Development of a Real-Time TaqMan RT-PCR Assay for the Detection of NADC34-like Porcine Reproductive and Respiratory Syndrome Virus.

NADC34-like porcine reproductive and respiratory syndrome virus first appeared in 2017 in a herd of pigs in Liaoning Province, China. The virus was subsequently found in other provinces. Given the potential for this virus to cause an epidemic, rapid, sensitive, and specific detection of NADC34-like PRRSV is required. The virus' ORF5 gene was artificially synthesized based on a Chinese reference strain, and specific primers/probes for the ORF5 gene were designed. Then, the amplified target fragment was cloned into the pMD19-T vector, and a series of diluted recombinant plasmids were used to generate a standard curve. An optimized real-time TaqMan RT-PCR method was established. The method was highly specific for NADC34-like PRRSV, without cross-reactions with other non-targeted pig viruses. The detection limit of this assay was 101 copies/µL. The method had an efficiency of 98.8%, a squared regression value (R2) of 0.999, and showed a linear range of 103-108 copies/µL of DNA per reaction. This method was shown to be analytically specific and sensitive with a low intra- and inter-assay coefficient of variation (<1.40%). A total of 321 clinical samples were tested using the established method, and four were shown to be positive (1.24%). This study confirmed the existence of NADC34-like PRRSV and HP-PRRSV co-infection in Sichuan and provided a promising alternative tool for the rapid detection of NADC34-like PRRSV.

The pathogenicity comparison of Lagovirus europaeus GI.1 and GI.2 strains in China by using relative quantitative assay.

Lagovirus europaeus GI.1 belongs to Lagovirus in the Caliciviridae family. GI.1 causes an acute, septic, and highly lethal disease in rabbits. Lagovirus europaeus GI.2, a new variant of GI.1, has caused explosive mortality in rabbits of all ages in Sichuan Province, China. To explore the differences in pathogenicity of rabbits infected with GI.1/GI.2, we investigated the virulence and disease progression of a naturally occurring GI.1/GI.2 in 4-week-old, 13-week-old, and 25-week-old New Zealand White laboratory rabbits after GI.1/GI.2 infection. Objective measures of disease progression were recorded using continuous body-temperature monitoring. We observed the kittens were infected with GI.2 during the most urgent course of the disease, and GI.1 was not lethal to kittens. We found that the target organ of both GI.1 and GI.2 was the liver, but the disease course of the two viruses was differed. Our study enriches the research on the pathogenicity of GI.1 and GI.2 under the same conditions.

Detection of a New Emerging Strain of Rabbit Haemorrhagic Disease Virus 2 (GI.2) in China.

Introduction: In May 2020, an outbreak of rabbit haemorrhagic disease 2 (RHD2) caused by the rabbit haemorrhagic disease virus 2 (RHDV2, GI.2) occurred in Sichuan, China. The acute onset and short disease course resulted in rabbit mortality as high as 42.86%. Currently, basic research on the aetiology and genetic characteristics of GI.2 is lacking in China. Material and Methods: Pathological changes in various tissues from infected rabbits were investigated and the viral genome was characterised. This study used RT-PCR, histopathology and scanning electron microscopy to identify the pathogen in samples from infected rabbits that had died. Phylogenetic trees were constructed based on whole genome sequence analysis, and recombination events were analysed. Results: RT-PCR identified the presence of GI.2. Histopathology revealed liver cell necrosis and haemorrhaging into lung alveoli. Electron microscopy demonstrated spherical GI.2 particles that were 40 nm in size. The gene sequence length of the isolate was 7,445 bp (GenBank accession number MW178244). A phylogenetic analysis based on the genome of the isolated strain and 60 reference strains showed that the isolate was grouped together with GI.2 strain MT586027.1 in a relatively independent sub-branch. The results of the recombination analysis showed that the strain was recombined from the MT586027.1 (major parent) and MN90145.1 (minor parent) strains, and recombination breakpoints were at locations in the 2858-5137 nt range. Conclusion: The results of this study extend our understanding of the molecular epidemiology of GI.2.

Whole Transcriptome Sequencing Identified CircRNA Profiles and the Related Networks in Schizophrenia.

