Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family
Abstract
:1. Introduction
2. Materials and Methods
2.1. The SCA1 Family with a Member Affected by ALS
2.2. DNA Extraction
2.3. Targeted Next-Generation Sequencing and Data Processing
2.4. Variant Prioritization and Assessment of Pathogenicity
2.5. NeuroArray aCGH Processing and Data Analysis
2.6. CNV Validation
2.7. Functional Enrichment Analysis of the CNV-Associated Gene Sets
2.8. Genomic Scale Profiling of ALS by Whole-Exome Sequencing
2.9. Visualization of the Protein–Protein Interaction Network
3. Results
3.1. Identification of Potentially Disease-Causing Sequence Variants in ALS Associated Genes
3.2. Identification of Copy Number Variants Related to ALS Phenotype
3.3. Functional and Pathway Enrichment Analysis of CNV-Driven Genes Identified Disease-Specific Molecular Signatures
3.4. WES-Based Mutation Profile Confirms the Functional Impact of Axon Guidance, Cell Adhesion and Immune Response in ALS
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ALS | amyotrophic lateral sclerosis |
ATXN-1 | ataxin-1 |
ATXN-2 | ataxin-2 |
ATXN-3 | Ataxin 3 |
ATXN7 | Ataxin 7 |
ATXN2L | Ataxin 2 Like |
SCA1 | spinocerebellar ataxia type I |
SCA2 | spinocerebellar ataxia type II |
aCGH | comparative genomic hybridization array |
WES | whole-exome sequencing |
NGS | next-generation sequencing |
SOD1 | Cu/Zn superoxide dismutase-1 |
FUS | fused in sarcoma/translocated in liposarcoma |
TARDBP/TDP-43 | transactive response DNA binding protein 43 kDa |
C9ORF72 | chromosome 9 open reading frame 72 |
ANG | Angiogenin |
SNV | single-nucleotide variant |
CNV | copy number variant |
MN | motor neuron |
CSF | cerebrospinal fluid |
MRI | magnetic resonance imaging |
EMG | Electromyography |
MUPs | motor unit potentials |
PSWs | positive sharp waves |
DSF | disease-free survival |
Cy5 | cyanine 5 |
Cy3 | cyanine 3 |
dUTP | deoxyuridine triphosphate |
ADM-2 | aberration detection method II algorithm |
FDR | Flase Discovery Rate |
CNVD | Copy Number Variation in Disease |
ACMG | American College of Medical Genetics |
DGV | Database of Genomic Variants |
UTR | untranslated region |
ncRNA | non coding RNA |
LoF | loss-of-function |
MAF | minor allele frequency |
EVS | Exome Variant Server |
HGMD | Human Gene Mutation Database |
LOVD | Leiden Open Variation Database |
OMIM | Online Mendelian Inheritance in Man |
GO | Gene Ontology |
BP | biological process |
MF | molecular function |
CC | Cellular Component |
PPI | protein–protein interaction |
SCN1A | sodium voltage-gated channel alpha subunit 1 |
WRN | Werner syndrome ATP-dependent helicase |
LPA | Lipoprotein(A) |
SCN7A | sodium voltage-gated channel alpha subunit 7 |
EPHA3 | Ephrin type-A receptor 3 |
EPHA1 | Ephrin type-A receptor 1 |
EPHA2 | Ephrin type-A receptor 2 |
EPHA4 | Ephrin type-A receptor 4 |
EPHA5 | Ephrin type-A receptor 5 |
EPHA6 | Ephrin type-A receptor 6 |
EPHB1 | Ephrin type-B receptor 1 |
EPHX1 | Epoxide Hydrolase 1 |
CHMP2B | Charged Multivesicular Body Protein 2B |
MAPT | Microtubule Associated Protein Tau |
VPS54 | Vacuolar Protein Sorting-Associated Protein 54 |
TTN | Titin |
AHR | Aryl Hydrocarbon Receptor |
NSF | N-Ethylmaleimide Sensitive Factor, Vesicle Fusing ATPase |
ARL13B | ADP Ribosylation Factor Like GTPase 13B |
MNVs | Multiple nucleotide variants |
INDEL | Insertion/Deletion |
CAPN2 | Calpain 2 |
DCC | DCC netrin 1 receptor |
LRRK1 | Leucine Rich Repeat Kinase 1 |
MMRN1 | Multimerin 1 |
NOS2 | Nitric Oxide Synthase 2 |
ARSB | Arylsulfatase B |
TMEM216 | Transmembrane Protein 216 |
LRP2 | LDL Receptor Related Protein 2 |
NOTCH4 | Notch Receptor 4 |
PCK1 | Phosphoenolpyruvate Carboxykinase 1 |
