In the last two years, the Tomm40 gene has caught the interest of Alzheimer’s researchers as a potential way to identify people at high risk of developing sporadic AD at relatively young ages. In the genome, Tomm40 (aka translocase of outer mitochondrial membrane 40 homologue) sits close to ApoE, the main genetic risk factor for late-onset AD, and, therefore, Tomm40 variants are co-inherited with particular ApoE alleles. Researchers led by Allen Roses at Duke University, Durham, North Carolina, first reported that, for people who carry the ApoE3 allele, genetic variants in Tomm40 help predict the age at which the disease will strike. Now, however, a large, case-control study has cast doubt on the strength of the association between Tomm40 variants and AD. Researchers led by Alison Goate at the Washington University, St. Louis, Missouri, report in the August Archives of Neurology that they saw no effect of Tomm40 polymorphisms on age of disease onset. In addition, they found only a small association between particular Tomm40 variants and AD risk, and this link pointed in the opposite direction to published data from Roses and colleagues.

It is not yet clear what the findings mean for research in this area. Roses notes methodological differences between his work and Goate’s that he said may explain the discrepancies. The issue will likely not be settled until data come in from even larger studies. For example, the Alzheimer's Disease Genetics Consortium is currently running a Tomm40 study with several thousand participants, said co-director of data analysis Lindsay Farrer at Boston University, Massachusetts. Meanwhile, Roses’ company, Zinfandel Pharmaceuticals, Durham, North Carolina, has a collaboration in the works with Takeda Pharmaceutical Company Limited, Osaka, Japan, that will seek to validate Tomm40’s status as a biomarker for individual AD risk, as well as test the ability of Takeda’s diabetes drug pioglitazone to delay AD progression (see Takeda press release). The trial is currently seeking FDA approval, Roses said, and will likely start in late 2012 with around 4,000 participants.

In 2009, Roses and colleagues first stirred up the Tomm40 buzz with their finding that the length of a variable poly-T repeat in an intron of the Tomm40 gene helped predict the age at which certain people will develop AD symptoms (see ARF related news story and Roses et al., 2009). The researchers repeated the finding in a small prospective cohort (see ARF related news story), showing that, in people who carry the ApoE3 allele, those with at least one short poly-T repeat develop AD about seven years later than those with two copies of long poly-T repeats. In other words, the short repeat seems to be protective, while longer repeats confer more risk.

Efforts to validate the finding have been mixed so far. Some research has supported the link; for example, scientists at the University of Wisconsin, Madison, found an association between Tomm40 variants and gray matter volume and cognition in middle-aged ApoE3/3 carriers that is consistent with Roses’ results (see Johnson et al., 2011). Likewise, researchers at New York University also turned up data suggesting that the short poly-T repeat is protective against AD (see Bruno et al., 2011). However, scientists at Carnegie Mellon University could not replicate Tomm40’s effect on onset age in a cohort of about 900 people (see Chu et al., 2011), while a study from the University of Navarra, Pamplona, Spain, showed inconsistent results (see Cervantes et al., 2011). The AlzGene database lists Tomm40 polymorphisms linked to AD.

To try to clarify the picture, Goate and colleagues undertook a large case-control study. First author Carlos Cruchaga combined data from two cohorts, for a total of around 1,600 AD patients and 1,200 controls. Roughly half the participants came from the Knight Alzheimer's Disease Research Center at WashU, the other half from the National Institute on Aging LOAD Family Study. Almost half of the participants had the crucial ApoE3/3 genotype. The authors defined onset as the age when clinical symptoms first appeared, as recorded in the clinical assessment, Cruchaga told ARF, but noted it can sometimes be difficult to be sure of the exact age of onset.

When they analyzed the data, Cruchaga and colleagues found a small but significant association suggesting that very long poly-T repeats confer a lower risk of AD in an ApoE3/3 background. This contradicts previously published results suggesting long repeats are high risk (but see below for Roses’ comments on unpublished data). Cruchaga and colleagues found no other significant associations, including no effect of Tomm40 variants on the AD age of onset. Separately, the authors examined about 120 postmortem brains from the WashU Neuropathology Core and found no links between Tomm40 variants and the expression of either ApoE or Tomm40 proteins in the brain. They also looked at cerebrospinal fluid biomarker levels in samples from WashU and from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), and again found no correlations with Tomm40 polymorphisms. Collectively, the data suggest that Tomm40 may be involved in disease pathways, but the mechanism is unlikely to involve expression levels or β amyloid or tau pathways, the authors note.

“It is still possible that this variant affects risk of the disease, but the effect is going to be very small,” Cruchaga suggested. “We do not think [the Tomm40 variant] is going to be useful to separate individuals with ApoE3 genotypes, based on our results.”

Farrer said the study by Cruchaga and colleagues was well designed and sufficiently powered to detect effects of the size seen in previous Tomm40 papers. Given the larger sample size in the new paper, Farrer suggested, “Unless there is some ascertainment bias in one of the studies, [the data] would have to favor the results of this study.” Farrer noted that the mitochondrial Tomm40 protein may still be an attractive candidate for scientists studying disease pathways, since several cellular investigations show a role for mitochondrial dysfunction in AD. Nonetheless, based solely on the results of this study and prior published studies, Farrer said, “To me it appears, at least in terms of the genetic variance of the disease, that [Tomm40] does not account for the genetic risk.”

