| Literature DB >> 35328582 |
Natalia Cullell1,2,3,4, Cristina Gallego-Fábrega1, Jara Cárcel-Márquez1,5, Elena Muiño1, Laia Llucià-Carol1, Miquel Lledós1, Jesús M Martín-Campos1, Jessica Molina2, Laura Casas2, Marta Almeria2, Israel Fernández-Cadenas1,2, Jerzy Krupinski2.
Abstract
Small vessel strokes (SVS) and intracerebral haemorrhages (ICH) are acute outcomes of cerebral small vessel disease (SVD). Genetic studies combining both phenotypes have identified three loci associated with both traits. However, the genetic cis-regulation at the protein level associated with SVD has not been studied before. We performed a proteome-wide association study (PWAS) using FUSION to integrate a genome-wide association study (GWAS) and brain proteomic data to discover the common mechanisms regulating both SVS and ICH. Dorsolateral prefrontal cortex (dPFC) brain proteomes from the ROS/MAP study (N = 376 subjects and 1443 proteins) and the summary statistics for the SVS GWAS from the MEGASTROKE study (N = 237,511) and multi-trait analysis of GWAS (MTAG)-ICH-SVS from Chung et al. (N = 240,269) were selected. We performed PWAS and then a co-localization analysis with COLOC. The significant and nominal results were validated using a replication dPFC proteome (N = 152). The replicated results (q-value < 0.05) were further investigated for the causality relationship using summary data-based Mendelian randomization (SMR). One protein (ICA1L) was significantly associated with SVS (z-score = -4.42 and p-value = 9.6 × 10-6) and non-lobar ICH (z-score = -4.8 and p-value = 1.58 × 10-6) in the discovery PWAS, with a high co-localization posterior probability of 4. In the validation PWAS, ICA1L remained significantly associated with both traits. The SMR results for ICA1L indicated a causal association of protein expression levels in the brain with SVS (p-value = 3.66 × 10-5) and non-lobar ICH (p-value = 1.81 × 10-5). Our results show that the association of ICA1L with SVS and non-lobar ICH is conditioned by the cis-regulation of its protein levels in the brain.Entities:
Keywords: PWAS; genome-wide association study (GWAS); intracerebral haemorrhage; proteome-wide association study; small vessel disease; small vessel stroke
Mesh:
Substances:
Year: 2022 PMID: 35328582 PMCID: PMC8951240 DOI: 10.3390/ijms23063161
Source DB: PubMed Journal: Int J Mol Sci ISSN: 1422-0067 Impact factor: 5.923
PWAS results for the stringent criteria. Significant PWAS associations using the stringent criteria in the discovery and replication. P0–P1: initial-final position for the analysed protein; pQTL ID: ID for the pQTL strongly associated with ICA1L; pQTL z-score: z-score for the pQTL strongly associated with ICA1L; pQTL z-score: z-score in the correspondent GWAS for the best pQTL; NSNP: number of SNPs in the locus; TWAS z-score: z-score for the PWAS association; PWAS p-value: p-value for the PWAS association; PP4: posterior probability 4 in the COLOC analysis; q-value: FDR-adjusted PWAS p-value.
| Discovery | Replication | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Trait | Protein | Chr | P0–P1 | pQTL ID | pQTL z-Score | pQTL GWAS z-Score | NSNP | PWAS z-Score | PWAS | PP4 | PWAS z-Score | PWAS | PP4 | ||
| SVS | ICA1L | 2 | 203640690 | rs7582720 | 7.21 | −4.426 | 81 | −4.43 | 9.60 × 10−6 | 0.90 | 1.42 × 10−2 | −3.55 | 3.91 × 10−4 | 0.99 | 5.08 × 10−3 |
| Non-lobar ICH | −4.801 | −4.80 | 1.58 × 10−6 | 0.93 | 2.33 × 10−3 | −4.07 | 4.76 × 10−5 | 0.99 | 6.19 × 10−4 | ||||||
SMR results.
| Trait | Protein | b_SMR | p_SMR |
|---|---|---|---|
| SVS | ICA1L | −2.78 | 3.66 × 10−5 |
| SVS | SPATA20 | −0.24 | 3.69 × 10−1 |
| ICH | ICA1L | −1.55 | 1.81 × 10−5 |
| Non-lobar ICH | ICA1L | −1.55 | 1.81 × 10−5 |
| Lobar ICH | SPATA20 | −0.05 | 7.98 × 10−1 |
Figure 1Significant SMR results for the significant and replicated PWAS results.Each “x” in figure represents a pQTL for ICA1L.
Figure 2GWAS results before conditioning by ICA1L levels (grey) or after conditioning by protein levels (blue).
