NEDD9 rs760678 polymorphism and the risk of Alzheimer's disease: a meta-analysis

Multi-omics analyses highlight molecular differences between clinical and neuropathological diagnoses in Alzheimer's disease

Both clinical diagnosis and neuropathological diagnosis are commonly used in literature to categorize individuals as Alzheimer's disease (AD) or non-AD in omics analyses. Whether these diagnostic strategies result in distinct profiles of molecular abnormalities is poorly understood. Here, we analysed one of the most commonly used AD omics datasets in the literature from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort and compared the two diagnosis strategies using brain transcriptome and metabolome by grouping individuals as non-AD and AD according to clinical or neuropathological diagnosis separately. Differentially expressed genes, associated pathways related with AD hallmarks and AD-related genes showed that the categorization based on neuropathological diagnosis more accurately reflects the disease state at the molecular level than the categorization based on clinical diagnosis. We further identified consensus biomarker candidates between the two diagnosis strategies such as 5-hydroxylysine, sphingomyelin and 1-myristoyl-2-palmitoyl-GPC as metabolite biomarkers and sphingolipid metabolism as a pathway biomarker, which could be robust AD biomarkers since they are independent of diagnosis strategies. We also used consensus AD and consensus non-AD individuals between the two diagnostic strategies to train a machine-learning based model, which we used to classify the individuals who were cognitively normal but diagnosed as AD based on neuropathological diagnosis (asymptomatic AD individuals). The majority of these individuals were classified as consensus AD patients for both omics data types. Our study provides a detailed characterization of both diagnostic strategies in terms of the association of the corresponding multi-omics profiles with AD.

The Contribution Plot: Decomposition and Graphical Display of the RV Coefficient, with Application to Genetic and Brain Imaging Biomarkers of Alzheimer's Disease

BACKGROUND/AIMS

Alzheimer's disease (AD) is a chronic neurodegenerative disease that causes memory loss and a decline in cognitive abilities. AD is the sixth leading cause of death in the USA, affecting an estimated 5 million Americans. To assess the association between multiple genetic variants and multiple measurements of structural changes in the brain, a recent study of AD used a multivariate measure of linear dependence, the RV coefficient. The authors decomposed the RV coefficient into contributions from individual variants and displayed these contributions graphically.

METHODS

We investigate the properties of such a "contribution plot" in terms of an underlying linear model, and discuss shrinkage estimation of the components of the plot when the correlation signal may be sparse.

RESULTS

The contribution plot is applied to simulated data and to genomic and brain imaging data from the Alzheimer's Disease Neuroimaging Initiative (ADNI).

CONCLUSIONS

The contribution plot with shrinkage estimation can reveal truly associated explanatory variables.

The Prognostic Role of NEDD9 and P38 Protein Expression Levels in Urinary Bladder Transitional Cell Carcinoma

Background. The most common malignant tumor of the urinary bladder is transitional cell carcinoma (TCC). Neural precursor cell-expressed developmentally downregulated protein 9 (NEDD9) is found to be a cell adhesion mediator. P38 Mitogen-Activated Protein Kinase is a serine/threonine kinases member which can mediate carcinogenesis through intracellular signaling. Methods. To assess their prognostic role; NEDD9 and p38 protein were evaluated in sections from 50 paraffin blocks of TCC. Results. The high expressions of NEDD9 and p38 protein were significantly associated with grade, stage, distant metastasis (p < 0.001), number of tumors, lymph node metastasis, and tumor size (p < 0.001, 0.002; 0.018, <0.001; and 0.004, 0.007, respectively). High NEDD9 and p38 detection had a worse 3-year OS (p = 0.041 and <0.001, respectively). By multivariate analysis the NEDD9 and p38 protein expression levels and various clinicopathological criteria including gender, grade, stage of the tumor, and regional lymph node involvement were independent prognostic parameters of TCC of the urinary bladder patients' outcome. Conclusion. NEDD9 and p38 protein expressions were poor prognostic markers of TCC.

