Overview of ALS Genetics - PowerPoint Presentation

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Overview of ALS Genetics Parts of what’s known and a glimpse of what’s next…

Patrick Dion,

Ph.D. Neurology and NeurosurgeryMcGill University

Human Genome Basics3 billions base pairs.

Contains protein-coding and noncoding DNA.19,000-20,000 protein-coding genes (2% of the genome).Exomes refers to the 2% coding DNA share.Noncoding is associated with regulation of expression, chromosome architecture and epigenetic regulation.First sequencing draft completed in 2001.Several thousands genomes have now been sequenced.Available through various databases (e.g. 1kGP,

ExaC, EVS).Regardless of race we are 99.9% identical at the genome level.

Human Genome BasicsDistinctive markers exist all across the genome.[Large] RFLP, tandem repeat, Copy Number Variants (CNVs)

[Small] Single nucleotide polymorphisms (SNPs).SNPs are common variants found in >1% of the population at 1,000 bp across.When in coding regions SNPs can be synonymous or nonsynonymous.Distinction between SNPs and single nucleotide variants (SNVs).

Discovery ApproachesClassical linkage analysis

Candidate genes associationGenome Wide Association Study (GWAS)Use of common variants to identify regions shared by affected.Whole Exome Sequencing (WES)Seeks to filter rare coding variants to identify to identify deleterious ones.No need for controls except when population specific.Whole Genome Sequencing (WGS)Seeks to filter all variants (coding and not coding)

WES and WGS data can also be used to conduct association studies using common variants and rare ones (e.g. Minor Allele Frequency < 1%)

Variants filtering of WES and WGS

FALS and SALSOverall ALS is the most common rare disease (2/100,00).

FALS (familial)5-10% of cases of ALSPrimarily autosomal dominant (AD) segregation of definite, probable or possible individuals.SALS (sporadic)No family historyClinically indistinguishable Except age of onset and sex distribution

This classification should not overshadow the fact that FALS and SALS DO share common genetic causes.Moreover environmental/stochastic factors can affect genetically susceptible individuals.

Just how many ALS genes are there?http://alsod.iop.kcl.ac.uk/home.aspx

Updated once a year.Between the discovery of the first causative gene (SOD1) in 1993 and now,126 genes were “linked” to ALS.[+] Classify the genes according to phenotype, geographical distribution and method of identification.[-] Includes > 50% of genes for which associations are either weak and/or were never replicated in independent studies.Nonetheless a valuable and objective online to use assessment tool to consult about the causal nature of specific variants.

The risk linked to ALS genes can be classified according to multiple factors.

High Risk Genes

Locus

Chromosome

Gene IDProtein/Function

Evidence

Inheritance

Mutation

Diagnosis

Onset

Replication studies

References

ALS1

21q22.11

SOD1

Cu/Zn superoxide dismutase 1, soluble / Oxidative stress

Linkage, Sanger

AD, AR

SNV

ALS, PMAAdultYes[1]ALS22q33.2ALS2Alsin / Rho guanine nucleotide exchange factorsLinkage, SangerARSNVALS, PLS, HSPJuvenileYes[2, 3]ALS49q34.13SETXSenataxin / RNA/DNA HelicaseLinkage, SangerADSNVALS, AOA2JuvenileYes[4]ALS515q21.1SPG11Spatacsin / transmembrane proteinLinkage, SangerARSNVALS, HSPJuvenileYes[5, 6]ALS616p11.2FUSFused in Sarcoma / RNA-binding protein, DNA repair, exon splicingLinkage, SangerADSNVALS, ALS-FTDAdultYes[7, 8]ALS720p13UnknownUnknownLinkageAD-ALSAdultNo[9]ALS820q13.33VAPBVesicle-associated membrane protein-associated protein B / Vesicular traffickingLinkage, SangerADSNVALS, SMAAdultYes[10, 11]ALS101p36.22TARDBPTAR DNA binding protein 43 / transcriptional repressor, splicing regulation Linkage, SangerADSNVALS, ALS-FTDAdultYes[12, 13]ALS149p13.3VCPvalosin-containing protein / ATP-binding protein, vesicle transport and fusionWES, linkage, SangerADSNVALS, ALS-FTD, FTD, IBMPFDAdultYes[14]ALS15Xp11.21UBQLN2ubiquilin 2 / ubiquitination, degradationLinkage, SangerX-linkedSNVALS, ALS-FTDJuvenile, AdulteYes[15]ALS169p13.3SIGMAR1sigma non-opioid intracellular receptor 1 / endoplasmic reticulum chaperoneHomozygosity mapping, SangerARSNVALS, FTDJuvenileNo[15] 12q24.11DAOD-amino-acid oxidase / unknownLinkage, SangerADSNVALSAdultNo[16]ALS1717p13.2PFN1profilin 1 / actin binding protein, actin polymerizationLinkage, WES, SangerADSNVALSAdultYes[17]ALS207p15.2/12q13.3hnRNPA2B1/A1Heterogenous nuclear ribonucleoprotein / mRNA processing, metabolism & transportLinkage, WES, SangerADSNVALS, IBMPFDAdultNo[18]ALS-FTD19q21-q22UnknownUnknownLinkageADSNVALS, ALS-FTD, FTDAdultNo[19]ALS-FTD29p21.2C9ORF72chromosome 9 open reading frame 72 / UnknownLinkage, GWAS, RP-PCR, Southern BlotAD, sporadic1G4C2 repeatALS, ALS-FTD, FTDAdultYes[20-28] 