PWAS results for the open criteria. The results for the discovery and replication of PWAS associations for proteins with a nominal p-value in the discovery (open criteria).
| Discovery | Replication | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Trait | Protein | Chr | pQTL ID | pQTL z-Score | pQTL GWAS z-Score | NSNP | PWAS z-Score | PWAS | PP4 | PWAS Z-Score | PWAS | PP4 | ||
| SVS | SPATA20 | 17 | rs878619 | −10.89 | −2.917 | 102 | 3.71 | 2.10 × 10−4 | 0.17 | 3.10 × 10−1 | 3.79 | 1.50 × 10−4 | 0.97 * | 1.95 × 10−3 |
| SVS | ALDH2 | 12 | rs4648328 | −7.25 | −3.437 | 61 | 3.58 | 3.38 × 10−4 | 0.29 | 4.99 × 10−1 | 3.38 | 7.28 × 10−4 | 0.27 | 9.46 × 10−3 |
| SVS | EXOC6 | 10 | rs980204 | 4.98 | −2.469 | 210 | −3.58 | 3.41 × 10−4 | 0.19 | 5.03 × 10−1 | 3.37 | 7.36 × 10−1 | - | 1 |
| SVS | OSBPL11 | 3 | rs2922170 | 4.11 | 3577 | 111 | 3.58 | 3.48 × 10−4 | 0.35 | 5.14 × 10−1 | - | - | - | |
| ICH | ICA1L | 2 | rs7582720 | 7.21 | −3.935 | 81 | −3.94 | 8.32 × 10−5 | 0.68 | 1.23 × 10−1 | −3.30 | 9.66 × 10−4 | 0.99 * | 1.25 × 10−2 |
| ICH | NRBF2 | 10 | rs4379723 | −4.19 | −3.96 | 77 | 3.85 | 1.19 × 10−4 | 0.18 | 1.76 × 10−1 | - | - | - | |
| ICH | DLGAP2 | 8 | rs7842425 | 4.32 | −3.742 | 225 | −3.74 | 1.83 × 10−4 | 0.12 | 2.70 × 10−1 | 1.14 | 2.54 × 10−1 | - | 1 |
| ICH | SPATA20 | 17 | rs878619 | −10.89 | −2.89 | 102 | 3.58 | 3.47 × 10−4 | 0.12 | 5.12 × 10−1 | 3.27 | 1.09 × 10−3 | 0.33 | 1.41 × 10−2 |
| ICH | MADD | 11 | rs11570115 | −9.09 | −2.565 | 99 | 3.54 | 4.06 × 10−4 | 0.03 | 5.99 × 10−1 | 1.88 | 6.04 × 10−2 | - | 0.78 |
| Non-lobar ICH | SPATA20 | 17 | rs878619 | −10.89 | −2.672 | 102 | 3.69 | 2.19 × 10−4 | 0.42 | 3.23 × 10−1 | 3.51 | 4.44 × 10−4 | 0.27 | 5.77 × 10−3 |
| Non-lobar ICH | NRBF2 | 10 | rs4379723 | −4.19 | −3.569 | 77 | 3.43 | 6.00× 10−4 | 0.29 | 8.90 × 10−1 | - | - | - | |
| Lobar ICH | MRVI1 | 11 | rs753002 | −5.36 | 2.452 | 211 | −3.69 | 2.20 × 10−4 | 0.02 | 3.25 × 10−1 | −1.87 | 6.22× 10−2 | - | 0.80 |
| Lobar ICH | NRBF2 | 10 | rs4379723 | −4.19 | −3.804 | 77 | 3.68 | 2.33 × 10−4 | 0.11 | 3.44 × 10−1 | - | - | ||
| Lobar ICH | SPATA20 | 17 | rs878619 | −10.89 | −3.186 | 102 | 3.51 | 4.44× 10−4 | 0.28 | 6.55 × 10−1 | 3.40 | 6.79× 10−4 | 0.55 * | 8.82 × 10−3 |
| Lobar ICH | ICA1L | 2 | rs7582720 | 7.21 | 81 | −3.30 | 9.6× 10−4 | 0.2 | 1 | −2.5692 | 1.02 × 10−2 | 0.9 | 0.13 | |
* Significant PP4 in the replication. pQTL ID: ID for the pQTL strongly associated with proteins; pQTL z-score: z-score for the pQTL strongly associated with proteins; pQTL z-score: z-score in the correspondent GWAS for the best pQTL; NSNP: number of SNPs in the locus; TWAS z-score: z-score for the PWAS association; PWAS p-value: p-value for the PWAS association; PP4: posterior probability 4 in the COLOC analysis; q-value: FDR-adjusted PWAS p-value.
Figure 3GWAS results before conditioning by the SPATA20 levels (grey) or after conditioning by protein levels (blue).
Figure 4Schematic study workflow considering the discovery and the replication PWAS but also the sensitivity analyses.