Alzheimer‘s disease (AD) is one of the most significant disorders facing our population. According to the US NIH Institute on Aging Citation[101], there are up to 4.5 million individuals living with AD in the USA alone. Age is the greatest risk factor for AD. As we continue to live longer as a society, the devastating personal, social and economic effects of AD will dramatically increase unless effective treatments or prevention strategies can be developed to slow or halt its progression.
In addition to age, a person‘s genetic makeup is another clear contributor to the risk of developing AD. There are approximately 200 known mutations in three different genes (APP, PSEN1 and PSEN2) that result in many cases of AD with dementia onset before 60 years of age (sometimes termed early onset AD) and are primarily inherited in an autosomal-dominant form of transmission Citation[1–5]. Twin studies have suggested that up to 80% of AD cases with dementia onset after 60 years of age (late-onset AD) are attributable to heritable risk factors. One well studied example of such a risk factor is the e4 variant of the APOE gene, which was first associated with AD risk over 15 years ago Citation[6,7]. This risk factor remains one of the strongest genetic associations for a common complex human disorder. Advances in the ability to scan the human genome at millions of single nucleotide polymorphism (SNP) markers, using a genome-wide association study (GWAS) design Citation[8,9], has greatly advanced the genetic study of AD as well as other disorders with purported common genetic roots. This approach at such depth is a relatively new tool in the search for additional common heritable risk factors. Several GWAS studies have been published for AD yielding multiple novel associations with surprisingly few overlapping loci Citation[10–15].
In a 2006 study led by Andreas Papassotiropoulos, my colleagues and I reported an association between a gene called KIBRA and human episodic memory performance in one of the first published studies using ultra-high density SNP genotyping arrays Citation[16]. In separate studies of two young adult groups and one late-middle-aged group, we found a significant association between absence of the T-allele at KIBRA rs17070145 SNP coupled with lower episodic memory task performance. Additionally, KIBRA transcripts were enriched in brain regions thought to play an important role in episodic memory, including the hippocampus. Finally, using functional MRI (fMRI), we found that the KIBRAT-allele noncarriers had an accentuated increase in hippocampal and parahippocampal gyrus activity during an episodic memory task, suggesting that these regions were ‘working harder‘ to perform the task in those individuals with the variant associated with risk for poor memory. The genetic association was subsequently independently confirmed in three separate studies Citation[17–19] and not supported in another study Citation[20].
In late 2007, a group utilizing patients from Northern Spain reported a putative genetic link between KIBRA and AD age-at-onset in a hypothesis-driven investigation of the exact same SNP our team had linked to memory performance Citation[21]. Their results suggested that the T-allele was associated with increased risk, something the authors suggested was inconsistent with what might be expected. Although their cohort was small, they were 71% powered to detect an association with an odds ratio greater than three. In 2008 we also reported an association between KIBRA and AD in 1026 cases and controls, many of whom were both clinically characterized and neuropathologically verified after death Citation[22]. In contrast to the Spanish findings, we found that T-allele noncarriers had elevated risk for AD, perhaps reflecting differences in geographical location, criteria utilized to classify cases and controls or other factors. In addition to our genetic data, we found significant transcriptional dysregulation of KIBRA and multiple biochemical interacting partners in laser-captured neurons from key brain regions in clinically characterized and neuropathologically verified cases and matched controls. Finally, we found that cognitively normal late-middle-aged KIBRAT-noncarriers had significantly reduced positron emission tomography (fluorodeoxyglucose [FDG]-PET) measurements of the cerebral metabolic rate for glucose in precuneus and posterior cingulate brain regions known to be preferentially affected by AD Citation[23,24]. Although we failed to detect an association between KIBRA and age at onset, Braak stage, Consortium to Establish a Registry for AD (CERAD) severity or the Mini Mental State Examination (MMSE) score in the subset of subjects with this data available. Larger studies and more sensitive and uniform methods may be needed to investigate these relationships with adequate statistical power.
