Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease

We performed an exome-wide association analysis in 1393 late-onset Alzheimer's disease (LOAD) cases and 8141 controls from the CHARGE consortium. We found that a rare variant (P155L) in TM2D3 was enriched in Icelanders (similar to 0.5% versus <0.05% in other European populations). In 433 LOAD cases and 3903 controls from the Icelandic AGES substudy, P155L was associated with increased risk and earlier onset of LOAD [odds ratio (95% CI) = 7.5 (3.5-15.9), p = 6.6x10(-9)]. Mutation in the Drosophila TM2D3 homolog, almondex, causes a phenotype similar to loss of Notch/Presenilin signaling. Human TM2D3 is capable of rescuing these phenotypes, but this activity is abolished by P155L, establishing it as a functionally damaging allele. Our results establish a rare TM2D3 variant in association with LOAD susceptibility, and together with prior work suggests possible links to the beta-amyloid cascade.Peer reviewe

Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease.

We performed an exome-wide association analysis in 1393 late-onset Alzheimer's disease (LOAD) cases and 8141 controls from the CHARGE consortium. We found that a rare variant (P155L) in TM2D3 was enriched in Icelanders (~0.5% versus &lt;0.05% in other European populations). In 433 LOAD cases and 3903 controls from the Icelandic AGES sub-study, P155L was associated with increased risk and earlier onset of LOAD [odds ratio (95% CI) = 7.5 (3.5-15.9), p = 6.6x10-9]. Mutation in the Drosophila TM2D3 homolog, almondex, causes a phenotype similar to loss of Notch/Presenilin signaling. Human TM2D3 is capable of rescuing these phenotypes, but this activity is abolished by P155L, establishing it as a functionally damaging allele. Our results establish a rare TM2D3 variant in association with LOAD susceptibility, and together with prior work suggests possible links to the β-amyloid cascade

Sequence alignment and domain structure of TM2D3.

<p>(A) Sequence alignment of TM2D3 homologs shows overall strong conservation but lack of conservation for P155L. Sequence alignment of human (TM2D3), mouse (Tm2d3), zebrafish (tm2d3), <i>Drosophila</i> (amx) and <i>C</i>. <i>elegans</i> (C41D11.9) using Clustal X2.1 is shown. The conserved amino acids are highlighted according to the standard color scheme of Clustal X. (B) Primary sequence and schematic diagram of the domain structure of human TM2D3.</p

<i>TM2D3</i>^<i>P155L</i> is a loss-of-function allele.

<p>(A-B) Embryos laid by <i>amx</i> mutant females exhibit a strong neurogenic phenotype. (A) Lateral view of a late stage control embryo shows properly patterned and organized central and peripheral nervous system structures. (B) Embryos laid by amx mutant females show dramatic increase in the number of neurons, labeled by Elav (neuronal nucleus, green) and Hrp (neuronal membrane, magenta). (C) Schematic diagram of the <i>amx</i> locus and genomic rescue constructs generated for this study. <i>amx</i>^<i>1</i> contains an 8 nucleotide deletion that introduces a frameshift followed by a stop codon after residue 184 (Michellod and Randsholt, 2008). <i>Df(1)Exel9049</i> is a molecularly defined deletion that covers <i>amx</i> and two neighboring genes. The genomic rescue construct contains a ~3.3 kb fragment that can fully rescue the sterility of <i>amx</i>^<i>1</i><i>/Df(1)Exel9049</i> mutant females and the neurogenic defects seen in the progeny (A, E). Coding region of Amx has been replaced by TM2D3 to “humanize” the fly <i>amx</i> gene. (D) Egg hatching assay reveals that <i>hTM2D3[+]</i> can partially suppress the female sterility of <i>amx</i>^<i>1</i><i>/Df(1)Exel9049</i> mutant females, while <i>hTM2D3[P155L]</i> cannot. Due to the lethality of <i>Df(1)Exel9049/Y</i> hemizygous male progeny, complete rescue of the <i>amx</i> phenotype is expected to lead to a maximum of ~75% egg hatching, as denoted by the Mendelian Expectation line (also see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006327#pgen.1006327.s004" target="_blank">S3 Fig</a>). (E-H) The developing nervous system is shown for embryos laid by <i>amx</i> mutant females with and without <i>amx[+]</i>, <i>TM2D3[+]</i>, and <i>TM2D3[P155L]</i> genomic rescue constructs. <i>TM2D3[+]</i> is capable of complete rescue of the <i>amx</i> neurogenic phenotype in some embryos (G), whereas all embryos with the <i>hTM2D3[P155L]</i> construct exhibit strong neurogenic phenotypes (H). Also see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006327#pgen.1006327.s006" target="_blank">S5 Fig</a> for assessment of rescue of the <i>amx</i> peripheral nervous system neurogenic phenotype. Scale bars = 100μm.</p

Sample characteristics and association results for P155L (rs139709573) in <i>TM2D3</i> in the two Icelandic AGES cohorts.

<p>Sample characteristics and association results for P155L (rs139709573) in <i>TM2D3</i> in the two Icelandic AGES cohorts.</p

Kaplan-Meier survival curves for <i>TM2D3</i>.

<p>Curves are based on incident data only. There was no evidence of bias due to competing risk of death (<b>Supporting results in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006327#pgen.1006327.s001" target="_blank">S1 Text</a></b>).</p