Semiparametric Bayes conditional graphical models for imaging genetics applications

Motivated by the need for understanding neurological disorders, large-scale imaging genetic studies are being increasingly conducted. A salient objective in such studies is to identify important neuroimaging biomarkers such as the brain functional connectivity, as well as genetic biomarkers, which are predictive of disorders. However, typical approaches for estimating the group level brain functional connectivity do not account for potential variation, resulting from demographic and genetic factors, while usual methods for discovering genetic biomarkers do not factor in the influence of the brain network on the imaging phenotype. We propose a novel semiparametric Bayesian conditional graphical model for joint variable selection and graph estimation, which simultaneously estimates the brain network after accounting for heterogeneity, and infers significant genetic biomarkers. The proposed approach specifies priors on the regression coefficients, which clusters brain regions having similar activation patterns depending on covariates, leading to dimension reduction. A novel graphical prior is proposed, which encourages modularity in brain organization by specifying denser and sparse connections within and across clusters, respectively. The posterior computation proceeds via a Markov chain Monte Carlo. We apply the approach to data obtained from the Alzheimer's disease neuroimaging initiative and demonstrate numerical advantages via simulation studies.

Preclinical and clinical studies of the NEDD9 scaffold protein in cancer and other diseases

Cancer progression requires a significant reprogramming of cellular signaling to support the essential tumor-specific processes that include hyperproliferation, invasion (for solid tumors) and survival of metastatic colonies. NEDD9 (also known as CasL and HEF1) encodes a multi-domain scaffolding protein that assembles signaling complexes regulating multiple cellular processes relevant to cancer. These include responsiveness to signals emanating from the T and B cell receptors, integrins, chemokine receptors, and receptor tyrosine kinases, as well as cytoplasmic oncogenes such as BCR-ABL and FAK- and SRC-family kinases. Downstream, NEDD9 regulation of partners including CRKL, WAVE, PI3K/AKT, ERK, E-cadherin, Aurora-A (AURKA), HDAC6, and others allow NEDD9 to influence functions as pleiotropic as migration, invasion, survival, ciliary resorption, and mitosis. In this review, we summarize a growing body of preclinical and clinical data that indicate that while NEDD9 is itself non-oncogenic, changes in expression of NEDD9 (most commonly elevation of expression) are common features of tumors, and directly impact tumor aggressiveness, metastasis, and response to at least some targeted agents inhibiting NEDD9-interacting proteins. These data strongly support the relevance of further development of NEDD9 as a biomarker for therapeutic resistance. Finally, we briefly discuss emerging evidence supporting involvement of NEDD9 in additional pathological conditions, including stroke and polycystic kidney disease.

Elevated expression of NEDD9 is associated with metastatic activity in gastric cancer

Objective

To investigate the protein and mRNA expression of NEDD9 in gastric cancer (GC) tissues, adjacent atypical hyperplasia tissues, and normal gastric mucosa tissues, and analyze its relationship with the pathological features and prognosis of GC.

Methods

Forty cases of GC tissues, 20 cases of adjacent atypical hyperplasia tissues, and 40 cases of normal gastric mucous tissues were collected. Immunohistochemistry and Western blot were used to examine the expression of NEDD9 protein in various tissues. Situ hybridization and reverse transcription polymerase chain reaction were applied to detect the expression of NEDD9 mRNA in various tissues. The correlation of NEDD9 expression with invasion and metastasis of GC was analyzed.

Results

The protein expression level of NEDD9 was significantly higher in GC tissues than in adjacent atypical hyperplasia tissues and normal gastric mucous tissues (P<0.05). The protein expression level of NEDD9 was positively related to the invasion depth of carcinoma and tumor lymph node metastasis (P<0.05), but unrelated to age, sex, tumor size, and clinical classification of cancer (P<0.05). The mRNA expression level of NEDD9 was also significantly higher in GC tissues than in adjacent atypical hyperplasia tissues and normal gastric mucous tissues (P<0.05), and positively related with the tumor lymph node metastasis and invasion depth of carcinoma (P<0.05).

Conclusion

NEDD9 is involved in the occurrence and development of GC, and it may be an important biological marker of GC metastasis and infiltration.