Schizophrenia (SCZ) is a complex psychiatric syndrome with uncertain etiology. This study aimed to uncover the expression profiles and related regulatory networks of circular RNA (circRNA) in SCZ. Whole transcriptome sequencing was performed to assess the expression profiles of circRNAs and microRNAs (miRNAs) in the peripheral blood of three patients with SCZ and three healthy controls. Five circRNAs were validated by quantitative real-time PCR (RT-qPCR). TargetScan, RNAhybrid, and miRanda were performed to predict the target miRNAs of the top 10 dysregulated circRNAs. MiRTarBase was applied to predict the target mRNAs of miRNAs to construct circRNA-miRNA-mRNA (ceRNA) networks. CatRAPID and StarBase were used to predict the target RNA-binding proteins (RBPs) of circRNAs to construct circRNA-RBP networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the potential functions of the maternal genes of circRNAs and target mRNAs. In total, 450 circRNAs and 160 miRNAs were found to be significantly differentially expressed, with hsa_circ_0003999 and hsa_circ_0030042 being significantly different between patients with SCZ and healthy controls (P < 0.05). The PI3K-AKT, MAPK, and cell cycle pathways were predicted to be associated with SCZ. GO analysis showed that focal adhesion was related to SCZ. The ceRNA networks, especially hsa_circ_0006151/hsa-miR-4685-3p/ZBTB16, hsa_circ_0000008/hsa-miR-1976/ZBTB16, and the hsa_circ_0007963/hsa-miR-3127-3p/UBE2K axes have the greatest probability of being involved in the pathophysiology of SCZ. The RBP networks, FXR1, FXR2, DGCR8, XRN2, FMR1, and QKI were the RBPs associated with SCZ. In conclusion, the circRNAs, ceRNAs, and RBP network expression patterns and related pathways indicate the potential role of circRNAs in the pathogenesis and development of SCZ.

Development of a Real-time TaqMan PCR Assay for The Detection of Porcine Circovirus 4.

Introduction: Porcine circovirus 4 (PCV4) was first discovered in 2019 in a herd of pigs with porcine respiratory disease, dermatitis and nephropathy syndrome in Hunan Province, China. It has subsequently been detected in other provinces and in South Korea. In consideration of the potential of the virus to cause an epidemic, rapid, sensitive, and specific detection of PCV4 is needed, as is the facilitation of further epidemiological research through elucidation of the whole genome of PCV4. This study had those two aims. Material and Methods: Fifty-five blood samples, two pig tissue samples, nine saliva swabs and one semen sample which all originated from Sichuan province pig farms were analysed. The virus' genome of 1,770 bp was synthesised artificially based on a Chinese reference strain and primers and probes for the ORF2 gene were designed. Then, the amplified target fragment was cloned into the pMD19-T vector and a series of diluted recombinant plasmids were used to generate a standard curve. An optimised real-time TaqMan PCR method was established. Results: The results of this study showed that the established method is specific for PCV4 but not for other viruses, and has amplification efficiency of 99.6%, a regression squared value (R2) of 1.000 and a detection limit of 2.2×10 DNA copies. This method was shown to be analytically specific and sensitive with a low intra- and inter-assay coefficient of variation (<1.67 %). Of a total of 67 clinical samples tested using the established method, three were shown to be positive (4%). Conclusion: This study confirms the existence of PCV4 in Sichuan and provides a promising alternative tool for rapid detection of PCV4.

The Antiviral Effect of Isatis Root Polysaccharide against NADC30-like PRRSV by Transcriptome and Proteome Analysis.

(1) Background: In recent years, the porcine reproductive and respiratory syndrome virus (PRRSV) has become a virulent pathogen that has caused devastating diseases and economic losses worldwide in the swine industry. IRPS has attracted extensive attention in the field of virology. However, it is not clear that IRPS has an antiviral effect on PRRSV at gene and protein levels. (2) Methods: We used transcriptomic and proteomic analysis to investigate the antiviral effect of IRPS against PRRSV. Additionally, a microbiome was used to explore the effects of IRPS on gut microbes. (3) Results: IRPS significantly extenuated the pulmonary pathological lesions and inflammatory response. We used transcriptomic and proteomic analysis to investigate the antiviral effect of IRPS against PRRSV. In the porcine model, 1669 differentially expressed genes (DEGs) and 370 differentially expressed proteins (DEPs) were identified. Analysis of the DEG/DEP-related pathways indicated immune-system and infectious-disease (viral) pathways, such as the NOD-like receptor (NLR) signaling pathway, toll-like receptor (TLR) signaling pathway, and Influenza A-associated signaling pathways. It is noteworthy that IRPS can inhibit NLR-dependent gene expression, then reduce the inflammatory damage. IRPS could exert beneficial effects on the host by regulating the structure of intestinal flora. (4) Conclusions: The antiviral effect of IRPS on PRRSV can be directly achieved by omics techniques. Specifically, the antiviral mechanism of IPRS can be better elucidated by screening target genes and proteins using transcriptome and proteome sequencing, and then performing enrichment and classification according to DEGs and DEPs.

