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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 Neurosurgery
McGill University
Human Genome Basics• 3 billions base pairs.
• Contains protein-coding and noncoding DNA.
• 19,000-20,000 protein-coding genes (2% of the genome).
o 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.
o Available through various databases (e.g. 1kGP, ExaC, EVS).
o Regardless of race we are 99.9% identical at the genome level.
Human Genome Basics• Distinctive markers exist all across the genome.
o [Large] RFLP, tandem repeat, Copy Number Variants (CNVs)
o [Small] Single nucleotide polymorphisms (SNPs).
• SNPs are common variants found in >1% of the
population at 1,000 bp across.
o When in coding regions SNPs can be synonymous or
nonsynonymous.
• Distinction between SNPs and single nucleotide variants
(SNVs).
Discovery Approaches• Classical linkage analysis
• Candidate genes association
• Genome Wide Association Study (GWAS)o Use of common variants to identify regions shared by affected.
• Whole Exome Sequencing (WES)o Seeks to filter rare coding variants to identify to identify deleterious ones.
o No need for controls except when population specific.
• Whole Genome Sequencing (WGS)o 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 SALS• Overall ALS is the most common rare disease (2/100,00).
• FALS (familial)
o 5-10% of cases of ALS
o Primarily autosomal dominant (AD) segregation of definite,
probable or possible individuals.
• SALS (sporadic)
o No family history
• Clinically indistinguishable
o Except age of onset and sex distribution
• This classification should not overshadow the fact that
FALS and SALS DO share common genetic causes.
o Moreover environmental/stochastic factors can affect
genetically susceptible individuals.
Just how many ALS genes are there?
• http://alsod.iop.kcl.ac.uk/home.aspx
o 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 GenesLocus
Chromosome
Gene ID Protein/Function EvidenceInheritance
Mutation
Diagnosis OnsetReplication studies
References
ALS1 21q22.11 SOD1Cu/Zn superoxide dismutase 1, soluble / Oxidative stress
Linkage, Sanger AD, AR SNV ALS, PMA Adult Yes [1]
ALS2 2q33.2 ALS2Alsin / Rho guanine nucleotide exchange factors
Linkage, Sanger AR SNVALS, PLS, HSP
Juvenile Yes [2, 3]
ALS4 9q34.13 SETXSenataxin / RNA/DNA Helicase
Linkage, Sanger AD SNVALS, AOA2
Juvenile Yes [4]
ALS5 15q21.1 SPG11Spatacsin / transmembrane protein
Linkage, Sanger AR SNV ALS, HSP Juvenile Yes [5, 6]
ALS6 16p11.2 FUSFused in Sarcoma / RNA-binding protein, DNA repair, exon splicing
Linkage, Sanger AD SNVALS, ALS-FTD
Adult Yes [7, 8]
ALS7 20p13 Unknown Unknown Linkage AD - ALS Adult No [9]
ALS8 20q13.33 VAPB
Vesicle-associated membrane protein-associated protein B / Vesicular trafficking
Linkage, Sanger AD SNV ALS, SMA Adult Yes [10, 11]
ALS10 1p36.22 TARDBP
TAR DNA binding protein 43 / transcriptional repressor, splicing regulation
Linkage, Sanger AD SNVALS, ALS-FTD
Adult Yes [12, 13]
ALS14 9p13.3 VCP
valosin-containing protein / ATP-binding protein, vesicle transport and fusion
WES, linkage, Sanger
AD SNVALS, ALS-FTD, FTD, IBMPFD
Adult Yes [14]
ALS15 Xp11.21 UBQLN2ubiquilin 2 / ubiquitination, degradation
Linkage, Sanger X-linked SNVALS, ALS-FTD
Juvenile,Adulte
Yes [15]
ALS16 9p13.3 SIGMAR1
sigma non-opioid intracellular receptor 1 / endoplasmic reticulum chaperone
Homozygosity mapping, Sanger
AR SNV ALS, FTD Juvenile No [15]
12q24.11 DAOD-amino-acid oxidase / unknown
Linkage, Sanger AD SNV ALS Adult No [16]
ALS17 17p13.2 PFN1profilin 1 / actin binding protein, actin polymerization
Linkage, WES, Sanger
AD SNV ALS Adult Yes [17]
ALS207p15.2/12q13.3
hnRNPA2B1/A1
Heterogenous nuclear ribonucleoprotein / mRNA processing, metabolism & transport
Linkage, WES, Sanger
AD SNVALS, IBMPFD
Adult No [18]
ALS-FTD1
9q21-q22 Unknown Unknown Linkage AD SNVALS, ALS-FTD, FTD
Adult No [19]
ALS-FTD2
9p21.2 C9ORF72chromosome 9 open reading frame 72 / Unknown
Linkage, GWAS, RP-PCR, Southern Blot
AD, sporadic
1G4C2
repeatALS, ALS-FTD, FTD
Adult Yes [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.