Superoxide Dismutase-1 SOD1 [ALS1]

Originally found using Classical linkage analysis and FALS.

Accounts for ~20% of FALS forms (2% of SALS).>160 mutations identified all over SOD1.All dominant except for D90A and D96N, recessive in some cases

Some mutations affect survival time: A4V

rapid progression D90A slow progression

Some affect disease onset:

G37R with early

onset

Most mutations trigger

a

shift of the folding equilibrium toward poorly structured SOD

monomers.

A great number of mechanisms are proposed to be involved, however, distinguishing cause from effect and identifying the critical processes remains

challenging

TAR DNA Binding ProteinTARDBP (TDP-43) [ALS10]

[Candidate gene approach]In 2008

the gene was screened for mutations as its product was a prominent product of ubiquitinated cytoplasmic inclusions in the CNS tissues of FTD and ALS. Accounts for ~4% of FALS forms (<1 % of SALS).

> 47 Missense and one truncating variants.All variants are dominants.

Pathogenic variants are mostly in the C-terminus which is involved in RNA binding and splicing.

Fused in SarcomaFUS [ALS6]

[Candidate gene approach and locus approaches] (2009) Accounts for ~4% of FALS forms (<1 % of SALS).Autosomal dominant and recessive.

Age of onset younger (< 40yrs with cases during teens).Faster progression than TARDBP and SOD1 cases

> 50 Missense and one truncating variants.All variants are dominants.

Pathogenic variants are mostly

in the C-terminus.

Chromosome 9 open reading frame C9orf72 [ALS-FTD]

[GWAS and locus approaches] (2011) Accounts for ~40% of European descent familial ALS-FTD cases (

10 % of Asians) and 7% of SALS.Large intronic repeat expansion (GGGGCC or G4C2).>30 repeats pathogenic, 15-30 not very pathogenic but recently observed to be with ATXN2 intermediate CAG expansion.

Both gain and loss of functions are under consideration.

Multiple pathogenic

avenues..

RNA foci and sequestration of RNA binding components.

Non-ATG (RAN) translation of repeat derived dipeptide accumulation in the CNS (GR > PR > GA > AP > GP).

Dysregulation of its potential DENN

Rab

-GEFs activity on membrane trafficking

.

Disrupts of nucleocytoplasmic transport of mRNA.

Low Risk Genes

Locus

Chromosome

Gene IDGene Name/Function

Evidence

Inheritance

Mutation

Diagnosis

Onset

Replication studies

References

ALS9

14q11.1

ANG

Angiogenin / Ribonuclease

Candidate Gene Association, Sanger

AD, sporadic

SNP, SNV

ALS, ALS-FTD, PDAdultYes[1-3]ALS116q21FIG4SAC1 lipid phosphatase domain containing (S. cerevisiae) / polyphosphoinositide phosphataseSangerAD, sporadicSNVALS, PLS, CMTAdultNo[4]ALS1210p13OPTNOptineurin / ocular tension, membrane and vesicle traffickingHomozygosity mapping, SangerAD/ARSNVALS, POAGAdultYes[5]ALS1312q24.12ATXN2ataxin 2 / ribosomal mRNA translation Repeat associationsporadicCAG repeatALS, SCA2AdultYes[6] 2p13.1DCTN1Dynactin / axonal transportSangerADSNVALSAdultYes[7]ALS173p11.2CHMP2BChromatin Modifying Protein 2B /SangerAD, sporadicSNVALS, FTDAdultYes[8] 7q36.2DPP6Dipeptidyl-peptidase 6 / GWASsporadicSNPALSAdultYes[9, 10] 6p21.1VEGFVascular Endothelial Growth Factor / angiogenic, vascular, growth, migration & apoptosis factorGene AssociationsporadicSNPALSAdultNo[11] 19p13.12UNC13AUnc-13 Homolog A / GWASsporadicSNPALSAdultYes[12, 13] 22q12.1-q13.1NEFHneurofilament, heavy polypeptide / intracellular transport to axons and dendritesSangersporadicSNVALSAdultNo[14] 12q13.12PRPHPeripherin / cytoskeletal proteinSangerAD, sporadicSNVALSAdultYes[15] 5q35.3SQSTM1sequestosome 1 /scaffold protein, NFKB signaling pathwaySangerAD, sporadicSNVALS, FTDAdultYes[16] 17q12TAF15TATA box binding protein (TBP)-associated factor / RNA polymerase II gene transcriptionSangerADSNVALSAdultYes[17] 8p21.1ELP3elongator acetyltransferase complex subunit 3 / transcript elongationCandidate Gene AssociationsporadicSNPALSAdultYes[18] 5q13.2SMN1survival of motor neuron 1QPCRAD, sporadicCNVALSAdultYes[19] 7q21.3PON1,2,3Paraoxonase / organophosphate hydrolysisCandidate Gene AssociationsporadicSNP, SNVALSAdultYes[20] 6p22.1HFEHemochromatosis / iron absorptionSangersporadic