Roses takes a different view. “I believe there are valid reasons why there are differences between their results and ours,” he wrote to ARF (see full comment below). One key factor is how the age of onset is determined. When onset ages are taken from a retrospective case-control study such as this one, inconsistencies in how ages are reported may lead to inaccurate data, Roses said. The best way to get accurate onset ages, he suggested, is to prospectively follow a cohort of cognitively normal people using neuropsychiatric tests to see when the first Alzheimer’s-like cognitive problems develop. He cited the work of Richard Caselli at the Mayo Clinic in Scottsdale, Arizona, as an example of this approach. Caselli presented preliminary data at the 2010 International Conference on Alzheimer’s Disease that supported Roses’ findings (see ARF related news story). In an update at the 2011 AAIC meeting, Caselli discussed more extensive results from a cohort of about 900 people that again replicate the association between Tomm40 variants and age of disease onset, Roses said. Cruchaga agrees that a case-control study does not provide as accurate an age of onset as a prospective study, but he notes that the decrease in accuracy is corrected for by the large sample size in his study. His sample had enough statistical power to detect an eight-year difference in disease onset, even if the ages of onset were misdiagnosed by as much as two years, Cruchaga told ARF.

In regard to the link between very long poly-T repeats and late ages of onset seen by Cruchaga and colleagues, Roses noted that his group has seen the same effect, which they described at the 2011 Alzheimer’s Association International Conference, held 16-21 July. The very long/very long genotype has a biphasic presentation, Roses said. Most people who develop late-onset AD before the age of 60 carry two copies of the very long poly-T repeats, indicating high risk associated with the genotype. However, these people make up a minority of those with the very long/very long genotype. The majority of people with this genotype instead have a late disease onset, typically over age 80. It is not yet clear why this is, Roses said, and he is currently investigating the phenomenon. He suggested there may be another genetic factor that discriminates between these groups. Roses noted that the planned Takeda-Zinfandel trial will be restricted to people between the ages of 62 and 83. Since people with the high-risk very long genotype typically develop symptoms before age 62 and will therefore not be included in the study, the very long genotype will be treated as protective in the trial design, Roses said.

Meanwhile, other scientists propose different interpretations for the Tomm40 results—for example, that variants in the ApoE promoter region, which affect ApoE expression, are responsible for the observed association. “The Tomm40 observations are really a reworking of the observation, mainly by Chartier-Harlin and colleagues, that the ApoE haplotype influenced disease risk,” wrote John Hardy at University College London, U.K., in an e-mail to ARF (see also ARF related news story and Lambert et al., 2002). However, Cruchaga noted that they did some fine mapping of the ApoE region and did not see any effect from common genetic variants on risk or age of onset, making this idea unlikely to explain their findings.—Madolyn Bowman Rogers


  1. It is positive that Cruchaga et al. support the association between the poly-T repeat (“523”) and risk of late-onset Alzheimer’s disease (LOAD) that we first reported in 2009. Additionally, this group completed a phylogenetic analysis of the ApoE-Tomm40 region that effectively confirmed the evolutionary-relatedness of the ApoE-523 haplotypes and allele frequencies in Caucasians, again reported by us in 2009. The two findings that differ from our original report are 1) longer alleles of 523 are associated with later onset and a protective effect and 2) lack of association between the 523 polymorphism and age of LOAD onset. Both are explainable by data not defined in the manuscript.

    1. We have reported (Hayden, K: AAIC meeting 2011) that there is a biphasic response associated with the 523-very long allele, and indeed have observed, for several clinical series, that very long (VL)/VL carriers can have a very late onset (>80 years of age). It is also observed that the very young onset subjects with late-onset Alzheimer's disease (2. Cruchaga reports that they did not find a relationship between “523” and age of onset. This stands in opposition to the robust results that we and others (Caselli) have reported from longitudinal studies of LOAD documenting earliest age of cognitive impairment. It is a shame that a longitudinal series of subjects defined by earliest neuropsychiatric data were not isolated from the dataset and scored for age of onset of cognitive impairment—especially since this center has such a long longitudinal experience. The authors attempted to re-create an analysis similar to a prospective analysis by including controls in the survival analysis (panel B of figure). However, there is a major difference between running a longitudinal study over time where you track events, record onset, and censor observations where events have not occurred, and retrospectively constructing a sample from cases and controls and placing them into a survival analysis. This may explain some of the discrepancy between the results, at least with respect to the survival analysis. However, the major difference is likely due to determination of the age of onset, especially in the ADNI cases (see below). Details are not provided in the paper as to how the age of onset was ascertained (self-reported, reported by physician as part of medical record, or reported by caregiver?), and age of onset of LOAD is recognized to be difficult to determine accurately.