o All dominant except for D90A and D96N, recessive in some cases
o Some mutations affect survival time: • A4V rapid progression D90A slow progression
o Some affect disease onset:• G37R with early onset
o 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.o 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).
o Autosomal dominant and recessive.
o Age of onset younger (< 40yrs with cases during teens).
o Faster progression than TARDBP and SOD1 cases
• > 50 Missense and one truncating variants.o 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).
o >30 repeats pathogenic, 15-30 not very pathogenic but recently observed to be
with ATXN2 intermediate CAG expansion.
o Both gain and loss of functions are under consideration.
o 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 GenesLocus Chromosome Gene ID Gene Name/Function Evidence
Inheritance
Mutation Diagnosis OnsetReplication studies
References
ALS9 14q11.1 ANG Angiogenin / Ribonuclease
Candidate Gene Association, Sanger
AD, sporadic
SNP, SNVALS, ALS-FTD, PD
Adult Yes [1-3]
ALS11 6q21 FIG4
SAC1 lipid phosphatase domain containing (S. cerevisiae) / polyphosphoinositide phosphatase
SangerAD, sporadic
SNVALS, PLS, CMT
Adult No [4]
ALS12 10p13 OPTNOptineurin / ocular tension, membrane and vesicle trafficking
Homozygosity mapping, Sanger
AD/AR SNV ALS, POAG Adult Yes [5]
ALS13 12q24.12 ATXN2ataxin 2 / ribosomal mRNA translation
Repeat association
sporadic CAG repeat ALS, SCA2 Adult Yes [6]
2p13.1 DCTN1 Dynactin / axonal transport Sanger AD SNV ALS Adult Yes [7]
ALS17 3p11.2 CHMP2B Chromatin Modifying Protein 2B / SangerAD, sporadic
SNV ALS, FTD Adult Yes [8]
7q36.2 DPP6 Dipeptidyl-peptidase 6 / GWAS sporadic SNP ALS Adult Yes [9, 10]
6p21.1 VEGF
Vascular Endothelial Growth Factor / angiogenic, vascular, growth, migration & apoptosis factor
Gene Association
sporadic SNP ALS Adult No [11]
19p13.12 UNC13A Unc-13 Homolog A / GWAS sporadic SNP ALS Adult Yes [12, 13]
22q12.1-q13.1 NEFHneurofilament, heavy polypeptide / intracellular transport to axons and dendrites
Sanger sporadic SNV ALS Adult No [14]
12q13.12 PRPH Peripherin / cytoskeletal protein SangerAD, sporadic
SNV ALS Adult Yes [15]
5q35.3 SQSTM1sequestosome 1 /scaffold protein, NFKB signaling pathway
SangerAD, sporadic
SNV ALS, FTD Adult Yes [16]
17q12 TAF15TATA box binding protein (TBP)-associated factor / RNA polymerase II gene transcription
Sanger AD SNV ALS Adult Yes [17]
8p21.1 ELP3elongator acetyltransferase complex subunit 3 / transcript elongation
Candidate Gene Association
sporadic SNP ALS Adult Yes [18]
5q13.2 SMN1 survival of motor neuron 1 QPCRAD, sporadic
CNV ALS Adult Yes [19]
7q21.3 PON1,2,3Paraoxonase / organophosphate hydrolysis
Candidate Gene Association
sporadic SNP, SNV ALS Adult Yes [20]
6p22.1 HFEHemochromatosis / iron absorption
