Heterozygous and Homozygous Variants in SORL1 Gene in Alzheimer's Disease Patients: Clinical, Neuroimaging and Neuropathological Findings

A novel SORL1 mutation in a pedigree affected by early-onset Alzheimer's disease

Familial cases of Alzheimer's disease (AD) with autosomal dominant transmission and early onset have a prevalence around 1%. Since only a small fraction of them has a monogenic inheritance due to APP, PSEN1, and PSEN2 genes, genetic studies are ongoing to unravel the missing heritability. By sequencing panels including multiple dementia-related genes, we identified a novel likely pathogenic mutation in SORL1 in a pedigree including five members affected by AD. This loss of function mutation may lead to a reduction of SORL1 receptor, worsening amyloidogenic burden. As the contribution of SORL1 mutations to heritability of AD is presently not well established, we think that it is very important to signal new familial (likely) pathogenic SORL1 mutations in order to define the actual genetic involvement of SORL1 in AD pathogenesis.

Exploration of the Key Pathways and Genes Involved in Osteoarthritis Genesis: Evidence from Multiple Platforms and Real-World Validation

Background

Osteoarthritis (OA), a degenerative and chronic joint disease, is essential for identifying novel biomarkers for the clinical diagnosis of OA.

Methods

We collected 35 OA patients and 32 healthy controls from four clinical cohorts and 8 real-world samples from our institute. The activation status of 7530 signalling pathways was calculated via the gene set enrichment analysis (GSEA) algorithm. Ten machine learning algorithms and 101 algorithm combinations were further applied to recognize the most diagnostic genes. KDELR3 was chosen for further validation via immunohistochemical staining to determine its diagnostic value in real-world samples.

Results

Sixteen pathways, namely, the cellular respiration chain, protein transport, lysosomal and endocytosis pathways, were activated in OA patients. A total of 101 types of algorithm combinations were considered for the diagnostic model, and 58 were successfully output. The two-step model of glmBoost plus RF had the highest average AUC value of 0.95 and was composed of LY86, SORL1, KDELR3, CSK, PTGS1, and PTGS2. Preferable consistency of the diagnostic mole and real conditions was observed in all four cohorts (GSE55235: Kappa=1.000, P<0.001; GSE55457: Kappa=0.700, P<0.001; GSE82107: Kappa=0.643, P=0.004; GSE1919: Kappa=1.000, P<0.001). KDELR3 was expressed at higher levels in OA patients than were the other genes, and with the help of immunohistochemistry (IHC), we confirmed that OA patients presented high levels of KDELR3 in synovial tissues. The infiltration of immunocytes, macrophages, and natural killer T cells was high in OA patients. KDELR3 might be involved in the activation and infiltration of effector memory CD4 T cells (Rpearson = 0.58, P < 0.001) and natural killer T cells (Rpearson = 0.53, P < 0.001).

Conclusion

We constructed and validated a six-gene diagnostic model for OA patients via machine learning, and KDELR3 emerged as a novel biomarker for OA.

The identification of key genes and pathways in polycystic ovary syndrome by bioinformatics analysis of next-generation sequencing data

Background

Polycystic ovary syndrome (PCOS) is a reproductive endocrine disorder. The specific molecular mechanism of PCOS remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS.

Methods

The next-generation sequencing (NGS) dataset GSE199225 was downloaded from the gene expression omnibus (GEO) database and NGS dataset analyzed is obtained from in vitro culture of PCOS patients’ muscle cells and muscle cells of healthy lean control women. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the gene ontology (GO) and REACTOME pathways of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed. The hub genes were validated by using receiver operating characteristic (ROC) curve analysis.

Results

We have identified 957 DEG in total, including 478 upregulated genes and 479 downregulated gene. GO terms and REACTOME pathways illustrated that DEG were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling, and aggregation. The top 5 upregulated hub genes including HSPA5, PLK1, RIN3, DBN1, and CCDC85B and top 5 downregulated hub genes including DISC1, AR, MTUS2, LYN, and TCF4 might be associated with PCOS. The hub gens of HSPA5 and KMT2A, together with corresponding predicted miRNAs (e.g., hsa-mir-34b-5p and hsa-mir-378a-5p), and HSPA5 and TCF4 together with corresponding predicted TF (e.g., RCOR3 and TEAD4) were found to be significantly correlated with PCOS.

Conclusions

These study uses of bioinformatics analysis of NGS data to obtain hub genes and key signaling pathways related to PCOS and its associated complications. Also provides novel ideas for finding biomarkers and treatment methods for PCOS and its associated complications.