TNK1 | Tyrosine Kinase Non Receptor 1 |
CNTN4 | Contactin 4 |
DIAPH3 | Diaphanous Related Formin 3 |
CDH13 | Cadherin 13 |
DYNC1H1 | Dynein Cytoplasmic 1 Heavy Chain 1; |
CPZ | Carboxypeptidase Z |
NEFH | Neurofilament Heavy |
TRPM7 | Transient Receptor Potential Cation Channel Subfamily M Member 7 |
VPS26A | Vacuolar Protein Sorting-Associated Protein 26, Retromer Complex Component A |
KIF1A | Kinesin Family Member 1A |
CYP2D6 | Cytochrome P450 Family 2 Subfamily D Member 6 |
GLE1 | GLE1 RNA Export Mediator |
SETX | Senataxin |
TAF15 | TATA-Box Binding Protein Associated Factor 15 |
ALS2 | Alsin Rho Guanine Nucleotide Exchange Factor ALS2 |
CCNF | Cyclin F |
PFN1 | Profilin 1 |
CEP112 | Centrosomal Protein 112 |
VAPB | Vesicle-Associated Membrane Protein Associated Protein B and C |
AVS | ALS variant server |
DPYD | Dihydropyrimidine Dehydrogenase |
SNARE | soluble NSF attachment protein receptor |
MATR3 | Matrin 3 |
ERBB4 | Erb-B2 Receptor Tyrosine Kinase 4 |
NEK1 | NIMA Related Kinase 1 |
OPTN | Optineurin |
SQSTM1 | Sequestosome 1 |
TBK1 | TANK Binding Kinase 1 |
TUBA4A | Tubulin Alpha 4a |
VCP | Valosin Containing Protein |
VEGFA | Vascular Endothelial Growth Factor A |
RPS27A | Ribosomal Protein S27a |
UBA52 | Ubiquitin A-52 Residue Ribosomal Protein Fusion Product 1 |
UBC | Ubiquitin C |
UBB | Ubiquitin B |
ANO2 | Anoctamin 2 |
CHCHD10 | Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 10 |
ELAVL4 | Embryonic Lethal, Abnormal Vision, Drosophila (ELAV)-Like 4 |
GRIN1 | Glutamate Ionotropic Receptor NMDA Type Subunit 1 |
NMDA | N-methyl-D-aspartate |
ZNF280A | Zinc Finger Protein 280A |
C22orf46 | Chromosome 22 Open Reading Frame 46 |
APEH | Acylaminoacyl-Peptide Hydrolase |
MST1 | Macrophage Stimulating 1 |
DCHS2 | Dachsous Cadherin-Related 2 |
FAT1 | FAT Atypical Cadherin 1 |
BACE1 | Beta-Secretase 1 |
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Genotype | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chr | Pos | Reference | Gene Symbol | Variant Class | Exonic | AA Change (Reference Gene) | ExAC_Freq | dbSNP | Polyphen/SIFT Prediction | IV-19 (ALS) | IV-15 (SCA1-MN) | V-4 (SCA1-MN) | V-26 (SCA1) |
2 | 202626479 | T | ALS2 | nonsynonymous SNV | 4 | p.Ser80Arg (NM_00113574) | . | . | Damaging/Pathogenic | T/G | T/G | - | - |
16 | 2498978 | G | CCNF | nonsynonymous SNV | 10 | p.Arg406Gln (NM_001323538) | 0.00 | rs146438723 | Damaging/Pathogenic | G/A | G/A | - | G/A |
22 | 29885908 | A | NEFH | nonsynonymous SNV | 4 | p.Asp760Gly (NM_021076) | . | . | Damaging/Pathogenic | A/G | A/G | - | - |
4 | 170428901 | C | NEK1 | nonsynonymous SNV | 22 | p.Ala626Thr (NM_001199397.1) | 0.05 | rs33933790 | Damaging/Pathogenic | C/T | - | C/T | - |
9 | 135204010 | T | SETX | nonsynonymous SNV | 10 | p.Lys992Arg (NM_001351527) | 0.02 | rs61742937 | Damaging/Pathogenic | T/C | - | T/C | - |
17 | 34171599 | - | TAF15 | frameshift insertion | 15 | p.Ser433fs (NM_139215) | . | . | Damaging/Pathogenic | C/CG | - | - | - |
Chr | Start | Stop | Probes | Log2 Ratio (Test/Control) | p-Value | Gene | Common CNV (DGV Frequency) | qPCR Validation | Clinical Interpretation | Detected in SCA1-MN Family Members (Patient Code) |
---|---|---|---|---|---|---|---|---|---|---|
1 | 98,164,881.00 | 98,187,177.00 | 6 | −0.63967 | 1.54 × 10−10 | DPYD | Yes (0.005–0.04%) | Likely pathogenic | No | |
2 | 64,146,992 | 64,211,176.00 | 25 | −0.3406 | 5.01 × 10−13 | VPS54 | Yes (0.003%) | X | Likely pathogenic | Yes (IV-18 *, IV-13, IV-15) |
2 | 166,852,501 | 166,870,328.00 | 14 | −0.5323 | 4.49 × 10−14 | SCN1A | Not | Likely pathogenic | No | |
