Gerard D. Schellenberg, PhDDepartment of Pathology and Laboratory Medicine

PI: Alzheimer’s Disease Genetics ConsortiumHead: Penn Neurodegeneration Genomics Center

Gene DiscoveryProgressive Supranuclear Palsy

Corticobasal Degeneration

• Study human disease mechanisms directly in humans

• Prediction

• Mechanism

• Drug targets

Human disease genetics

Gene Protein Mechanism/ DrugPathway target

• Study human disease mechanisms directly in humans

• Prediction

• Mechanism

• Drug targets

Human disease genetics

Does this work?

Gene Protein Mechanism/ DrugPathway target

1. Dewey et al., NEJM (2017, online)2. Graham et al., NEJM (2017, online)3. Crosby et al. NEJM 371, 22 (2014)4. Jorgensen et al., NEJM 371, 32 (2014)5. Gaudet et al., NEJM 371, 2200 (2014)

Gene target trial drug

2006 2011 2016

PCSK9 Coronary artery disease

protective loss-of-function mutations

PCSK9 LOF mutations monoclonal antibodies

ANGPTL3 LOF mutations monoclonal antibodies1

antisense oligonucleotide2

APOC3 LOF mutations3,4 antisense oligonucleotide5

Gene Protein Mechanism/ DrugPathway target

Target Disorder Drug

HMG co-A reductase Heart disease statinsNPC1L1 Heart disease Zetia (ezetimibe)PCSK9 Heart disease monoclonal antibodyVCAM1 MS natalizumabIL2RA MS daclizumabTNF-α RA infliximabSLC30A8/KCNJ11 Type 2 diabetes ZnT-8 antagonists/GlyburidePADI Rheumatoid Arthritis BB-Cl-amidine/ToclilizumabTNFR1/PTGER4/TYK2 Ankylosing Spondylitis (AS) TNF-inhibitors/NSAIDS/fostamatinibIL23A Psoriasis (Ps) RisankizumabRANKL/ESR1 Osteoporosis Denosumab/Raloxifene and HRTDRD2 Schizophrenia anti-psychoticsIL12B AS, Ps, Psoriatic arthritis UstekinumabANGPTL3 Heart disease monoclonal Ab/antisense oligosAPOC3 Heart disease antisense oligos

Drug targets – supported by genetics Visscher et al. Am J. Hum. Genet. 101, 5-22 (2017)

Gene Protein Mechanism/ DrugPathway target

PSP GWASChr/band Closest Gene SNV OR (CI) P

1q25 STX6rs1411478 0.79 (0.74 – 0.85) 2.3 x 10-10

2p11 EIF2AK3 rs7571971 0.85 (0.69 – 0.81) 3.2 x 10-13

3p22 MOBP rs1768208 0.72 (0.67 – 0.78) 1.0 x 10-16

17q21 MAPT rs8070723 5.64 (4.72 – 6.31) 1.5 x 10-116

MAPT mutationsPSP CBD

exon 1 R5Lexon 10 S285R, ∆296, G303V, S305S N296H, N296N, P301S intron 10 E10+11, E10+16exon 13 G415S

PSP Genetics

b

MAPT encodes tau – protein in neurofibrillary tangles

MAPT

MAPT

NSFexons 1-13

NSFexons 1-21

NSFexons 1-21

NSFexons 1-13

H1

Stefansson et al (2005) Nature Genet. 37, 129

H2

KANSL1

KANSL1

863 kb

rs242557 rs17662853Thr-Ile 3’ UTR variant

NSF

Interpretations:

• KANSL1 is tagging a regulatory element that alters MAPT expression/splicing

• KANSL1 variant influences risk for PSP through activity of the KANSL1 protein

Boettger et al., Nature Genetics 44:8, 2012

rs17662853

PSP riskOne copy of KANSL1 5’ endOne – four copies NSF 5’ endOne copy of NSF 5’ end

