Racing Toward New Alzheimer’s Mutations with Runs of Homozygosity

While scientists lay the lion’s share of the blame for late-onset Alzheimer’s disease on genetics, they have yet to identify many of the genes that must account for the disease. In the August 26 JAMA Neurology online, researchers from the University of Toronto, Canada, and Columbia University, New York, describe a way to seek out new, recessive mutations. They focused on a population they knew was likely to be a rich source. Due to their high degree of relatedness, many Caribbean Hispanics possess long runs of homozygosity (ROHs), that is, regions where both maternal and paternal copies of a given chromosome are identical. By finding chromosomal spots where people with AD tend to have these ROHs, the researchers were able to home in on places where Alzheimer’s genes are likely to reside. This approach of focusing on people in whom the probability of AD genes is high can help scientists more easily fish out mutations, said senior author Ekaterina Rogaeva of the University of Toronto. Her work led to two potential new regions for AD genes, though the researchers still have to sequence to identify specific mutations.

Rogaeva, Peter St George-Hyslop of UToronto, and colleagues looked for Alzheimer’s cases who had more ROHs than controls, in the hope that some of those runs might harbor a recessive mutation that increases risk for the disease. A few other researchers have tried a similar approach, with some finding ROH are linked to Alzheimer’s (Nalls et al., 2009) and others uncovering no such association for common variants in a heterogeneous population (Sims et al., 2011). The key, Rogaeva said, is to start with a population where ROHs are plentiful. Though everyone has them, ROHs are more common in certain populations, such as those where inbreeding is common.

Study collaborator Richard Mayeux of Columbia University in New York spent years collecting data and DNA from Caribbean Hispanics in New York City and in the Dominican Republic. This ethnic group, hailing from the Dominican Republic and Puerto Rico, underwent a population bottleneck due to past disease, warfare, and slavery. Such dramatic reductions in population size eliminate some of the genetic variation in that population, resulting in a more homogeneous gene pool even after the population grows again. When the researchers analyzed gene samples for relatedness, they found that Caribbean Hispanics were as closely linked as if second-cousin marriages were a regular practice. “I was shocked at the degree of relatedness,” Rogaeva said. This does not mean that Caribbean Hispanics regularly wed relatives. Rather, it likely indicates that the bottleneck produced relatedness on the same level as cousin intermarriage would, Rogaeva said.

The tragic history of these Caribbean islands created an opportunity for geneticists that Mayeux and colleagues have used repeatedly (Lee et al., 2011, Ghani et al., 2012, Athan et al., 2001). By picking a relatively homogeneous ethnic group with triple the normal risk for AD (Tang et al., 2001), first author Mahdi Ghani and colleagues boosted their chances of finding rare mutations, even though their sample of about 1,100 participants was relatively small. The researchers further upped the odds in their favor by including people with a family history of AD in half of their case population. “It is a very clever approach,” commented Julie Williams of Cardiff University in the U.K., who was not involved with the study.

With DNA from 547 cases and 542 controls, the researchers used gene chips to genotype single nucleotide polymorphisms. From these data, they could pick out ROHs longer than one megabase. They found that people with AD tended to have longer ROHs than controls, a clue that recessive genes were lurking in those parts of the genome. They reasoned that regions where the ROHs of several cases overlapped should point them toward likely loci for recessive AD mutations.

However, none of these individual loci reached statistical significance until the scientists stratified their population further. Even among homogeneous Caribbean Hispanics, a divide exists. Based on genotyping, the researchers split the subjects into those of mainly African ancestry and those of mostly European ancestry. When they looked specifically at the European group, they saw that a single locus passed statistical tests for significance. The only gene in this region, on chromosome seven, is exocyst complex component 4 (EXOC4). “It is our best target for the white Hispanic subpopulation,” Rogaeva said. In the nervous system, the exocyst complex is involved in delivering NMDA receptors to the synapse (Sans et al., 2003). This gene is not listed in the Alzgene database.

In the African subgroup, the most significant association was with locus of α-catenin CTNNA3 http://www.alzgene.org/geneoverview.asp?geneid=45. The link between this gene and AD was “borderline significant” due to small sample size, Rogaeva said. Only 10 cases, and no controls, had ROHs covering this region. This locus has been linked with AD before (Myers et al., 2000, Ertekin-Taner et al., 2000, Miyashita et al., 2007), though no specific mutation has been found. The protein interacts with presenilin 1 at synapses (Georgakopoulos et al., 1999). Both EXOC4 and CTNNA3 also participate in endocytosis. Endocytosis is a cellular process that has emerged repeatedly among confirmed AD GWAS hits, and could link these two gene products to amyloid precursor protein (APP) processing (D’Souza-Schorey and Chavrier, 2006).

Williams believes these genes may indeed contribute to AD. She would like to see corroboration of these chromosomal regions as AD hotspots in another population. Finding ROH-associated loci is but the first step in the project, Rogaeva said. Next, the team will do deep sequencing of the regions they identified in the Caribbean cases who had those same stretches of homozygosity. This should yield mutations, which the researchers can then genotype in a wider, more heterogeneous population. Once confirmed, the new genes should provide clues to the process of Alzheimer’s degeneration, Williams said. Rogaeva hopes the work could eventually lead to clinical genetic screens for AD risk as well.—Amber Dance
 

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References

Paper Citations

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External Citations

  1. EXOC4

Further Reading

Papers

  1. Reitz C, Mayeux R. Genetics of Alzheimer's Disease in Caribbean Hispanic and African American Populations. Biol Psychiatry. 2013 Jul 25; PubMed.
  2. Reitz C, Conrad C, Roszkowski K, Rogers RS, Mayeux R. Effect of Genetic Variation in LRRTM3 on Risk of Alzheimer Disease. Arch Neurol. 2012 Mar 5; PubMed.
  3. Lee JH, Barral S, Cheng R, Chacon I, Santana V, Williamson J, Lantigua R, Medrano M, Jimenez-Velazquez IZ, Stern Y, Tycko B, Rogaeva E, Wakutani Y, Kawarai T, St George-Hyslop P, Mayeux R. Age-at-onset linkage analysis in Caribbean Hispanics with familial late-onset Alzheimer's disease. Neurogenetics. 2008 Feb;9(1):51-60. PubMed.
  4. Bertram L, Mullin K, Parkinson M, Hsiao M, Moscarillo TJ, Wagner SL, Becker KD, Velicelebi G, Blacker D, Tanzi RE. Is alpha-T catenin (VR22) an Alzheimer's disease risk gene?. J Med Genet. 2007 Jan;44(1):e63. PubMed.
  5. Martin ER, Bronson PG, Li YJ, Wall N, Chung RH, Schmechel DE, Small G, Xu PT, Bartlett J, Schnetz-Boutaud N, Haines JL, Gilbert JR, Pericak-Vance MA. Interaction between the alpha-T catenin gene (VR22) and APOE in Alzheimer's disease. J Med Genet. 2005 Oct;42(10):787-92. PubMed.

Primary Papers

  1. Ghani M, Sato C, Lee JH, Reitz C, Moreno D, Mayeux R, St George-Hyslop P, Rogaeva E. Evidence of Recessive Alzheimer Disease Loci in a Caribbean Hispanic Data Set: Genome-wide Survey of Runs of Homozygosity. JAMA Neurol. 2013 Aug 26; PubMed.

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