, the methionine synthase reaction, is also exquisitely sensitive to oxidative stress. We have proposed a complementary mechanism whereby such stress impairs methionine synthase activity (McCaddon et al 2002; McCaddon and Kelly, 1992, and see Alzheimer Research Forum "A cobalaminergic hypothesis.")

Taken together, these two mechanisms suggest that it might be important to address oxidative stress as well as B vitamin deficiency in cognitively impaired patients presenting with...  Read more

Homocysteine, oxidative stress, and AD: An even more vicious cycle!
Commenting on Hasegawa et al., Dwyer and collaborators note that elevated homocysteine may participate in a vicious cycle involving iron dysregulation, resulting in oxidative stress seen in AD (Dwyer et al., 2004). Their proposed mechanism suggests that localized heme deficiency in AD brain could result in loss of cystathionine β-synthase redox responsiveness and incur increased homocysteine during periods of oxidative stress.

It is also important to note that the other major route of homocysteine metabolism, the methionine synthase reaction, is also exquisitely sensitive to oxidative stress. We have proposed a complementary mechanism whereby such stress impairs methionine synthase activity (McCaddon et al 2002; McCaddon and Kelly, 1992, and see Alzheimer Research Forum "A cobalaminergic hypothesis.")

Taken together, these two mechanisms suggest that it might be important to address oxidative stress as well as B vitamin deficiency in cognitively impaired patients presenting with hyperhomocysteinaemia. We have observed promising clinical effects using such an approach in several recent cases [McCaddon A, Davies G. Int.J.Ger.Psych. 2005 (in press)]. A randomized controlled clinical trial is now underway to formally evaluate this novel synergistic approach in these patients.

References:
Dwyer BE, Raina AK, Perry G, Smith MA. Homocysteine and Alzheimer's disease: a modifiable risk? Free Radic Biol Med. 2004 Jun 1;36(11):1471-5. Abstract

McCaddon A, Regland B, Hudson P, Davies G. Functional vitamin B(12) deficiency and Alzheimer disease. Neurology. 2002 May 14;58(9):1395-9. Abstract

McCaddon A, Kelly CL. Alzheimer's disease: A "cobalaminergic" hypothesis. Med Hypotheses. 1992 Mar;37(3):161-5. Review. Abstract Reproduced on ARF at: The "Cobalaminergic" hypothesis)

McCaddon A. Davies G. Co-administration of N-acetylcysteine, vitamin B12 and folate in cognitively impaired hyperhomocysteinaemic patients Int J Ger Psych. 2005 (in press).

View all comments by Andrew McCaddon

I look at the results reported bearing in mind that homocysteine is one of the products of S-adenosylmethionine metabolism. It has been recently reported by my group (Scarpa et al., 2003 and Fuso et al., 2005) that both PS1 and BACE are regulated by DNA methylation and that accumulation of homocysteine, obtained by starvation of B12 and folate in the culture medium, increased amyloid production. As far as amyloid release (Fig. 1) and the ratio between intracellular and extracellular concentrations of the two Aβ species, my comment is that HA administration, by changing the methylation status of membrane lipids, among several other events, could decrease the fluidity of the membranes and therefore the secretion. Consequently, amyloid accumulates inside the cells (Fig. 3A and 4).

I think it is important to look carefully at the main metabolism in which homocysteine is involved. The main product in the pathway is S-adenosylmethionine, the donor of all the methylation reactions. The...  Read more

I look at the results reported bearing in mind that homocysteine is one of the products of S-adenosylmethionine metabolism. It has been recently reported by my group (Scarpa et al., 2003 and Fuso et al., 2005) that both PS1 and BACE are regulated by DNA methylation and that accumulation of homocysteine, obtained by starvation of B12 and folate in the culture medium, increased amyloid production. As far as amyloid release (Fig. 1) and the ratio between intracellular and extracellular concentrations of the two Aβ species, my comment is that HA administration, by changing the methylation status of membrane lipids, among several other events, could decrease the fluidity of the membranes and therefore the secretion. Consequently, amyloid accumulates inside the cells (Fig. 3A and 4).

I think it is important to look carefully at the main metabolism in which homocysteine is involved. The main product in the pathway is S-adenosylmethionine, the donor of all the methylation reactions. The accumulation of homocysteine, either pathologic or administered (please note that Frauscher, in the paper cited by the authors, used the thiolactone that produces both HC and HA), reverses the reaction controlled by S-adenosylhomocysteine-hydrolase, blocking the methylation reaction cycle and therefore inducing a generalized hypomethylation.

View all comments by Sigfrido Scarpa

Zou et al. (1) report that γ-secretase is involved in the processing of megalin. In view of the fact that megalin binds cubilin, the receptor for B12-intrinsic factor complex, and mediates uptake of the vitamin B12-transcobalamin complex (2), what are the implications for AD?

References:
1. Zou Z, Chung B, Nguyen T, Mentone S, Thomson B, Biemesderfer D. Linking receptor-mediated endocytosis and cell signaling: evidence for regulated intramembrane proteolysis of megalin in proximal tubule. J Biol Chem. 2004 Aug 13;279(33):34302-10. Epub 2004 Jun 4. Abstract

2. Gliemann J. Receptors of the low density lipoprotein (LDL) receptor family in man. Multiple functions of the large family members via interaction with complex ligands. Biol Chem. 1998 Aug-Sep;379(8-9):951-64. Review. Abstract

View all comments by Mary Reid

Does homocysteic acid also induce expression of HERP ( Homocysteine- and endoplasmic reticulum stress-inducible protein, ubiquitin-like domain-containing, 1)? Sai et al. (1) report that HERP increases the generation of amyloid beta-protein (Abeta) and that Herp interacts with presenilin (PS).

