Neurodegenerative diseases, such as AD, PD, FTD, ALS and prion disease, are a group of disorders characterized by aggregation of abnormal proteins in neurons and progressive degeneration of affected neurons. Neurodegenerative diseases have some neuropathology, clinical and genetic crossover. To determine whether genetic mutations in neurodegenerative diseases could have a role in FAD etiology, we performed a targeted sequencing of 277 candidate genes related to neurodegenerative disease in 75 FAD probands. Casual and risk variants were found to be segregated within AD families, and showed strong association when combined with ExAC East Asian control data and our case-control cohort. This result indicated a potential role for rare variants from AD risk genes and genes linked to other NBDs in FAD etiology.
A novel missense mutation, p.P410S, of PLD3 was identified in one of our AD families. PLD3 was identified as a new risk gene by a next-generation sequencing study on a large LOFAD cohort of European descent. p.V232M was found to segregate with disease status in two large late-onset families and showed strong association with disease status in a large LOAD cohort (4,998 cases and 6,356 controls)(19). Since then, multiple replication studies in different ethnicities (Belgian, Germany, French, Chinese, etc) have been performed on rare variants of PLD3, but they showed controversial association consequences with AD risk (20–22). Notably, in a northern Han Chinese population study of 960 LOAD cases and 2,290 controls, the authors found the rare variants p.I163M and c.1020-8G > A that conferred considerable risk of LOAD in their cohort; they detected a p.V232M carrier but found no association of p.V232M with the LOAD risk in their cohort(23), which indicated that the role of PLD3 to AD risk was still unclear and that it showed strong ethnic diversity. The p.P410S identified in our study was segregated in an EOAD family. Pathogenicity predictions revealed that p.P410S was damaging using SIFT, Polyphen2, and Mutationtaster. p.P410s is absent in the Exome Sequencing Project, 1000 Genomes Project, ExAc database, and our case-control cohort, indicating that p.P410S might be a causative mutation to this EOAD family. Our result indicated that rare variants of PLD3 may also play an important role in EOAD family as well as LOAD as previously described. Large family sample studies should be conducted on PLD3 in the future.
Mutations of LRRK2 is a main genetic cause for both familial and sporadic PD firstly identified by Zimprich et al. in 2004(24). Most of the previous reported LRRK2 mutations are G2019S and R1441C/G/H (25, 26). The I2012T mutation mostly occurs in Asian PD patients (27, 28), which lies in the activation loop of kinase domain and could decrease LRRK2 kinase activity in several studies (26, 29). The clinical spectrum of I2012T mutation carriers varies widely, ranges from typical late-onset levodopa-responsive PD to FTD with parkinsonism. We found a missense substitution p.I2012T of the LRRK2 gene in an EOAD family. The proband showed a typical AD clinical course with episodic memory loss, progressive apathy and fewer words, but no typical FTD symptoms or parkinsonism were found in the proband or his relatives. Brain MRI showed mild to moderate atrophy in the hippocampus, temporal and parietal areas, suggesting a diagnose of probable AD. As we know, in the precious studies on relationship between AD cognitive impairment and LRRK2 mutations, the R1396G mutation in LRRK2 seemed to have a protective effect on cognitive impairment in LRRK2-related PD. The G2019S carriers had a lower executive performance than non-carriers in the Ashkenazi Jewish group, while with a negative result in an Italy AD cohort(30). To date, neither AD nor dementia but without parkinsonism phenotype has been reported in I2012T mutation carriers. Our research reported a new clinical presentation of LRRK2 I2012T mutation, and which propose that screening of LRRK2 mutation is needed in the genetic cause unknown FAD patients.
In the follow-up genotyping, the p.P143S, rs192694824 in ABCA7 and rs374551420 in CR1 were significantly associated with FAD risk, and the rs200820365 in TREM2 was significantly associated with AD risk when they were compared with the allele frequency of the Asian data in ExAc. No previously reported risk variants were found in this study, suggesting region specificity and race specificity of the rare variants in AD risk. ABCA7 encoded a protein that is involved in phospholipid transmembrane transport, phagocytosis of apoptotic cells, and microglia-mediated clearance of Aβ (31, 32). In the previous study, several risk variants that contributed to AD in ABCA7 differed between people of different ethnic origins. In a European population, targeted resequencing identified an intronic variant in ABCA7(10), whereas among African-Americans, the most strongly associated SNP is rs115550680(33). In this study, 2 rare variants in exons that showed strong association were identified in the Chinese FAD population. CR1, which encodes a large type 1 transmembrane glycoprotein involved in the immune complement cascade, was among the first susceptibility genes for AD to be identified (34). To date, no rare variants in CR1 have been reported to be associated with AD. Findings from a genome-wide CNV association study confirmed association between an intragenic CNV and AD (35). A rare coding variant, rs4844609, located outside the CNV region, was reported to explain the GWAS association (36). However, that finding has yet to be replicated. In this study, rs374551420 in CR1 was significantly associated with FAD, existing in 2 LOFAD families and absent in controls or unaffected family members. The rare variant R47H in TREM2 was first detected with strong association with LOAD with an effect size similar to that of APOE ε4 from two NGS-based studies (7). The genetic association between TREM2 R47H and AD has been widely replicated. R47H was absent in our sequencing data; instead, we found that rs200820365 in TREM2 showed a strong association with AD in this study. The rs200820365 was overrepresented in EOAD families and SAD, supporting its causative role in both EOAD and LOAD. Taken together, our study above confirmed that AD risk genes may have a high burden of deleterious variants in both EOAD and LOAD, but differences in the observed mutations could be due to ethnicity, capture, coverage differences and sample size in different studies. The biological impact of these variants remains to be investigated.
A total of 257 rare damaging mutations in FTD-, VD-, PD-, and ALS-related and functionally related genes were identified in this study. These variants were located in the conservative domain, and had at least one computer-based software predicting damage, supporting their potential causative role. Their association with AD needs a large cohort study to elucidate. Notably, the variant p. G222del in FUS was frequent in AD cases. Through follow-up genotyping in our case-control cohort, it was found in 3 FAD families and 3 sporadic AD cases. By Fisher’s exact test, p. G223del in FUS was significantly associated with FAD. Variants in FUS have been identified as causal and risk for ALS, essential tremor, and FTD (37–40). The p. G223del was located in the G-rich region of FUS that is not strongly conserved in closely related organisms, suggesting it may be a benign variant. Its association with FAD needs further validation. We also detected 2 families carrying p.A104T in PARK7/DJ-1. The p.A104T of PARK7/DJ-1 was first reported in a sporadic PD patient in 2003(41). Previous studies on PARK7/DJ-1 and PD supposed that mutations in the heterozygous state in the parkin gene may represent risk factors (42). As the role of p.A104T in PD remains unclear, the association of p.A104T with FAD needs large cohort and functional study for confirmation.