Sanger sporadic SNV ALS Adult Yes [21]
1q24.2 KIFAP3kinesin-associated protein 3 / small G protein
GWAS sporadic SNP ALS Adult Yes [22]
14q11.2 APEX1APEX nuclease 1 / Apurinic/apyrimidinic endonuclease
Candidate Gene Association
soradic SNP ALS Adult No [1]
17q21.31 PGRNProgranulin / cell growth regulator
Sanger sporadic SNV ALS, FTLD Adult Yes [23]
5q13.2 ARHGEF28rho guanine nucleotide exchange factor 28
Sanger AD SNV ALS Adult No [24]
Percentage of ALS genetically explained
Nat Neurosci. 2014 Jan; 17(1): 17–23.
New genes 2015 and upLocus Chromosome Gene ID Gene Name/Function Evidence
Inheritance
Mutation Diagnosis OnsetReplication studies
References
4q33 NEK1 NIMA-Related Kinase 1Exome gene-burden
unknown
unknown ALS Adult Yes (1)
12q14.2 TBK1 TANK-Binding KinaseExome-gene burden
Familial/Sporadic
SNV FTD/ALS Adult Yes (2)
ALS21 5q31.2 MATR3 Matrin-3 ExomeFamilial/Sporadic
SNV ALS Adult Yes (3)
16p13.3 CCNF Cyclin F LinkageFamilial/Sporadic
SNV FTD/ALS Adult No (4)
21q22.3 C21ORF2Chromosome 21 Open Reading Frame 2
GWASunknown
unknown unknownunknown
No (5)
3p22.1 MOBPMyelin-Associated Oligodendrocyte Basic Protein
GWASunknown
unknown unknownunknown
No (5)
14q12 SCFD1 Sec1 Family Domain Containing 1 GWASunknown
unknown unknownunknown
No (5)
ALS19 2q34 ERBB4Tyrosine Kinase-Type Cell Surface Receptor HER4
Linkage Sporadic SNV ALSunknown
Yes (6)
9q34.11 GLE1 Homolog of S. Cerevisiae GLE1Sanger/Exome
unknown
SNV ALSunknown
No (7)
2p13 TIA1T cell-restricted intracellular antigen-1
Exome-geneburden
FamilialSporadic
SNV FTD/ALS Adult No ( )
10q23.1 ANXA11 Annexin A11Exome-gene burden
FamilialSporadic
SNV ALS Adult No ( )
*
*
*
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*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 TIA1SCFD1 ANXA11CCNF
Rate of gene discovery• “Plateau” Stage
o Several candidate genes without strong evidence
o Functional relevance unknown
• Limit reached for current technologieso Require larger cohorts to detect small effect sizes
• Deep phenotyping and extreme phenotypes
• New directions: • Large consortia (MinE)
• Whole genome sequencing
• Rare and small structural variants
• Epigenetics
Other themes tested for ALS Genetics
• Oligogenicityo Possibility that ALS is caused by two (or more) variants concurrently that
would not independently cause disease.
o Studies have observed patients with multiple mutations in “causal” genes.
• e.g. C9orf72 expansion with an OPTN mutation of unknown
pathogenicity
o Does severity of disease increase with more ALS mutations?
• De novo mutationso Mutations can occur in germinal cells, not present in either parent
• Sporadic ALS patients have no family history, but could pass new
mutations to children?
o De novo is not commonly observed in genetic studies, not a common
cause of ALS
Thank [email protected]