2 | 166,911,120 | 166,913,035.00 | 5 | −0.67504 | 5.51 × 10−11 | SCN1A | Yes (0.1%) | Likely pathogenic | No | |
2 | 167,328,904 | 167,334,011.00 | 6 | −0.75482 | 4.24 × 10−11 | SCN7A | Yes (0.005–1%) | X | Likely pathogenic | No |
2 | 179,536,740 | 179,540,750.00 | 9 | −0.57381 | 1.35 × 10−10 | TTN | Yes (0.4%) | Likely pathogenic | No | |
3 | 87,299,007 | 89,814,870.00 | 10 | −0.45231 | 1.51 × 10−10 | CHMP2B, EPHA3 | Yes (0.003–1%) | X | Uncertain clinical significance | No |
3 | 93,772,085 | 113,652,487.00 | 20 | −0.28537 | 4.68 × 10−11 | ARL13B | Yes (0.006–0.03%) | Uncertain clinical significance | No | |
6 | 161,026,135 | 161,067,305.00 | 17 | 0.477799 | 2.80 × 10−21 | LPA | Yes (>70%) | Likely benign | No | |
7 | 17,362,101 | 17,375,411.00 | 12 | −0.64847 | 3.43 × 10−22 | AHR | Yes (0.0034–0.04%) | Likely pathogenic | Yes (IV-13) | |
8 | 30,947,985 | 30,999,316.00 | 23 | −0.30766 | 1.60 × 10−11 | WRN | Not | Likely pathogenic | No | |
9 | 27,558,554 | 27,573,862.00 | 13 | −0.39928 | 2.08 × 10−11 | C9orf72 | Not | X | Likely pathogenic | No |
10 | 70,892,631 | 70,931,418.00 | 15 | −0.36405 | 4.32 × 10−10 | VPS26A | Yes (>10%) | Likely benign | No | |
17 | 44,301,037 | 44,771,900.00 | 16 | −0.61264 | 4.50 × 10−29 | NSF | Yes | X | Likely benign | Yes (IV-18, IV-13, IV-15) |
21 | 38,791,571 | 38,865,493.00 | 15 | −0.35809 | 8.53 × 10−11 | DYRK1A | Yes (0.003–5%) | Uncertain clinical significance | Yes (IV-13) | |
X | 108,902,635 | 108,906,573.00 | 6 | −0.73236 | 5.03 × 10−10 | ACSL4 | Yes (2%) | Likely benign | No |
GO Biological Processes | ALS | SCA IV-18 | SCA IV-13 | SCA IV-15 |
growth | ||||
vacuolar transport | ||||
circadian rhythm | ||||
peptidyl-tyrosine modification, phosphorylation | ||||
regulation of hydrolase activity | ||||
cell morphogenesis | ||||
regulation of endocytosis | ||||
regulation of growth rate | ||||
lysosomal transport | ||||
membrane depolarization during action potential | ||||
regulation of microtubule cytoskeleton organization | ||||
neuronal action potential | ||||
regulation of microtubule-based process | ||||
endosomal transport | ||||
Golgi vesicle transport | ||||
autophagy | ||||
regulation of microtubule cytoskeleton organization | ||||
Pathway Name | ALS | SCA IV-18 | SCA IV-13 | SCA IV-15 |
Interaction between L1 and Ankyrins | ||||
Phase 0 - rapid depolarization | ||||
Retrograde transport at the Trans-Golgi-Network | ||||
Muscle contraction | ||||
L1CAM interactions | ||||
Cardiac conduction | ||||
Intra-Golgi and retrograde Golgi-to-ER traffic | ||||
Axon guidance | ||||
Membrane Trafficking | ||||
Fatty acid, triacylglycerol, and ketone body metabolism | ||||
Endocytosis | ||||
Vesicle-mediated transport |
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Share and Cite
Morello, G.; Gentile, G.; Spataro, R.; Spampinato, A.G.; Guarnaccia, M.; Salomone, S.; La Bella, V.; Conforti, F.L.; Cavallaro, S. Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family. J. Pers. Med. 2020, 10, 262. https://doi.org/10.3390/jpm10040262
Morello G, Gentile G, Spataro R, Spampinato AG, Guarnaccia M, Salomone S, La Bella V, Conforti FL, Cavallaro S. Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family. Journal of Personalized Medicine. 2020; 10(4):262. https://doi.org/10.3390/jpm10040262
Chicago/Turabian StyleMorello, Giovanna, Giulia Gentile, Rossella Spataro, Antonio Gianmaria Spampinato, Maria Guarnaccia, Salvatore Salomone, Vincenzo La Bella, Francesca Luisa Conforti, and Sebastiano Cavallaro. 2020. "Genomic Portrait of a Sporadic Amyotrophic Lateral Sclerosis Case in a Large Spinocerebellar Ataxia Type 1 Family" Journal of Personalized Medicine 10, no. 4: 262. https://doi.org/10.3390/jpm10040262