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. 2019 Jun;137(6):879-899.
doi: 10.1007/s00401-019-01962-9. Epub 2019 Feb 9.

Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD

Cyril Pottier  1 Yingxue Ren  2 Ralph B Perkerson 3rd  1 Matt Baker  1 Gregory D Jenkins  3 Marka van Blitterswijk  1 Mariely DeJesus-Hernandez  1 Jeroen G J van Rooij  4 Melissa E Murray  1 Elizabeth Christopher  1 Shannon K McDonnell  3 Zachary Fogarty  3 Anthony Batzler  3 Shulan Tian  3 Cristina T Vicente  1 Billie Matchett  1 Anna M Karydas  5 Ging-Yuek Robin Hsiung  6 Harro Seelaar  4 Merel O Mol  4 Elizabeth C Finger  7 Caroline Graff  8   9 Linn Öijerstedt  8   9 Manuela Neumann  10   11 Peter Heutink  10   12 Matthis Synofzik  10   12 Carlo Wilke  10   12 Johannes Prudlo  10   13 Patrizia Rizzu  10 Javier Simon-Sanchez  10   12 Dieter Edbauer  14   15 Sigrun Roeber  16 Janine Diehl-Schmid  17 Bret M Evers  18 Andrew King  19   20 M Marsel Mesulam  21 Sandra Weintraub  21   22 Changiz Geula  21 Kevin F Bieniek  1   23 Leonard Petrucelli  1 Geoffrey L Ahern  24 Eric M Reiman  25 Bryan K Woodruff  26 Richard J Caselli  26 Edward D Huey  27 Martin R Farlow  28 Jordan Grafman  29 Simon Mead  30 Lea T Grinberg  5   31 Salvatore Spina  5 Murray Grossman  32 David J Irwin  32 Edward B Lee  33 EunRan Suh  33 Julie Snowden  34 David Mann  35 Nilufer Ertekin-Taner  1   36 Ryan J Uitti  36 Zbigniew K Wszolek  36 Keith A Josephs  37 Joseph E Parisi  37 David S Knopman  37 Ronald C Petersen  37 John R Hodges  38 Olivier Piguet  39 Ethan G Geier  5 Jennifer S Yokoyama  5 Robert A Rissman  40   41 Ekaterina Rogaeva  42 Julia Keith  43   44 Lorne Zinman  43 Maria Carmela Tartaglia  42   45 Nigel J Cairns  46 Carlos Cruchaga  47 Bernardino Ghetti  48 Julia Kofler  49 Oscar L Lopez  24   50 Thomas G Beach  51 Thomas Arzberger  14   16   52 Jochen Herms  14   16 Lawrence S Honig  53 Jean Paul Vonsattel  54 Glenda M Halliday  38   55 John B Kwok  38   55 Charles L White 3rd  18 Marla Gearing  56 Jonathan Glass  56 Sara Rollinson  57 Stuart Pickering-Brown  57 Jonathan D Rohrer  58 John Q Trojanowski  33 Vivianna Van Deerlin  33 Eileen H Bigio  21 Claire Troakes  19 Safa Al-Sarraj  19   20 Yan Asmann  2 Bruce L Miller  5 Neill R Graff-Radford  36 Bradley F Boeve  37 William W Seeley  5   31 Ian R A Mackenzie  59 John C van Swieten  4 Dennis W Dickson  1 Joanna M Biernacka  3 Rosa Rademakers  60
Affiliations

Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD

Cyril Pottier et al. Acta Neuropathol. 2019 Jun.

Abstract

Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) represents the most common pathological subtype of FTLD. We established the international FTLD-TDP whole-genome sequencing consortium to thoroughly characterize the known genetic causes of FTLD-TDP and identify novel genetic risk factors. Through the study of 1131 unrelated Caucasian patients, we estimated that C9orf72 repeat expansions and GRN loss-of-function mutations account for 25.5% and 13.9% of FTLD-TDP patients, respectively. Mutations in TBK1 (1.5%) and other known FTLD genes (1.4%) were rare, and the disease in 57.7% of FTLD-TDP patients was unexplained by the known FTLD genes. To unravel the contribution of common genetic factors to the FTLD-TDP etiology in these patients, we conducted a two-stage association study comprising the analysis of whole-genome sequencing data from 517 FTLD-TDP patients and 838 controls, followed by targeted genotyping of the most associated genomic loci in 119 additional FTLD-TDP patients and 1653 controls. We identified three genome-wide significant FTLD-TDP risk loci: one new locus at chromosome 7q36 within the DPP6 gene led by rs118113626 (p value = 4.82e - 08, OR = 2.12), and two known loci: UNC13A, led by rs1297319 (p value = 1.27e - 08, OR = 1.50) and HLA-DQA2 led by rs17219281 (p value = 3.22e - 08, OR = 1.98). While HLA represents a locus previously implicated in clinical FTLD and related neurodegenerative disorders, the association signal in our study is independent from previously reported associations. Through inspection of our whole-genome sequence data for genes with an excess of rare loss-of-function variants in FTLD-TDP patients (n ≥ 3) as compared to controls (n = 0), we further discovered a possible role for genes functioning within the TBK1-related immune pathway (e.g., DHX58, TRIM21, IRF7) in the genetic etiology of FTLD-TDP. Together, our study based on the largest cohort of unrelated FTLD-TDP patients assembled to date provides a comprehensive view of the genetic landscape of FTLD-TDP, nominates novel FTLD-TDP risk loci, and strongly implicates the immune pathway in FTLD-TDP pathogenesis.

Keywords: DPP6; HLA; Immunity; TBK1; UNC13A; Whole-genome sequencing FTLD-TDP.

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Figures

Figure 1.
Figure 1.. Age distributions in each FTLD-TDP pathological subtype
Age at onset, age at death and survival after onset are represented as histogram per FTLD-TDP pathological subtype. A density curve is superimposed to the histograms.
Figure 2.
Figure 2.. Common variant whole genome sequencing association study and DPP6 locus
(a) Manhattan plot of the FTLD-TDP patients versus control association study. The red dotted line represents the genome-wide significance level (p=5e-08). (b)Regional association (locus zoom) plot of the DPP6 locus. Each dot represents a genotyped variant. The purple dot is the most significant variant (rs4726389) among variants in the region. Dots are colored from red to blue according to their r2 value, showing their degree of linkage disequilibrium with rs4726389 (grey indicates an r2 of zero). The light blue line shows the estimated recombination rate. (c) DPP6 mRNA expression levels in function of the rs4726389 genotypes without correction for cellular composition in custom RNAseq frontal cortex dataset. (d) DPP6 mRNA expression levels in function of the rs4726389 genotypes with correction for cellular composition in custom RNAseq frontal cortex dataset. (e) Differential DPP6 mRNA expression levels in FTLD-TDP patients and controls without correction for cellular composition. (f) Differential DPP6 mRNA expression levels in FTLD-TDP patients and controls with correction for cellular composition.

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