    3. When we analyzed the ADNI data made available to us, we came to a similar conclusion about the relationship between “523” and age of onset—effectively, we also did not find a statistically significant relationship between these variables. However, we also did not find a statistically significant difference in age of onset between ApoE3/3 and ApoE3/4 individuals in this dataset either, which stands in contrast to over 18 years of experience with ApoE (after the first report by Roses and Saunders) and LOAD. Looking over how these cases were ascertained, and by what criteria age of onset were scored, we felt that we could not compare or report the ADNI data. Our collaborators confirmed the non-uniformity of the age of onset (of what, it is not clear...cognitive impairment, diagnosis, etc.?) in this series collected from more than 50 centers for a totally different purpose.

    4. The most accurate series for determining the age of onset of cognitive impairment of the Alzheimer's type is by prospective, serial testing of cognitively normal individuals. In prospective series followed less than eight to 10 years, like that reported by Caselli et al., it is unclear what proportion of cognitively impaired patients will go on to defined AD (as collected by Cruchaga et al.). The rate of progression to AD and the proportion affected over time is currently being monitored in several large prospective collections. Retrospective cohort series are also being investigated, but we judge these analyses to be less robust, as accurate neuropsychiatric data at a given age is often not the first characteristic scored in these series.

    I suspect these same observations will apply to other AD case-control series that have variable ascertainment and are retrospective. To be clear, we have never claimed that the 523 data, or the ApoE4 data, should be used for the diagnosis of AD. We have published these data to support the use of the data for pharmacogenetic enrichment of a high-risk population selected from a geographically defined area who are neuropsychiatric tested at entry and found to be normal by currently accepted standards. This is not an "AD study," but a study of prognostic prediction that will be qualified by the clinical trial population. I believe there are valid reasons why there are differences between the results of Cruchaga et al. and ours. Since the delay of the onset of cognitive impairment study that will be done, with regulatory oversight already in progress, claims of non-confirmation will be viewed with the same degree of interest as that of the lack of confirmation of ApoE in the first years after we published almost 20 years ago. It is an interesting note that several of the overt ApoE skeptics of 1993-1995 were also the same negative voices heard at ICAD 2011. As Yogi Berra, legendary catcher, and later manager of the New York Yankees, commented: "It's like déjà vu all over again!"

    View all comments by Allen Roses
  2. Allen Roses referred to my work, so I'd like to clarify that in a longitudinal study of more than 600 cognitively normal individuals, we found a difference between the VL/VL and S/S variants among ApoE3/3 individuals prior to age 60 (presented at the Alzheimer's Association International Conference last month; paper under review). The VL/VL group showed little evidence of a test-retest effect (on the long-term memory measure/trial 7 of the auditory verbal learning test) in our longitudinal study, and that is not normal. On the other hand, we did not find any evidence for accelerated decline after age 60. The results are therefore complex, and I am all in favor of additional clinical data with age of onset defined as clearly as possible. If there are cohorts of younger individuals that might be in a position to replicate (or refute) our findings, that too would be of obvious importance and (together with the new perspective of preclinical stage AD) underscores the need for inclusion of younger individuals in AD research. For example, might Tomm40 contribute to a cognitive phenotype that fosters earlier clinical recognition even in the absence of actual Tomm40-mediated accelerated decline? This is an example of the kind of new model we may need to consider, though certainly not the only possibility.

    View all comments by Richard Caselli

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News Citations

  1. Las Vegas: AD, Risk, ApoE—Tomm40 No Tomfoolery
  2. Honolulu: Tomm40 Reported to Track With Brain Atrophy, Cognition

Paper Citations

  1. . A TOMM40 variable-length polymorphism predicts the age of late-onset Alzheimer's disease. Pharmacogenomics J. 2010 Oct;10(5):375-84. Epub 2009 Dec 22 PubMed.
  2. . The effect of TOMM40 poly-T length on gray matter volume and cognition in middle-aged persons with APOE ε3/ε3 genotype. Alzheimers Dement. 2011 Jul;7(4):456-65. PubMed.
  3. . Cerebrospinal fluid cortisol concentrations in healthy elderly are affected by both APOE and TOMM40 variants. Psychoneuroendocrinology. 2011 Jul 30; PubMed.
  4. . TOMM40 poly-T repeat lengths, age of onset and psychosis risk in Alzheimer disease. Neurobiol Aging. 2011 Dec;32(12):2328.e1-9. PubMed.
  5. . Genetic variation in APOE cluster region and Alzheimer's disease risk. Neurobiol Aging. 2011 Nov;32(11):2107.e7-17. PubMed.
  6. . Contribution of APOE promoter polymorphisms to Alzheimer's disease risk. Neurology. 2002 Jul 9;59(1):59-66. PubMed.

External Citations

  1. Alzheimer's Disease Genetics Consortium
  2. Takeda press release
  3. Tomm40
  4. Alzheimer’s Disease Neuroimaging Initiative

Further Reading

Primary Papers

  1. . Association and expression analyses with single-nucleotide polymorphisms in TOMM40 in Alzheimer disease. Arch Neurol. 2011 Aug;68(8):1013-9. PubMed.