| Literature DB >> 32095376 |
Shi Chen1,2,3,4,5, Mengqi Li1,3,4, Wenqiang Xin1,3,4, Shengze Liu2, Linfei Zheng2, Yan Li6, Mengyao Li7, Mengxiong Zhan2, Xinyu Yang1,3,4.
Abstract
PURPOSE: The development of intracranial aneurysm (IA) has been linked to genetic factors. The current study examines the potential role of genes encoding disintegrin and metalloproteinase using thrombospondin motifs (ADAMTS) in IA development.Entities:
Keywords: ADMTSL1; Bioinformatics; Hemorrhagic stroke; Single-nucleotide variants
Year: 2020 PMID: 32095376 PMCID: PMC7025701 DOI: 10.7717/peerj.8596
Source DB: PubMed Journal: PeerJ ISSN: 2167-8359 Impact factor: 2.984
Figure 1Discovery corhort and imaging diagnosis.
(A–L) Diagrams showing 20 cases of intracranial aneurysm (IA), collected from 11 pedigrees. (M-FF) Imaging diagnosis: Digital subtraction angiography (DSA) or computed tomography angiography (CTA) images of 20 Han Chinese IA patients in this study.
Prediction of single-nucleotide variations (SNVs) related to intracranial aneurysm.
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| G | A | Ser >Leu | ADAMTS4 | exonic | 0.144,T | 0.994,D | 4.34 | 14.88 |
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| A | T | Leu >Pro | ADAMTS12 | exonic | 0.0,D | 1.000,D | 5.57 | 22.0 |
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| G | C | Pro >Ala | ADAMTS6 | exonic | 0.059,T | 1,D | 4.86 | 16.94 |
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| C | T | Gly >Ser | ADAMTS2 | exonic | 0.107,T | 0.951,D | 4.72 | 22.9 |
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| C | T | Val >Met | ADAMTS2 | exonic | 0.087,T | 0.989,N | 4.23 | 20.6 |
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| G | A | Asp >Asn | ADAMTSL1 | exonic | 0.479,T | 0.978,D | 5.77 | 18.75 |
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| C | T | Arg >Trp | ADAMTS14 | exonic | 0.103,T | 0.895,D | . | 15.30 |
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| A | T | N/A | ADAMTS8 | splicing | . | . | . | 11.19 |
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| G | C | Glu >Gln | ADAMTS15 | exonic | 0.02,D | 1.000,D | 3.49 | 20.5 |
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| G | A | Arg >Ter | ADAMTS20 | exonic | . | 1,A | 2.86 | 40 |
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| G | A | Thr >Ile | ADAMTS7 | exonic | 0.098,T | 0.968,D | 4.57 | 14.50 |
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| G | A | Thr >Met | ADAMTS7 | exonic | 0.005,D | 0.031,P | 2.85 | 16.30 |
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| G | A | Arg >His | ADAMTSL3 | exonic | 0.005,D | 1.000,D | 5.45 | 25.1 |
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| C | G | Gly >Arg | ADAMTS18 | exonic | 0.0,D | 1.000,D | 5.54 | 28.1 |
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| C | T | Cys >Tyr | ADAMTS18 | exonic | 0.003,D | 0.815,D | 4.23 | 14.96 |
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| G | A | Pro >Leu | ADAMTSL5 | exonic | 0.0,D | 1,D | 4.28 | 19.09 |
Notes.
alternative allele
reference
SIFT score indicates whether the variation is likely to cause changes in protein structure or function: “D”, deleterious (sift ≤ 0.05); “T”, tolerated (sift > 0.05).
MutationTaster predicts the effect of the mutation on the protein sequence: “A”, “disease_causing_automatic”; “D”, “disease_causing”; “N”, “polymorphism”; “P”, ”polymorphism_automatic”.
Variations with a gerp++gt2 score > 2 are considered conservative.
CADD score >15 means that the variation affects protein function.
Deleterious single-nucleotide polymorphisms in ADAMTS genes in patients with intracranial aneurysm.