SNV

ALS

AdultYes

[

21

]

1q24.2

KIFAP3

kinesin-associated protein 3 / small G protein

GWAS

sporadic

SNP

ALS

Adult

Yes

[22] 14q11.2APEX1APEX nuclease 1 / Apurinic/apyrimidinic endonucleaseCandidate Gene AssociationsoradicSNPALSAdultNo[1] 17q21.31PGRNProgranulin / cell growth regulatorSangersporadicSNVALS, FTLDAdultYes[23] 5q13.2ARHGEF28rho guanine nucleotide exchange factor 28SangerADSNVALSAdultNo[24]

Percentage of ALS genetically explained

Nat Neurosci. 2014 Jan; 17(1): 17–23.

New genes 2015 and up

Locus

Chromosome

Gene ID

Gene Name/Function

Evidence

Inheritance

Mutation

Diagnosis

Onset

Replication studies

References

4q33

NEK1

NIMA-Related Kinase 1

Exome gene-burden

unknown

unknownALSAdultYes(1) 12q14.2TBK1TANK-Binding KinaseExome-gene burdenFamilial/SporadicSNVFTD/ALSAdultYes(2)ALS215q31.2MATR3Matrin-3ExomeFamilial/SporadicSNVALSAdultYes(3) 16p13.3CCNFCyclin FLinkageFamilial/SporadicSNVFTD/ALSAdultNo(4) 21q22.3C21ORF2Chromosome 21 Open Reading Frame 2 GWASunknownunknownunknownunknownNo(5) 3p22.1MOBPMyelin-Associated Oligodendrocyte Basic ProteinGWASunknownunknownunknownunknownNo(5) 14q12SCFD1Sec1 Family Domain Containing 1GWASunknownunknownunknownunknownNo(5)ALS192q34ERBB4Tyrosine Kinase-Type Cell Surface Receptor HER4LinkageSporadicSNVALSunknownYes(6) 9q34.11GLE1Homolog of S. Cerevisiae GLE1Sanger/ExomeunknownSNVALSunknownNo(7) 2p13TIA1T cell-restricted intracellular antigen-1Exome-gene burdenFamilialSporadicSNVFTD/ALSAdultNo( ) 10q23.1ANXA11Annexin A11Exome-gene burdenFamilialSporadicSNVALSAdultNo( )*****Aggregation tests termed as burden tests collapse information for multiple genetic variants into a single genetic score and test for association between this score and a trait. A simple approach summarizes genotype information by comparing the number of minor alleles (˂ 1%) across all variants in the sequencing data of multiple cases and controls.

Growing percentage of SALS genetically explained

Nat Neurosci. 2014 Jan; 17(1): 17–23.

17 %

Neurology 2017;89:226-233

A rapidly increasing number of ALS genes

Bettencourt

& Houlden, Nat Neuroscience 2015

Rate of ALS gene Discovery

2017

Rate of new gene discovery has reached a plateau despite increased sequencing efforts

>100 ALS genes?

C21ORF2 UNC13A

MOBP TIA1

SCFD1 ANXA11

CCNF

Rate of gene discovery“Plateau” StageSeveral candidate genes without strong evidenceFunctional relevance unknownLimit reached for current technologies

Require larger cohorts to detect small effect sizesDeep phenotyping and extreme phenotypesNew directions: Large consortia (MinE)Whole genome sequencingRare and small structural variantsEpigenetics

Other themes tested for ALS GeneticsOligogenicityPossibility that ALS is caused by two (or more) variants concurrently that would not independently cause

disease.Studies have observed patients with multiple mutations in “causal” genes.e.g. C9orf72 expansion with an OPTN mutation of unknown pathogenicityDoes severity of disease increase with more ALS mutations?De novo mutationsMutations

can occur in germinal cells, not present in either parentSporadic ALS patients have no family history, but could pass new mutations to children?De novo is not commonly observed in genetic studies, not a common cause of ALS

Thank you!

patrick.a.dion@mcgill.ca