SNP CH Closest Gene/Region

Meta-Analysis

OR (95% CI) P

rs2732703 17 KANSL1/LRRC37A 0.73 (0.65-0.81) 5.8x10-9

APOE ε4 positive

APOE ε4 negative

AD

PSP Genetics

• GWAS array data

• Whole exome sequence data

• Whole genome sequence data

• Imputed genotypes

Combined approaches

Gene Protein Mechanism/ DrugPathway target

PSP Genetics:

• 700 WES• 2,000 WGS• Controls: ~8,000 (ideal?)• Controls available: ~5,000 for WES, 1,600 for WGS

Challenges:

• Cases sequenced at different times and different platforms• Controls sequenced separately from cases• Controls sequenced at different times and different platforms• WES capture – different reagents• Case/control data needs to be identically processed• Methods to detect structural variants not reliable

Deletion Size Frequency50-500 bp

Alu Insertion Peak

37% deletions (37%) are known SVs (dbSNP144)

Alzheimer’s Disease Sequence Project, TOPMed, and others

Controls

WES

5,000 unrelated AD cases5,000 elderly normal controls – Caucasians (non-

Hispanics)1,000 cases from multiplex families – one/family

WGS

Multiplex families: 1,000 subjects, 158 families~40% Caucasians (non-Hispanics)

Caucasians: 500 cases/500 normal controlsAfrican Americans: 500 cases/500 normal controlsCaribbean Hispanics: 500 cases/500 normal controlsADSP planned (funded): 15,000 - ~2,000 control

Caucasians

TOPMed, CCDG, and others:ADNI 800, 200 Caucasian controlsMESA 4,300 - 2,000 Caucasians many more

GCAD: Call all data – HG38

Generate gVCF files: GATKATLAS (?)

Consensus call set

Harmonized project level VCF - all data sets

Goal: All variant positions called in all data sets

Model Organisms and TauopathiesGene Discovery

Loss-of-function mutations

Brian Kraemer, Ph.D.

• Veterans Affairs Medical Center – Seattle

• Associate Professor - Department of Medicine, University of Washington

• Acting Director – Research at the Geriatric Research Education and Clinical Center, Seattle VA

Cure PSP Society Charles D. Peebler Foundation NIA/NIH

Andrew Lees

Bernie Devlin

Chang-En Yu

Dennis Dickson

Gerard D. Schellenberg

Günter U. Höglinger

Hakon Hakonarson

John HardyLi-San WangLaura Cantwell

Matthew J. Farrer

Nadine Melham

Patrick Sleiman

Rohan de Silva

Rosa Rademakers

Ulrich Müller

Alberto RabanoAlessandro PadovaniAlexandra DurrAlexis BriceAndrew LiebermanAngelo AntoniniAnna KarydasBarbara BorroniBernardino GhettiBill SeeleyBrit MollenhauerBruce MillerCarlo ColosimoCharles WhiteChris MorrisChris ZarroClaire TroakesClaudia TrenkwalderDaniela Befg

Donatella Ottaviani

J. Raphael GibbsMark R. CooksonAndrew SingletonMarcel P. van der Brug

Doug GalaskoDr. Alex RajputDr. GaigDr. Salvatore SpinaEduardo Tolosa Eliezer MasliahFairlie HintonFrancine M. BenesGiovanni FabbriniHoward HurtingHuw MorrisIrene LitvanIsabelle Le BerJean Paul G. VonsattelJesus AvilaJohn TrojanowskiJohn van SwietenJonathan RohrerJuan C. TroncosoJusto García de YébenesLili-Naz HazratiManuela SchmidtMaria StamelouMario EzquerraMarla Gearing

Martin RossorMatthew FroschMurray GrossmanPau PastorPeter de DeynPeter St George-HyslopRobyn FlookRoger AlbinSigrun RoeberStefano Goldwurm Steve ArnoldStuart Pickering-BrownThomas BeachThomas BirdThomas GasserVirginia LeeVivianna Van DeerlinWallace TourtellotteWalter Maetzler Werner Poewe

PSP/CBD GWAS Collaborators

Thank you