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| ADAMTS4 | A | A/G=1/19 | T/C=7/244892 | 0.001 | 1,841 | 216 | 15,697 |
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| ADAMTS12 | T | T/A=1/19 | T/A=548/245962 | 0.044 | 24 | 3 | 177 |
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| ADAMTS6 | C | C/G=1/19 | C/G=318/245638 | 0.026 | 41 | 5 | 305 |
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| ADAMTS2 | T | T/C=1/19 | T/C=6/149126 | 0.001 | 1,308 | 150 | 11,391 |
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| ADAMTS2 | T | T/C=1/20 | T/C=409/234580 | 0.034 | 30 | 4 | 226 |
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| ADAMTSL1 | A | A/G=1/20 | A/G=85/245886 | 0.007 | 152 | 20 | 1,150 |
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| ADAMTS14 | T | T/C=3/17 | T/C=1077/246088 | <0.001 | 40 | 11 | 138 |
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| ADAMTS8 | T | T/A=3/17 | T/A=628/245972 | <0.001 | 69 | 20 | 236 |
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| ADAMTS15 | C | C/G=1/19 | C/G=692/235086 | 0.057 | 18 | 2 | 134 |
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| ADAMTS20 | A | A/G=1/19 | A/G=14/220938 | 0.001 | 831 | 104 | 6,635 |
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| ADAMTS7 | A | A/G=1/19 | no data | ||||
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| ADAMTS7 | A | A/G=12/8 | A/G=80464/245590 | 0.12 | 2 | 0.8 | 4.9 |
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| ADAMTSL3 | A | A/G=3/17 | A/G=417/246136 | <0.001 | 104 | 30 | 357 |
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| ADAMTS18 | G | G/C=1/19 | G/C=4/245924 | <0.001 | 3,236 | 346 | 30,303 |
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| ADAMTS18 | T | T/C=1/19 | T/C=6/171256 | 0.001 | 1,502 | 173 | 13,081 |
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| ADAMTSL5 | A | A/G=1/19 | A/G=103/213450 | 0.01 | 109 | 14 | 822 |
Notes.
confidence interval
genome aggregation database
odds ratio
single-nucleotide polymorphism identification
ADAMTS genes differentially expressed between individuals with intracranial aneurysm and controls.
| 2.88 × 10−4 | <0.001 | 5.433435 | 3.296323 | |
| 2.63 × 10−3 | <0.001 | 4.393505 | 2.777007 | |
| 1.58 × 10−5 | <0.001 | 6.82637 | 1.786802 | |
| 5.44 × 10−3 | <0.001 | 4.049965 | 1.650133 | |
| ADAMTS9 | 1.38 × 10−1 | 0.026 | 2.330043 | 1.404467 |
| ADAMTS15 | 1.21 × 10−1 | 0.022 | 2.411667 | 1.096499 |
| ADAMTS4 | 2.04 × 10−1 | 0.047 | 2.063526 | 0.751622 |
| ADAMTSL4 | 1.58 × 10−1 | 0.032 | 2.241619 | 0.708539 |
| ADAMTSL1 | 1.42 × 10−1 | 0.028 | −2.311788 | −0.678263 |
| ADAMTS3 | 1.05 × 10−1 | 0.018 | −2.49951 | −0.76742 |
| ADAMTS17 | 7.83 × 10−2 | 0.012 | −2.67964 | −0.77946 |
| 2.52 × 10−2 | 0.002 | −3.29649 | −1.24966 | |
| ADAMTSL3 | 5.51 × 10−2 | 0.007 | −2.87834 | −1.36329 |
| 3.74 × 10−2 | 0.004 | −3.09323 | −1.44272 | |
| 2.39 × 10−2 | 0.002 | −3.32586 | −1.77612 | |
| 8.23 × 10−9 | 2.86 × 10−12 | −11.0591 | −2.87598 |
Notes.
log fold change
statistic from Student’s t test
The data sourced from GEO database (http://www.ncbi.nlm.nih.gov/geo/GSE75436). Differentially expressed genes identified with multiple correction are shown in bold.
Figure 2Differentially expressed ADAMTS genes and the network of interactions among proteins encoded by the overlapping genes.
(A) Heatmap of differentially expressed ADAMTS genes. Different colors represent different levels of expression. The row above the heatmap corresponds to sample numbers, and the column on the right side of the heatmap corresponds to differentially expressed genes. CA, cerebral artery; IA, intracranial aneurysm. (B) Overlap among ADAMTS genes with deleterious variants (mutant genes), ADAMTS genes differentially expressed (DEGs) in IA, and ADAMTS genes abnormally methylated in IA. Seven genes overlapped among the three sets: ADAMTS15, ADAMTS2, ADAMTS4, ADAMTS7, ADAMTS8, ADAMTSL1, and ADAMTSL3. (C) A network of interactions among proteins encoded by the seven overlapping genes was predicted using String (https://string-db.org/) in order to identify the genes most likely to be relevant to IA. ADAMTSL1 is at the center of this network, suggesting that it acts upstream of the other overlapping genes.
Figure 3Expression of ADAMTSL1 in IA issue and cerebral artery.
(A) Identification of IA tissue based on computed tomography angiography: Patient 1, Patient 2, Patient 3 and Patient 4. Red arrows indicate the location of IA. (B) ADAMTSL1 was expressed at lower levels in IA tissue than in cerebral artery.
SNVs rs11750568 in ADAMSTS2 and rs2301612 and rs2285489 in ADAMSTS13.
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| A | ADD | 0.970 | 0.133 | 0.746 | 1.26 | 0.817 | 1 | 1 |
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| T | ADD | 0.931 | 0.124 | 0.731 | 1.187 | 0.565 | 1 | 1 |
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| G | ADD | 0.958 | 0.15 | 0.765 | 1.2 | 0.710 | 1 | 1 |
Notes.
Multiple-testing correction methods were BONF and FDR_BY.
single- nucleotide variants
Bonferroni single-step adjusted P-values
Benjamini & Yekutieli (2001) step-up FDR control