Large Genetic Analysis Pays Off With New AD Risk Genes

Casting a larger net boosts the chance of landing fish. The same goes for genes. Over the last few years, researchers have been pushing genomewide association studies (GWAS) as a means to find genetic variants that put people at risk for Alzheimer’s disease. The strategy tallies hundreds of thousands of genetic variants in the genomes of thousands of people to identify those that more likely occur in AD patients than normal controls. Most of the catch is under legal size quotas—statistically speaking—and has to be tossed back into the gene pool. Those are the variants that fall short of genomewide significance. But enlarge the net and the chance of finding genuine risk genes grows. Indeed, this approach just paid off. In today’s Nature Genetics, two back-to-back papers report strong evidence for four new AD risk genes, and one that was previously linked to the disease in families. “It’s an exciting time for genetics,” said Christine Van Broeckhoven, University of Antwerp, Belgium, one of the many coauthors. “I’m really interested to see how this plays out for patients,” she told ARF.

In addition to new genes, the studies also confirmed ApoE4, the strongest risk gene for late-onset AD to date, and PICALM, CR1, CLU, and BIN1, genes previously identified in smaller genomewide analyses (see ARF related news story and ARF news story). This brings the total GWAS gene haul for case-control studies to 10, according to the authors. Genes previously claimed to be associated with AD in family and case-control GWAS include ATXN1 (Bertram et al., 2008 and Bettens et al., 2009), PCDH11X (Carrasquillo et al., 2009; Beecham et al., 2010), and MTHFD1L (Naj et al., 2010).

The new genes were not detected before simply because the samples were too few, said Gerard Schellenberg, University of Pennsylvania, senior author on one of the papers. Schellenberg and well over 100 colleagues at the Alzheimer’s Disease Genetics Consortium (ADGC), carried out a meta-analysis of datasets from previous cohorts to look at genomewide variation among 8,309 AD patients and 7,366 normal controls. Joint first authors Adam Naj, University of Miami, Florida, and Gyungah Jun, Boston University, Massachusetts, and colleagues then carried out two more replications of the analysis using yet different datasets, one comprising about 3,500 cases and roughly the same number of controls, while the third had almost 7,000 cases and roughly 24,600 controls. The latter were provided by the authors of the second study.

Those researchers, primarily in Europe and led by Julie Williams at Cardiff University in Wales, also carried out a three-stage meta-analysis. Step 1 comprised primarily European samples with some input from American datasets (total of almost 7,000 cases and just over 13,600 controls), while stage 2 added further samples from Iceland and Germany (almost 5,000 each of controls and AD samples). In stage 3 (8,200 cases and 21,200 controls), joint first authors Paul Hollingworth, Denise Harold, Rebecca Sima, and Amy Gerrish at Cardiff University, and Jean-Charles Lambert, University of North Lille, France, and Minerva Carrasquillo at the Mayo Clinic, Jacksonville, Florida, added a mix of samples from Europe and the U.S.

The two consortia came up with almost identical results. Both found that genetic variants in four genes—CD2AP, MS4A4/MS4A6E, EPHA1, and CD33—associated with AD. The data passed strict statistical standards for genomewide significance. CD33 was previously identified as a potential AD risk gene by researchers led by Rudy Tanzi at Massachusetts General Hospital, Charlestown (see ARF related news story on Bertram et al., 2008), though the variants identified by these latest GWAS and Tanzi’s group are different. Naj and colleagues were unable to find a link between the previously identified CD33 variant and AD, but noted that the two are in weak linkage disequilibrium, or in other words, not necessarily inherited together. The fifth gene identified, ABCA7, came only from the European study.

What does this news mean for the general public? The minor allele frequencies for the genes ranged from about 19 to 39 percent. The genetic variations are not uncommon, said Schellenberg, and may be in 20-30 percent of the population. Each susceptibility variant was associated with a small increase in risk for the disease of about 10-12 percent. ApoE4, by comparison, is believed to increase risk by two- to fourfold if one copy is inherited, and by up to 15-fold when two copies are present. Naj and colleagues calculated the population attributable fraction (PAF), or the percentage of Alzheimer’s cases that could be eliminated if the genetic risk factors were taken out of the picture, at between 3 and 6 percent for each of the nine non-ApoE genes and perhaps 30 percent for the nine combined. But Schellenberg cautioned that their study was not set up to address this question, and that the real PAF might be different. Williams reckons with all the genetic analysis done to date, scientists can now account for about 32 percent of the genetic risk for AD and about 20 percent of the total risk.