References:
FEBS Lett. 2003 Oct 9;553(1-2):151-6. The ubiquitin-like domain of Herp is involved in Herp degradation, but not necessary for its enhancement of amyloid beta-protein generation. Sai X, Kokame K, Shiraishi H, Kawamura Y, Miyata T, Yanagisawa K, Komano H. Department of Dementia Research, National Institute for Longevity Sciences, Obu, Aichi, Japan. Herp is an endoplasmic reticulum (ER)-stress-inducible membrane protein, which has a ubiquitin-like domain (ULD). However, its biological function is as yet unknown. Previously, we reported that a high expression level of Herp in cells increases the generation of amyloid beta-protein (Abeta) and that Herp interacts with presenilin (PS). Here, we addressed the role of the ULD of Herp in Abeta generation and intracellular Herp stability. We found that the ULD is not essential for the enhancement of Abeta generation by Herp expression and the interaction of Herp with PS, but is involved in the rapid degradation of Herp, most likely via the ubiquitin/proteasome pathway. Thus, the ULD of Herp most likely plays a role in the regulation of the intracellular level of Herp under ER stress. PMID: 14550564 [PubMed - indexed for MEDLINE]

View all comments by Mary Reid

This study’s conclusion that memory is not lost but is somehow "locked in" prompted me to write with my own experience. For the last 10 years of his life, my father lived in a care home near mine and I saw him daily.

Initially he had Parkinson disease, but in the years that followed he suffered from a series of mini-strokes and eventually cancer. During this time he also suffered from senility—whether strictly speaking Alzheimer's or not I can't say—but he was increasingly confused, forgetful, and entirely unable to carry out the most basic self care, so that ultimately he was asleep virtually all the time, waking only to be fed, and speaking very rarely.

By the time he spent his last Christmas day with us at home, he was in a most pathetic state, and had not spoken more than a word or two in many months. At 5 p.m., as we were sitting around him after opening presents, we had a most odd experience. He suddenly "came to life."

It was as though someone had flipped a switch in his brain, and for the next 45 minutes he laughed and chatted and “remembered,” and...  Read more

This study’s conclusion that memory is not lost but is somehow "locked in" prompted me to write with my own experience. For the last 10 years of his life, my father lived in a care home near mine and I saw him daily.

Initially he had Parkinson disease, but in the years that followed he suffered from a series of mini-strokes and eventually cancer. During this time he also suffered from senility—whether strictly speaking Alzheimer's or not I can't say—but he was increasingly confused, forgetful, and entirely unable to carry out the most basic self care, so that ultimately he was asleep virtually all the time, waking only to be fed, and speaking very rarely.

By the time he spent his last Christmas day with us at home, he was in a most pathetic state, and had not spoken more than a word or two in many months. At 5 p.m., as we were sitting around him after opening presents, we had a most odd experience. He suddenly "came to life."

It was as though someone had flipped a switch in his brain, and for the next 45 minutes he laughed and chatted and “remembered,” and we watched in utter amazement at this complete return of his old self. He appeared to have no recollection of his illness and no sense that "normal service had been interrupted." It was obvious that his memory and sense of humor were absolutely intact.

For three quarters of an hour, we watched in delight as he shared anecdotes of past Christmases, teased his grandchildren, and made jokes—and then, as suddenly as the switch had flipped on, it flipped off again, and he never spoke again until his death more than 2 years later.

I realize this is just one anecdotal experience, but it was obvious to me then that his memory had absolutely not been wiped clean, as I had supposed, but that those memories had somehow been rendered inaccessible by his illness.

View all comments by Geraldine Durrant

The Bjornsson et al. study provides further evidence that DNA methylation differences between individuals increase with age. However, the study not only confirms this principle, but shows that genetic factors play a role in inter-individual methylation differences. It highlights the complexities when studying DNA methylation in aging. While it is thought that "environmental" factors such as alcohol, diet, perhaps medications, etc., play a role in modifying DNA methylation patterns in the genome, genetic factors could play a role as well. Recently, we identified in a postmortem brain study 2/50 gene loci that showed significant alterations in Alzheimer's subjects, as compared to controls (Siegmund et al., 2007). Interestingly, the changes in the Alzheimer's cohort, in terms of DNA methylation, appeared to reflect an acceleration of normal aging. Therefore, one could assume that the findings of Bjornsson et al. will be of great interest for aging-related disorders, including Alzheimer disease.

View all comments by Schahram Akbarian

These are indeed highly interesting papers.

To add to the story of epigenetic influences in the aging process, a new and fascinating study was published in PLoS ONE. The group around Axel Schumacher et al. at the Technical University Munich/Germany could show that people with late-onset Alzheimer disease have indeed an increased “epigenetic drift” in genes that may be responsible for some of the observed phenotypes. Additionally, the group found that some genes that participate in amyloid-β processing and methylation homeostasis show a significant interindividual epigenetic variability, which may contribute to disease predisposition. The observed epigenetic pattern would complement and support the aforementioned data, showing that the changes in the Alzheimer brain appeared to reflect an acceleration of normal aging. This could indicate that everybody has a certain likelihood of developing the disease.

References:
Wang SC, Oelze B, Schumacher A. Age-specific epigenetic drift in late-onset Alzheimer's disease. PLoS ONE. 2008;3(7):e2698. Abstract

View all comments by Jutta Bremer