Integrative analysis of gene expression profiles of substantia nigra identifies potential diagnosis biomarkers in Parkinson's disease

Parkinson's disease (PD) is a progressive neurodegenerative disease whose etiology is attributed to development of Lewy bodies and degeneration of dopaminergic neurons in the substantia nigra (SN). Currently, there are no definitive diagnostic indicators for PD. In this study, we aimed to identify potential diagnostic biomarkers for PD and analyzed the impact of immune cell infiltrations on disease pathogenesis. The PD expression profile data for human SN tissue, GSE7621, GSE20141, GSE20159, GSE20163 and GSE20164 were downloaded from the Gene Expression Omnibus (GEO) database for use in the training model. After normalization and merging, we identified differentially expressed genes (DEGs) using the Robust rank aggregation (RRA) analysis. Simultaneously, DEGs after batch correction were identified. Gene interactions were determined through venn Diagram analysis. Functional analyses and protein-protein interaction (PPI) networks were used to the identify hub genes, which were visualized through Cytoscape. A Lasso Cox regression model was employed to identify the potential diagnostic genes. The GSE20292 dataset was used for validation. The proportion of infiltrating immune cells in the samples were determined via the CIBERSORT method. Sixty-two DEGs were screened in this study. They were found to be enriched in nerve conduction, dopamine (DA) metabolism, and DA biosynthesis Gene Ontology (GO) terms. The PPI network and Lasso Cox regression analysis revealed seven potential diagnostic genes, namely SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1, were subsequently validated in peripheral blood samples obtained from healthy control (HC) and PD patients, as well as in the GSE20292 dataset. The results revealed the exceptional sensitivity and specificity of these genes in PD diagnosis and monitoring. Moreover, PD patients exhibited a higher number of plasma cells, compared to HC individuals. The SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1 are potential diagnostic biomarkers for PD. Our findings also reveal the essential roles of immune cell infiltration in both disease onset and trajectory.

BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies

Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single-cell resolution spatial transcriptomics. BASS performs cell type clustering at the single-cell scale and spatial domain detection at the tissue regional scale, with the two tasks carried out simultaneously within a Bayesian hierarchical modeling framework. We illustrate the benefits of BASS through comprehensive simulations and applications to three datasets. The substantial power gain brought by BASS allows us to reveal accurate transcriptomic and cellular landscape in both cortex and hypothalamus.

The Endometrial Transcriptome of Metabolic and Inflammatory Pathways During the Window of Implantation Is Deranged in Infertile Obese Polycystic Ovarian Syndrome Women

Introduction and Aim: Obese women with polycystic ovarian syndrome (PCOS) have a reduced rate of spontaneous conception even when their cycles are ovulatory. Endometrial receptivity is an important factor for poor implantation and increased miscarriage rates. Mechanisms in which both pathologies modify the endometrium are not fully clarified. The aim of our study was to compare the endometrial transcriptomic profiles between infertile obese PCOS (O-PCOS) women and infertile normal weight subjects during the window of implantation in ovulatory menstrual cycles. Methods: We conducted a prospective transcriptomic analysis of the endometrium using RNA sequencing. In this way, potential endometrial mechanisms leading to the poor reproductive outcome in O-PCOS patients could be characterized. Endometrial samples during days 21-23 of the menstrual cycle were collected from infertile O-PCOS women (n = 11) and normal weight controls (n = 10). Subgroups were defined according to the ovulatory/anovulatory status in the natural cycles, and O-PCOS women were grouped into the O-PCOS ovulatory (O-PCOS-ovul) subgroup. RNA isolation, sequencing with library reparation, and subsequent RNAseq data analysis were performed. Results: Infertile O-PCOS patients had 610 differentially expressed genes (DEGs), after adjustment for multiple comparisons with normal weight infertile controls, related to obesity (MXRA5 and ECM1), PCOS (ADAMTS19 and SLC18A2), and metabolism (VNN1 and PC). In the ovulatory subgroup, no DEGs were found, but significant differences in canonical pathways and the upstream regulator were revealed. According to functional and upstream analyses of ovulatory subgroup comparisons, the most important biological processes were related to inflammation (TNFR1 signaling), insulin signaling (insulin receptor signaling and PI3/AKT), fatty acid metabolism (stearate biosynthesis I and palmitate biosynthesis I), and lipotoxicity (unfolded protein response pathway). Conclusions: We demonstrated that endometrial transcription in ovulatory O-PCOS patients is deranged in comparison with the control ovulatory endometrium. The most important pathways of differentiation include metabolism and inflammation. These processes could also represent potential mechanisms for poor embryo implantation, which prevent the development of a successful pregnancy. ClinicalTrials.gov ID: NCT03353948.

The Potential Effect of Rhizoma coptidis on Polycystic Ovary Syndrome Based on Network Pharmacology and Molecular Docking

Background

Rhizoma coptidis (RC) showed a significant effect on PCOS, but its mechanism in PCOS remains unclear.

Methods

The components of RC were searched by TCMSP. The Smiles number of the active ingredients was queried through PubChem, and the predicted targets were obtained from the SwissTargetPrediction database. The DrugBank, GeneCards, and DisGeNET databases were retrieved to acquire the related targets of PCOS. Then, the network of compound-target was constructed. The core targets were analyzed using protein-protein interaction (PPI) analysis, and the binding activities were verified by molecular docking. The enriched pathways of key targets were examined by GO and KEGG.