“Although the significance of any particular gene is relatively small, the biological significance is much bigger because we are finding definite pathways pointing in directions of disease mechanisms,” said Williams. There are now several genes that seem to play a role in lipid processing (ApoE4, ABCA7, CLU), in the immune system (CD33, CLU, CR1, ABCA7, and EPHA1), and in endocytosis or membrane trafficking (CD2AP, PICALM, BIN1, and CD33).

Tanzi agreed. “We are beginning to see binning or boxing of genes. For me, the most interesting is the innate immunity box,” he told ARF. In addition to the immune-related genes that have emerged from GWAS, there are also a number of other genes linked to AD in the AlzGene database that are intimately involved in immunity, including IL1A, IL1B, IL8, which is number 10 in the AlzGene hit parade, and TNFα.

Van Broeckhoven is optimistic that, going forward, even more genes will be found. Both consortia are now joining forces in a mega-meta-analysis. The International Genomics of Alzheimer’s Project, or IGAP (see ARF related news story) is already underway, and researchers expect to see the first analysis of that published within the year. Williams predicts that new genes will emerge that are in the same mechanistic pathways as those already discovered. “History shows that when you have done enough GWAS to get to the stage where we are now, that further, more powerful studies will confirm the pathway already identified,” she said. Genetic analysis of multiple sclerosis and Crohn’s disease bear this out.

With a huge dataset like the one IGAP is analyzing (roughly 20,000 cases and controls), van Broeckhoven predicts that researchers can begin to ask more detailed questions. For example, which genetic variants are linked to earlier age at onset, to fluid biomarkers, epigenetics? Which genes interact with each other? “There is so much work to be done,” said van Broeckhoven. “We don’t know if we will need a mouse model for every variant, or if a cell model will suffice.” When and how the GWAS information is translated into the clinic remains to be seen.—Tom Fagan

Comments

    • User Profile Image Rudy Tanzi
      Massachusetts General Hospital
    • Posted:

    The two new Alzheimer's GWAS reports from the NIA-ADGC (Naj et al., 2011) and European consortium (Hollingworth et al., 2011) provide further support for roles of the innate immune system, cholesterol metabolism, and protein trafficking in the etiology and pathogenesis of Alzheimer's disease (Bertram et al., 2010).

    With regard to innate immunity, CD33 is a particularly compelling AD candidate gene, both genetically and biologically. In 2008, we reported CD33 to show genomewide significant association with AD in a large family-based GWAS: genomewide significance for association in the NIMH family sample, and replication in two other large AD family samples from the NIA AD family collection. This study (Bertram et al., 2008), was part of the Cure Alzheimer's Fund Alzheimer's Genome Project. Thus, CD33 now exhibits genomewide significant association in both family-based and case-control GWAS study designs, albeit with different SNPs. The AD-associated SNP that we had reported in CD33 increases risk for AD (Bertram et al., 2008). However, the neighboring SNP in CD33 reported by the ADGC in the case-control study confers protection against AD (Naj et al., 2011).

    CD33 controls the initiation of the innate immune system. Thus, it will be important to determine whether the problem in AD is that CD33 does not sufficiently trigger innate immunity and, for example, microglial degradation of β amyloid. Or, perhaps, in AD, CD33 triggers innate immunity too robustly, leading to excessive inflammation and secondary neurodegeneration. In any event, the combined genetic findings from the new case-control GWAS (Naj et al., 2011, Hollingworth et al., 2011) and the previous family-based GWAS (Bertram et al., 2008) clearly warrant further study of the genetics and role of CD33 (and innate immunity) in AD.

    References:

    Naj AC, Jun G, Beecham GW, Wang LS, Vardarajan BN, Buros J, Gallins PJ, Buxbaum JD, Jarvik GP, Crane PK, Larson EB, Bird TD, Boeve BF, Graff-Radford NR, De Jager PL, Evans D, Schneider JA, Carrasquillo MM, Ertekin-Taner N, Younkin SG, Cruchaga C, Kauwe JS, Nowotny P, Kramer P, Hardy J, Huentelman MJ, Myers AJ, Barmada MM, Demirci FY, Baldwin CT, Green RC, Rogaeva E, St George-Hyslop P, Arnold SE, Barber R, Beach T, Bigio EH, Bowen JD, Boxer A, Burke JR, Cairns NJ, Carlson CS, Carney RM, Carroll SL, Chui HC, Clark DG, Corneveaux J, Cotman CW, Cummings JL, DeCarli C, DeKosky ST, Diaz-Arrastia R, Dick M, Dickson DW, Ellis WG, Faber KM, Fallon KB, Farlow MR, Ferris S, Frosch MP, Galasko DR, Ganguli M, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Gilman S, Giordani B, Glass JD, Growdon JH, Hamilton RL, Harrell LE, Head E, Honig LS, Hulette CM, Hyman BT, Jicha GA, Jin LW, Johnson N, Karlawish J, Karydas A, Kaye JA, Kim R, Koo EH, Kowall NW, Lah JJ, Levey AI, Lieberman AP, Lopez OL, Mack WJ, Marson DC, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Parisi JE, Perl DP, Peskind E, Petersen RC, Poon WW, Quinn JF, Rajbhandary RA, Raskind M, Reisberg B, Ringman JM, Roberson ED, Rosenberg RN, Sano M, Schneider LS, Seeley W, Shelanski ML, Slifer MA, Smith CD, Sonnen JA, Spina S, Stern RA, Tanzi RE, Trojanowski JQ, Troncoso JC, Van Deerlin VM, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Williamson J, Woltjer RL, Cantwell LB, Dombroski BA, Beekly D, Lunetta KL, Martin ER, Kamboh MI, Saykin AJ, Reiman EM, Bennett DA, Morris JC, Montine TJ, Goate AM, Blacker D, Tsuang DW, Hakonarson H, Kukull WA, Foroud TM, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet. 2011 May;43(5):436-41. Epub 2011 Apr 3 PubMed.

    Hollingworth P, Harold D, Sims R, Gerrish A, Lambert JC, Carrasquillo MM, Abraham R, Hamshere ML, Pahwa JS, Moskvina V, Dowzell K, Jones N, Stretton A, Thomas C, Richards A, Ivanov D, Widdowson C, Chapman J, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Holmes C, Mann D, Smith AD, Beaumont H, Warden D, Wilcock G, Love S, Kehoe PG, Hooper NM, Vardy ER, Hardy J, Mead S, Fox NC, Rossor M, Collinge J, Maier W, Jessen F, Rüther E, Schürmann B, Heun R, Kölsch H, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Gallacher J, Hüll M, Rujescu D, Giegling I, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Sleegers K, Bettens K, Engelborghs S, De Deyn PP, Van Broeckhoven C, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Pankratz VS, Sando SB, Aasly JO, Barcikowska M, Wszolek ZK, Dickson DW, Graff-Radford NR, Petersen RC, , van Duijn CM, Breteler MM, Ikram MA, DeStefano AL, Fitzpatrick AL, Lopez O, Launer LJ, Seshadri S, Berr C, Campion D, Epelbaum J, Dartigues JF, Tzourio C, Alpérovitch A, Lathrop M, Feulner TM, Friedrich P, Riehle C, Krawczak M, Schreiber S, Mayhaus M, Nicolhaus S, Wagenpfeil S, Steinberg S, Stefansson H, Stefansson K, Snædal J, Björnsson S, Jonsson PV, Chouraki V, Genier-Boley B, Hiltunen M, Soininen H, Combarros O, Zelenika D, Delepine M, Bullido MJ, Pasquier F, Mateo I, Frank-Garcia A, Porcellini E, Hanon O, Coto E, Alvarez V, Bosco P, Siciliano G, Mancuso M, Panza F, Solfrizzi V, Nacmias B, Sorbi S, Bossù P, Piccardi P, Arosio B, Annoni G, Seripa D, Pilotto A, Scarpini E, Galimberti D, Brice A, Hannequin D, Licastro F, Jones L, Holmans PA, Jonsson T, Riemenschneider M, Morgan K, Younkin SG, Owen MJ, O'Donovan M, Amouyel P, Williams J. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet. 2011 May;43(5):429-35. PubMed.

    Bertram L, Lill CM, Tanzi RE. The genetics of Alzheimer disease: back to the future. Neuron. 2010 Oct 21;68(2):270-81. PubMed.

    Bertram L, Lange C, Mullin K, Parkinson M, Hsiao M, Hogan MF, Schjeide BM, Hooli B, Divito J, Ionita I, Jiang H, Laird N, Moscarillo T, Ohlsen KL, Elliott K, Wang X, Hu-Lince D, Ryder M, Murphy A, Wagner SL, Blacker D, Becker KD, Tanzi RE. Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE. Am J Hum Genet. 2008 Nov;83(5):623-32. PubMed.