Input of exome sequencing in early-onset cerebral amyloid angiopathy

INTRODUCTION

Genetics of cerebral amyloid angiopathy (CAA) remains understudied.

METHODS

We assessed variants in Alzheimer's disease (AD) risk factor genes and differential diagnosis genes by performing exome sequencing among 78 patients with early-onset definite or probable CAA, after negative screening for APP mutation or duplication.

RESULTS

Among 14 genes involved in non-Aβ CAA, or vascular leukoencephalopathies, we detected pathogenic NOTCH3 variants in two patients, who exhibited lobar hematomas at the ages of 58 and 65, leading to a diagnosis redirection toward CADASIL. Of the remaining 76 patients, 23.1% carried at least one apolipoprotein E (APOE) ε2 allele and 43.6% carried at least one APOE ε4 allele, known as CAA risk factors. A total of 15 out of 76 (19.7%) carried either a loss-of-function or a rare predicted damaging missense or known AD risk variant in SORL1, TREM2, ABCA7, ABCA1, and ATP8B4.

DISCUSSION

Exome sequencing allowed the redirection toward CADASIL in two patients and suggested shared genetic factors between AD and CAA, beyond the APOE gene.

Highlights

The genetic component of cerebral amyloid angiopathy (CAA) remains understudied.Rare differential diagnoses such as CADASIL should be considered, even in cases of cerebral hemorrhage.Our study suggests shared genetic factors between AD and CAA, beyond the APOE gene.Rare variants in SORL1, TREM2, ABCA7, ABCA1 and ATP8B4 might be susceptibility factors in early-onset CAA.

A familial missense variant in the Alzheimer's disease gene SORL1 impairs its maturation and endosomal sorting

The SORL1 gene has recently emerged as a strong Alzheimer's Disease (AD) risk gene. Over 500 different variants have been identified in the gene and the contribution of individual variants to AD development and progression is still largely unknown. Here, we describe a family consisting of 2 parents and 5 offspring. Both parents were affected with dementia and one had confirmed AD pathology with an age of onset > 75 years. All offspring were affected with AD with ages at onset ranging from 53 years to 74 years. DNA was available from the parent with confirmed AD and 5 offspring. We identified a coding variant, p.(Arg953Cys), in SORL1 in 5 of 6 individuals affected by AD. Notably, variant carriers had severe AD pathology, and the SORL1 variant segregated with TDP-43 pathology (LATE-NC). We further characterized this variant and show that this Arginine substitution occurs at a critical position in the YWTD-domain of the SORL1 translation product, SORL1. Functional studies further show that the p.R953C variant leads to retention of the SORL1 protein in the endoplasmic reticulum which leads to decreased maturation and shedding of the receptor and prevents its normal endosomal trafficking. Together, our analysis suggests that p.R953C is a pathogenic variant of SORL1 and sheds light on mechanisms of how missense SORL1 variants may lead to AD.

Finding memo: versatile interactions of the VPS10p-Domain receptors in Alzheimer’s disease

The family of VPS10p-Domain (D) receptors comprises five members named SorLA, Sortilin, SorCS1, SorCS2 and SorCS3. While their physiological roles remain incompletely resolved, they have been recognized for their signaling engagements and trafficking abilities, navigating a number of molecules between endosome, Golgi compartments, and the cell surface. Strikingly, recent studies connected all the VPS10p-D receptors to Alzheimer’s disease (AD) development. In addition, they have been also associated with diseases comorbid with AD such as diabetes mellitus and major depressive disorder. This systematic review elaborates on genetic, functional, and mechanistic insights into how dysfunction in VPS10p-D receptors may contribute to AD etiology, AD onset diversity, and AD comorbidities. Starting with their functions in controlling cellular trafficking of amyloid precursor protein and the metabolism of the amyloid beta peptide, we present and exemplify how these receptors, despite being structurally similar, regulate various and distinct cellular events involved in AD. This includes a plethora of signaling crosstalks that impact on neuronal survival, neuronal wiring, neuronal polarity, and synaptic plasticity. Signaling activities of the VPS10p-D receptors are especially linked, but not limited to, the regulation of neuronal fitness and apoptosis via their physical interaction with pro- and mature neurotrophins and their receptors. By compiling the functional versatility of VPS10p-D receptors and their interactions with AD-related pathways, we aim to further propel the AD research towards VPS10p-D receptor family, knowledge that may lead to new diagnostic markers and therapeutic strategies for AD patients.