The Role of Rare Coding Variants in Parkinson's Disease GWAS Loci

Introduction: Genome-wide association studies (GWAS) have identified multiple loci associated with Parkinson's disease (PD) risk. The presence of rare variants within these loci that may account for the increased susceptibility requires further investigation.

Methods: Using exome sequencing, we performed a comprehensive rare variant screen of genes located within 56 novel PD loci. We first analyzed exomes from 109 subjects in the discovery cohort (85 diagnosed with PD and 24 healthy controls) and filtered for rare coding variants with minor allele frequency <0.01 and combined annotation-dependent depletion > 15. Further investigation of exome data from a replication cohort of 2,859 European patients with PD (International Parkinson's Disease Genomics Consortium) and 24,146 non-Finnish European controls from gnomAD were used for association testing of specific rare variants found in the discovery cohort.

Results: Our genetic screening identified 54 potential disease-relevant variants in 71 genes in 109 subjects. Six out of 54 variants were found in two or more patients and were not observed in healthy controls: DNAH1 p.A3639T, STAB1 p.S1089G, ANK2 p.V3634D, ANK2 p.R3906W, SH3GL2 p.G276V, and NOD2 p.G908R. Replication in the International Parkinson's Disease Genomics Consortium (IPDGC) confirmed the association with PD risk for three out of the six identified variants (STAB1 p.S1089G, SH3GL2 p.G276V, and NOD2 p.G908R) (p < 10⁻³).

Conclusion: Our study suggests that some of the associations identified in PD risk loci can be ascribed to rare variants with likely functional effects that modify PD risk.

Identification of STAB1 in Multiple Datasets as a Prognostic Factor for Cytogenetically Normal AML: Mechanism and Drug Indications

Cytogenetically normal acute myeloid leukemia (CN-AML) presents with diverse outcomes in different patients and is categorized as an intermediate prognosis group. It is important to identify prognostic factors for CN-AML risk stratification. In this study, using the TCGA CN-AML dataset, we found that the scavenger receptor stabilin-1 (STAB1) is a prognostic factor for poor outcomes and validated it in three other independent CN-AML datasets. The high STAB1 expression (STAB1^high) group had shorter event-free survival compared with the low STAB1 expression (STAB1^low) group in both the TCGA dataset (n = 79; p = 0.0478) and GEO: GSE6891 dataset (n = 187; p = 0.0354). Differential expression analysis between the STAB1^high and STAB1^low groups revealed that upregulated genes in the STAB1^high group were enriched in pathways related to cell adhesion and migration and immune responses. We confirmed that STAB1 suppression inhibits cell growth in KG1a and NB4 leukemia cells. Expression correlation analyses between STAB1 and cancer drug targets suggested that patients in the STAB1^low group are more sensitive to the BCL2 inhibitor venetoclax, and we confirmed it in cell lines. In conclusion, we identified STAB1 as a prognostic factor for CN-AML in multiple datasets, explored its underlying mechanism, and provided potential therapeutic indications.

Identification of novel human glioblastoma-specific transcripts by serial analysis of gene expression data mining

BACKGROUND

Glioblastoma multiforme (GBM) remains the most common and aggressive primary brain tumor in adults with a poor median survival, and molecular biomarkers for GBM pathogenesis are in need.

PURPOSE

The objective of this study is to identify potential novel genes for GBM pathogenesis by gene expression data mining.

MATERIALS AND METHODS

Available SAGE libraries of GBM, astrocytoma, and normal brain tissues were collected from the Cancer Genome Anatomy Project (CGAP). Significance analysis for microarray (SAM) and CGAP-SAGE-Genie-DGED were used to identify differentially expressed tags, and specific tags that were differentially expressed only in GBM were further selected. Tags to genes association was performed by CGAP-SAGE-Genie-SAV. Immunohistochemistry was used to investigate distribution and validate expression of the interested gene.

RESULTS

Three genes were significantly differentially expressed just in brain. up-regulated expression of STAB1 and down-regulated expression of SH3GL2 and DNM3. Immunohistochemistry assay indicated that STAB1 mainly expressed in vascular endothelial cells and over-expressed in GBM samples compared to normal samples.

CONCLUSIONS

Our study shows that data mining of public sources of gene expression is an effective way to identify novel tumor-associated genes, and this work may contribute to the identification of candidate genes for GBM angiogenesis.

Increased expression of factor XIII-A in patients with chronic rhinosinusitis with nasal polyps

BACKGROUND

Profound edema or formation of a pseudocyst containing plasma proteins is a prominent characteristic of nasal polyps (NP). However, the mechanisms underlying NP retention of plasma proteins in the submucosa remain unclear. Recently, we reported that impairment of fibrinolysis causes excessive fibrin deposition in NP and this might be involved in the retention of plasma proteins. Although the coagulation cascade plays a critical role in fibrin clot formation at extravascular sites, the expression and role of coagulation factors in NP remain unclear.

OBJECTIVE

The objective of this study was to investigate the expression of coagulation factors in patients with chronic rhinosinusitis (CRS).

METHODS

Sinonasal tissues were collected from patients with CRS and control subjects. We assayed mRNA for factor XIII-A (FXIII-A) by using real-time PCR and measured FXIII-A protein by means of ELISA, immunohistochemistry, and immunofluorescence.

RESULTS

FXIII-A mRNA levels were significantly increased in NP tissue from patients with CRS with NP (P < .001) compared with uncinate tissue from patients with CRS or control subjects. Similarly, FXIII-A protein levels were increased in NP. Immunofluorescence analysis revealed that FXIII-A expression in inflammatory cells and FXIII-A(+) cell numbers were significantly increased in NP. Most FXIII-A staining was observed within CD68(+)/CD163(+) M2 macrophages in NP. Levels of FXIII-A correlated with markers of M2 macrophages, suggesting that M2 macrophages are major FXIIIA-producing cells in NP.

CONCLUSION

Overproduction of FXIII-A by M2 macrophages might contribute to the excessive fibrin deposition in the submucosa of NP, which might contribute to the tissue remodeling and pathogenesis of CRS with NP.