Could it be that the KIBRA effect is entirely due to a delicate alteration in cognitive reserve Citation[25–27]? Although not significant, we did observe a trend for later AD age at onset in carriers of the T-allele. Perhaps it is due to effects on the default pathway of brain activity Citation[28] through the metabolic changes in the precuneus and cingulate cortex? KIBRA has been shown to participate in the endocytic recycling pathway Citation[29] – could it be that KIBRA is altering the cellular re-uptake of β-amyloid and impacting plaque formation Citation[30]? The jury is still out on these questions but I feel that after addressing these remaining issues a clear link between KIBRA and AD will be established.
The combined odds ratio for KIBRA in our study was 1.24 (95% CI: 1.09–1.41; p = 0.0012). Such subtle associations are sometimes not significant enough to be prioritized for follow-up after GWAS. Instead one tends to focus on SNPs that approach or exceed genome-wide significance. Of course this is out of necessity as these investigations now assess upwards of 1 million SNPs simultaneously and follow-up of all the significant associations is typically cost prohibitive, even though one understands that false-negatives abound in this data owing to multiple hypothesis testing. This begs the question, how many significant loci are we ignoring simply owing to their marginal association statistics? The fact is that KIBRA would not have been investigated as an AD susceptibility gene had it not been first identified in the episodic memory study – it just simply is not significant enough from a genome-wide standpoint. However, in a hypothesis-driven investigation, the genetics meet statistical muster and the associated biological evidence is very convincing. Can these subtle yet valid associations yield important biological, diagnostic, or drug development clues for disease? If the answer to this last question is yes, the identification of such associations becomes a clear opportunity and challenge for AD and human genetics in general.
One way to empower the investigation of such subtle associations is to publicly and openly share all GWAS data. A quick look into a new data set can help make the case for further follow-up. The sharing of GWAS data and DNA samples has started in the AD field and a continuation of this effort is needed. Such efforts are exemplified by the National Institute on Aging sponsored AD Genetics Consortium and the National Cell Repository for Alzheimer‘s Disease (NCRAD) biospecimen bank Citation[102], as well as several other emerging initiatives. Another take home message from the KIBRA work is that there is clearly still room for hypothesis-driven candidate gene investigations in AD. However, one has to be cautious not to stop at the genetic association level alone, but to go the next step and demonstrate the importance of a specific gene in the context of disease. Demonstration of biological and/ordisease significance will be required not only for the subtle associations, but also for the strongest. Lastly, single SNP association analysis of GWAS data should be deprioritized for more intensive methods of multi-SNP ‘set association‘ or other compound genetic analyses that evaluate the relationships among multiple major and minor susceptibility genes Citation[31,32]. Most researchers consider late-onset AD to be a common and complex disease – one that is governed by multiple environmental and genetic risks. Although it is computationally intensive and the methods for analysis are still in their infancy, it will likely be an important direction for the field to move, namely, in treating AD as a disorder that will require an aggregate genetic score for the most accurate presymptomatic assessment of risk.
Even as we grapple with this question of how to handle the significant and important associations lost in the ‘noise‘ of GWAS data, the field of human genomics is undergoing yet another rapid and exciting change ushering in the era of affordable whole-genome resequencing with new attempts to simultaneously assess the association of billions of data points with disease. These ‘next generation‘ sequencing technologies promise to revolutionarize the field of human genetics as they put us very close to the goal of sequencing an entire person‘s three billion base pair genome for US$1000 Citation[33–35]. One has to wonder if we are truly ready to handle the statistical analysis of such large data sets in such a fashion where we won‘t throw out the proverbial baby with the bath water.
Acknowledgements
The field of Alzheimer‘s disease genetics would not be possible without the selfless patients, their families and caregivers who donate their time and biological specimens in the hope of eradicating Alzheimer‘s disease.
Financial & competing interests disclosure
Matthew J Huentelman is indebted to funding from the NIH-NINDS R01-NS059873, NIH-NIA P30-AG19610 and the State of Arizona. The author has no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
No writing assistance was utilized in the production of this manuscript.
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Websites
- Alzheimer‘s disease fact sheet. US NIH National Institute on Aging www.nia.nih.gov/Alzheimers/Publications/adfact.htm
- The national cell repository for Alzheimer‘s disease (NCRAD) http://ncrad.iu.edu