Results

13 components and 250 targets of RC on PCOS were screened. The core network was filtered based on topological parameters, and the key components were palmatine, berberine, berberrubine, quercetin, and epiberberine. The key targets included DRD2, SLC6A4, CDK2, DPP4, ESR1, AKT2, PGR, and AKT1. Molecular docking displayed that the active ingredients of RC had good binding activities with potential targets of PCOS. After enrichment analysis, 30 functional pathways were obtained, including neuroactive ligand-receptor interaction, dopaminergic synapse, and cAMP signaling pathway.

Conclusion

In summary, this study clarified the potential effect of RC on PCOS, which is helpful to provide references for clinical practice. It is also conducive to the secondary development of RC and its monomer components.

Advances in the Regulation of Mammalian Follicle-Stimulating Hormone Secretion

Simple Summary

The reproduction of mammals is regulated by the hypothalamic-pituitary-gonadal axis. Follicle stimulating hormone, as one of the gonadotropins secreted by the pituitary gland, plays an immeasurable role. This article mainly reviews the molecular basis and classical signaling pathways that regulate the synthesis and secretion of follicle stimulating hormone, and summarizes its internal molecular mechanism, which provides a certain theoretical basis for the research of mammalian reproduction regulation and the application of follicle stimulating hormone in production practice.

Abstract

Mammalian reproduction is mainly driven and regulated by the hypothalamic-pituitary-gonadal (HPG) axis. Follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, is a key regulator that ultimately affects animal fertility. As a dimeric glycoprotein hormone, the biological specificity of FSH is mainly determined by the β subunit. As research techniques are being continuously innovated, studies are exploring the underlying molecular mechanism regulating the secretion of mammalian FSH. This article will review the current knowledge on the molecular mechanisms and signaling pathways systematically regulating FSH synthesis and will present the latest hypothesis about the nuclear cross-talk among the various endocrine-induced pathways for transcriptional regulation of the FSH β subunit. This article will provide novel ideas and potential targets for the improved use of FSH in livestock breeding and therapeutic development.

The Gene Polymorphism of VMAT2 Is Associated with Risk of Schizophrenia in Male Han Chinese

OBJECTIVE

To investigate the association between gene polymorphism of vesicular monoamine transporter type 2(VMAT2) and schizophrenia in Han Chinese population.

METHODS

430 patients with schizophrenia and 470 age-sex matched controls were recruited from four mental health centers. All patients were diagnosed by two psychiatrists based on the Structured Clinical Interview for DSM Disorders (SCID). The ligase detection reactions (LDR) method was used to assess the polymorphism of the two SNPs (rs363371 and rs363324) of VMAT2.

RESULTS

No associations of two SNPs with schizophrenia was found. When we stratified males and females for the analysis, we found that that in the recessive model of rs363371, there was an obvious significant association between rs363371 and schizophrenia in males (OR=0.564, 95% CI=0.357-0.892, p=0.014) but not females. For the association between rs363324 and schizophrenia, no association was found in either males or females. No association was found when stratifying early-onset schizophrenia and late-onset schizophrenia.

CONCLUSION

Our findings indicate that both rs363371 and rs363324 were not associated with schizophrenia, while it seemed that the AA genotype of rs363371 plays a protective effect in male Chinese in developing schizophrenia.

A genome-wide association study identifies FSHR rs2300441 associated with follicle-stimulating hormone levels

Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play critical roles in female reproduction, while the underlying genetic basis is poorly understood. Genome-wide association studies (GWASs) of FSH and LH levels were conducted in 2590 Chinese females including 1882 polycystic ovary syndrome (PCOS) cases and 708 controls. GWAS for FSH level identified multiple variants at FSHR showing genome-wide significance with the top variant (rs2300441) located in the intron of FSHR. The A allele of rs2300441 led to a reduced level of FSH in the PCOS group (β = -.43, P = 6.70 × 10^-14 ) as well as in the control group (β = -.35, P = 6.52 × 10^-4 ). In the combined sample, this association was enhanced after adjusting for the PCOS status (before: β = -.38, P = 1.77 × 10^-13 ; after: β = -.42, P = 3.33 × 10^-16 ), suggesting the genetic effect is independent of the PCOS status. The rs2300441 explained sevenfold higher proportion of the FSH variance than the total variance explained by the two previously reported FSHR missense variants (rs2300441 R² = 1.40% vs rs6166 R² = 0.17%, rs6165 R² = 0.03%). GWAS for LH did not identify any genome-wide significant associations. In conclusion, we identified genome-wide significant association between variants in FSHR and circulating FSH first, with the top associated variant rs2300441 might be a primary contributor at the population level.

Hyperandrogenemia and insulin resistance: The chief culprit of polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is one of the most common systemic reproductive endocrine diseases, which has a variety of effects on a woman's health. Because of the involvement of multiple pathways and the lack of common clues, PCOS demonstrates multifactorial properties and heterogeneity of symptoms. Recent studies have demonstrated that the core etiology and primary endocrine characteristics of PCOS are hyperandrogenemia (HA) and insulin resistance (IR). HA and IR are the main causes of PCOS and they can interplay each other in the occurrence and development of PCOS. Just because of this, the study about the effects of HA and IR on pathophysiology of various related symptoms of PCOS is very important to understand the pathogenesis of PCOS. This paper reviews the main symptoms of PCOS, including neuroendocrine disorders, reproductive processes, dyslipidemia, obesity, hypertension, nonalcoholic fatty liver disease (NAFLD), and sleep disordered breathing, which seriously affect the physical and mental health of PCOS women. The increasing knowledge of the development pattern of HA and IR in PCOS suggests that changes in diet and lifestyle, and the discovery of potential therapeutic agents may improve PCOS. However, further studies are needed to clarify the mutual influence and relation of HA and IR in development of PCOS. This review provides an overview of the current knowledge about the effects of HA and IR on PCOS.