    View all comments by Rudy Tanzi

Make a Comment

To make a comment you must login or register.

References

News Citations

  1. LOADing Up—Largest GWAS to Date Confirms Two, Adds Two Risk Genes
  2. Repeat Offenders—CLU, CR1, PICALM Hold Up in Association Studies
  3. Four New Acts Debut on GWAS Screen
  4. Mind the IGAP—Transatlantic Consortium to Map AD Genes

Paper Citations

  1. Bertram L, Lange C, Mullin K, Parkinson M, Hsiao M, Hogan MF, Schjeide BM, Hooli B, Divito J, Ionita I, Jiang H, Laird N, Moscarillo T, Ohlsen KL, Elliott K, Wang X, Hu-Lince D, Ryder M, Murphy A, Wagner SL, Blacker D, Becker KD, Tanzi RE. Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE. Am J Hum Genet. 2008 Nov;83(5):623-32. PubMed.
  2. Bettens K, Brouwers N, van Miegroet H, Gil A, Engelborghs S, De Deyn PP, Vandenberghe R, Van Broeckhoven C, Sleegers K. Follow-Up Study of Susceptibility Loci for Alzheimer's Disease and Onset Age Identified by Genome-Wide Association. J Alzheimers Dis. 2009 Dec 14; PubMed.
  3. Carrasquillo MM, Zou F, Pankratz VS, Wilcox SL, Ma L, Walker LP, Younkin SG, Younkin CS, Younkin LH, Bisceglio GD, Ertekin-Taner N, Crook JE, Dickson DW, Petersen RC, Graff-Radford NR. Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease. Nat Genet. 2009 Feb;41(2):192-8. PubMed.
  4. Beecham GW, Naj AC, Gilbert JR, Haines JL, Buxbaum JD, Pericak-Vance MA. PCDH11X variation is not associated with late-onset Alzheimer disease susceptibility. Psychiatr Genet. 2010 Dec;20(6):321-4. PubMed.
  5. Naj AC, Beecham GW, Martin ER, Gallins PJ, Powell EH, Konidari I, Whitehead PL, Cai G, Haroutunian V, Scott WK, Vance JM, Slifer MA, Gwirtsman HE, Gilbert JR, Haines JL, Buxbaum JD, Pericak-Vance MA. Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities. PLoS Genet. 2010 Sep;6(9) PubMed.

External Citations

  1. ATXN1
  2. PCDH11X
  3. MTHFD1L
  4. Alzheimer’s Disease Genetics Consortium
  5. CD33
  6. ApoE4
  7. CLU
  8. CR1
  9. PICALM
  10. BIN1
  11. IL1A
  12. IL1B
  13. IL8
  14. TNFα

Further Reading

Papers

  1. Corneveaux JJ, Myers AJ, Allen AN, Pruzin JJ, Ramirez M, Engel A, Nalls MA, Chen K, Lee W, Chewning K, Villa SE, Meechoovet HB, Gerber JD, Frost D, Benson HL, O'Reilly S, Chibnik LB, Shulman JM, Singleton AB, Craig DW, Van Keuren-Jensen KR, Dunckley T, Bennett DA, De Jager PL, Heward C, Hardy J, Reiman EM, Huentelman MJ. Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. Hum Mol Genet. 2010 Aug 15;19(16):3295-301. PubMed.
  2. Grupe A, Abraham R, Li Y, Rowland C, Hollingworth P, Morgan A, Jehu L, Segurado R, Stone D, Schadt E, Karnoub M, Nowotny P, Tacey K, Catanese J, Sninsky J, Brayne C, Rubinsztein D, Gill M, Lawlor B, Lovestone S, Holmans P, O'Donovan M, Morris JC, Thal L, Goate A, Owen MJ, Williams J. Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. Hum Mol Genet. 2007 Apr 15;16(8):865-73. Epub 2007 Feb 22 PubMed.