Nedd9 restrains renal cystogenesis in Pkd1-/- mice

Mutations inactivating the cilia-localized Pkd1 protein result in autosomal dominant polycystic kidney disease (ADPKD), a serious inherited syndrome affecting ∼ 1 in 500 people, in which accumulation of renal cysts eventually destroys kidney function. Severity of ADPKD varies throughout the population, for reasons thought to involve differences both in intragenic Pkd1 mutations and in modifier alleles. The scaffolding protein NEDD9, commonly dysregulated during cancer progression, interacts with Aurora-A (AURKA) kinase to control ciliary resorption, and with Src and other partners to influence proliferative signaling pathways often activated in ADPKD. We here demonstrate Nedd9 expression is deregulated in human ADPKD and a mouse ADPKD model. Although genetic ablation of Nedd9 does not independently influence cystogenesis, constitutive absence of Nedd9 strongly promotes cyst formation in the tamoxifen-inducible Pkd1fl/fl;Cre/Esr1(+) mouse model of ADPKD. This cystogenic effect is associated with striking morphological defects in the cilia of Pkd1(-/-);Nedd9(-/-) mice, associated with specific loss of ciliary localization of adenylase cyclase III in the doubly mutant genotype. Ciliary phenotypes imply a failure of Aurora-A activation: Compatible with this idea, Pkd1(-/-);Nedd9(-/-) mice had ciliary resorption defects, and treatment of Pkd1(-/-) mice with a clinical Aurora-A kinase inhibitor exacerbated cystogenesis. In addition, activation of the ADPKD-associated signaling effectors Src, Erk, and the mTOR effector S6 was enhanced, and Ca(2+) response to external stimuli was reduced, in Pkd1(-/-);Nedd9(-/-) versus Pkd1(-/-) mice. Together, these results indicated an important modifier action of Nedd9 on ADPKD pathogenesis involving failure to activate Aurora-A.

Adaptors for disorders of the brain? The cancer signaling proteins NEDD9, CASS4, and PTK2B in Alzheimer's disease

No treatment strategies effectively limit the progression of Alzheimer's disease (AD), a common and debilitating neurodegenerative disorder. The absence of viable treatment options reflects the fact that the pathophysiology and genotypic causes of the disease are not well understood. The advent of genome-wide association studies (GWAS) has made it possible to broadly investigate genotypic alterations driving phenotypic occurrences. Recent studies have associated single nucleotide polymorphisms (SNPs) in two paralogous scaffolding proteins, NEDD9 and CASS4, and the kinase PTK2B, with susceptibility to late-onset AD (LOAD). Intriguingly, NEDD9, CASS4, and PTK2B have been much studied as interacting partners regulating oncogenesis and metastasis, and all three are known to be active in the brain during development and in cancer. However, to date, the majority of studies of these proteins have emphasized their roles in the directly cancer relevant processes of migration and survival signaling. We here discuss evidence for roles of NEDD9, CASS4 and PTK2B in additional processes, including hypoxia, vascular changes, inflammation, microtubule stabilization and calcium signaling, as potentially relevant to the pathogenesis of LOAD. Reciprocally, these functions can better inform our understanding of the action of NEDD9, CASS4 and PTK2B in cancer.

Overexpression of Nedd9 is a prognostic marker of human gastric cancer

The present study was designed to evaluate the expression and prognostic significance of neural precursor cell-expressed, developmentally downregulated 9 (Nedd9) in patients with gastric cancer. Overexpression of Nedd9 was detected in a number of human cancers and was associated with progression and poor prognosis of the diseases. The expression of Nedd9 and focal adhesion kinase (FAK) were detected using the tissue microarray technique and immunohistochemical method and compared with clinicopathological parameters of patients with gastric cancer. The expressions of Nedd9 and FAK were upregulated in gastric cancer lesions compared with their expression in adjacent non-malignant tissues. High expression of Nedd9 correlated with age, location of tumor, tumor size, depth of invasion, vessel invasion, lymph node metastasis, and distant metastasis, and also with expression of FAK. Further, multivariate analysis suggested that expression of Nedd9 and FAK were independent prognostic indicators for gastric cancer. Cumulative 5-year survival rates of patients with high expression of both Nedd9 and FAK was significantly lower than those with low expression of both. Nedd9 was implicated in the progression of gastric cancer. Based on the TNM stage, Nedd9 and FAK proteins could be useful prognostic marker to predict tumor progression and prognosis in gastric cancer.