Primary Papers

  1. Naj AC, Jun G, Beecham GW, Wang LS, Vardarajan BN, Buros J, Gallins PJ, Buxbaum JD, Jarvik GP, Crane PK, Larson EB, Bird TD, Boeve BF, Graff-Radford NR, De Jager PL, Evans D, Schneider JA, Carrasquillo MM, Ertekin-Taner N, Younkin SG, Cruchaga C, Kauwe JS, Nowotny P, Kramer P, Hardy J, Huentelman MJ, Myers AJ, Barmada MM, Demirci FY, Baldwin CT, Green RC, Rogaeva E, St George-Hyslop P, Arnold SE, Barber R, Beach T, Bigio EH, Bowen JD, Boxer A, Burke JR, Cairns NJ, Carlson CS, Carney RM, Carroll SL, Chui HC, Clark DG, Corneveaux J, Cotman CW, Cummings JL, DeCarli C, DeKosky ST, Diaz-Arrastia R, Dick M, Dickson DW, Ellis WG, Faber KM, Fallon KB, Farlow MR, Ferris S, Frosch MP, Galasko DR, Ganguli M, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Gilman S, Giordani B, Glass JD, Growdon JH, Hamilton RL, Harrell LE, Head E, Honig LS, Hulette CM, Hyman BT, Jicha GA, Jin LW, Johnson N, Karlawish J, Karydas A, Kaye JA, Kim R, Koo EH, Kowall NW, Lah JJ, Levey AI, Lieberman AP, Lopez OL, Mack WJ, Marson DC, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Parisi JE, Perl DP, Peskind E, Petersen RC, Poon WW, Quinn JF, Rajbhandary RA, Raskind M, Reisberg B, Ringman JM, Roberson ED, Rosenberg RN, Sano M, Schneider LS, Seeley W, Shelanski ML, Slifer MA, Smith CD, Sonnen JA, Spina S, Stern RA, Tanzi RE, Trojanowski JQ, Troncoso JC, Van Deerlin VM, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Williamson J, Woltjer RL, Cantwell LB, Dombroski BA, Beekly D, Lunetta KL, Martin ER, Kamboh MI, Saykin AJ, Reiman EM, Bennett DA, Morris JC, Montine TJ, Goate AM, Blacker D, Tsuang DW, Hakonarson H, Kukull WA, Foroud TM, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet. 2011 May;43(5):436-41. Epub 2011 Apr 3 PubMed.
  2. Hollingworth P, Harold D, Sims R, Gerrish A, Lambert JC, Carrasquillo MM, Abraham R, Hamshere ML, Pahwa JS, Moskvina V, Dowzell K, Jones N, Stretton A, Thomas C, Richards A, Ivanov D, Widdowson C, Chapman J, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Holmes C, Mann D, Smith AD, Beaumont H, Warden D, Wilcock G, Love S, Kehoe PG, Hooper NM, Vardy ER, Hardy J, Mead S, Fox NC, Rossor M, Collinge J, Maier W, Jessen F, Rüther E, Schürmann B, Heun R, Kölsch H, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Gallacher J, Hüll M, Rujescu D, Giegling I, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Sleegers K, Bettens K, Engelborghs S, De Deyn PP, Van Broeckhoven C, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Pankratz VS, Sando SB, Aasly JO, Barcikowska M, Wszolek ZK, Dickson DW, Graff-Radford NR, Petersen RC, , van Duijn CM, Breteler MM, Ikram MA, DeStefano AL, Fitzpatrick AL, Lopez O, Launer LJ, Seshadri S, Berr C, Campion D, Epelbaum J, Dartigues JF, Tzourio C, Alpérovitch A, Lathrop M, Feulner TM, Friedrich P, Riehle C, Krawczak M, Schreiber S, Mayhaus M, Nicolhaus S, Wagenpfeil S, Steinberg S, Stefansson H, Stefansson K, Snædal J, Björnsson S, Jonsson PV, Chouraki V, Genier-Boley B, Hiltunen M, Soininen H, Combarros O, Zelenika D, Delepine M, Bullido MJ, Pasquier F, Mateo I, Frank-Garcia A, Porcellini E, Hanon O, Coto E, Alvarez V, Bosco P, Siciliano G, Mancuso M, Panza F, Solfrizzi V, Nacmias B, Sorbi S, Bossù P, Piccardi P, Arosio B, Annoni G, Seripa D, Pilotto A, Scarpini E, Galimberti D, Brice A, Hannequin D, Licastro F, Jones L, Holmans PA, Jonsson T, Riemenschneider M, Morgan K, Younkin SG, Owen MJ, O'Donovan M, Amouyel P, Williams J. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet. 2011 May;43(5):429-35. PubMed.

Annotate

To make an annotation you must Login or Register.