Genome-wide association studies-supported rs12966547 variant of the long noncoding RNA LOC105372125 is significantly associated with susceptibility to schizophrenia and bipolar disorder in Han Chinese women.

OBJECTIVE: Genome-wide association studies have found that rs12966547 polymorphism was associated with susceptibility to schizophrenia in European populations. Recent studies showed that a genetic overlap may exist in schizophrenia and bipolar disorder. Here, we analyzed the associations between LOC105372125 rs12966547 polymorphism and schizophrenia and bipolar disorder in the Han Chinese population. METHODS: Our study recruited 548 schizophrenia patients, 512 bipolar disorder patients, and 598 healthy controls. Genotyping of rs12966547 were performed using the Sequenom MassARRAY platform. RESULTS: A significant association between rs12966547 polymorphism and susceptibility to bipolar disorder was observed after adjusting for sex and age (additive model: Padj = 0.040, recessive model: Padj = 0.044). However, no significant association was found between rs12966547 polymorphism and schizophrenia risk (all P > 0.05). In the analysis of gender, rs12966547 polymorphism was significantly associated with bipolar disorder (additive model: Padj = 0.027) and schizophrenia (dominant model: Padj = 0.039) in women. However, no significant association was found between rs12966547 polymorphism and the risk of bipolar disorder or schizophrenia in men (all Padj > 0.05). CONCLUSIONS: Polymorphism of rs12966547 on the long noncoding RNA LOC10537215 are a shared genetic variant of schizophrenia and bipolar disorder in Han Chinese women.

Influence of the rs6736 Polymorphism on Ischemic Stroke Susceptibility in Han Chinese Individuals via the Disruption of miR-7-1 Binding to the C14orf119 Gene.

This study investigates the association between the C14orf119 gene rs6736 polymorphism and ischemic stroke (IS) susceptibility, and explores the influence of the rs6736 polymorphism on the binding between miR-7-1 and the C14orf119 gene. mRNA expression levels were determined in 45 IS patients and 45 matched controls via real-time quantitative PCR. A total of 774 IS patients and 793 matched controls were recruited from a Han Chinese population for genotyping, performed with the Sequenom MassARRAY iPLEX platform. A dual-luciferase reporter assay was used for the analysis of miRNA-mRNA binding. The results showed that the mRNA expression of C14orf119 differed significantly between IS patients and controls (t = -2.235, P = 0.030). Significant associations were noted between the C14orf119 gene rs6736 polymorphism and IS susceptibility in Han Chinese individuals under the additive model [ORadj (95% CI) = 0.87 (0.76-1.00) Padj = 0.048] and dominant model [ORadj (95% CI) = 0.76 (0.61-0.94), Padj = 0.014], with adjustment for age and sex. Mutations in the rs6736 polymorphism disrupted the binding of miR-7-1 and the C14orf119 gene. The results of this study show that the rs6736 polymorphism in the 3'-untranslated region of the C14orf119 gene not only is associated with IS but also modifies the binding between miR-7-1 and the C14orf119 gene. The C14orf119 gene may participate in the relationship between IS and miR-7-1.

LncRNA SERPINB9P1 expression and polymorphisms are associated with ischemic stroke in a Chinese Han population.

Long noncoding RNAs (lncRNAs) were reported to play important roles in the pathogenesis of ischemic stroke (IS). Our study aimed to investigate the role of lncRNA SERPINB9P1 expression in ischemic stroke and the association between SERPINB9P1 polymorphisms and IS risk, as well as examine the correlation of SERPINB9P1 expression and variants with clinical parameters of IS. The SERPINB9P1 levels in human participants and oxygen-glucose deprivation (OGD)-treated human A172 cells were measured by qRT-PCR. The SERPINB9P1 polymorphisms (rs375556 and rs318429) were genotyped by the MassARRAY platform. We found that the SERPINB9P1 expression was significantly downregulated in patients with IS compared with that in healthy controls. On the 14th day in the hospital, the SERPINB9P1 level in patients with moderate and severe stroke was significantly downregulated compared with the normal group. After stratification by gender, the rs375556 polymorphism was significantly associated with susceptibility to female IS in the recessive model, and the significant association remained after adjusting for age. After adjusting for gender and age, rs318429 was significantly associated with FPG and D-D levels, and rs375556 was significantly associated with INR and PTA levels in IS cases. Besides, the lncRNA SERPINB9P1 expressed downregulated in OGD/reoxygenation-treated human A172 cells. In conclusion, the lncRNA SERPINB9P1 may protect against cerebral ischemia-reperfusion injury and neurological impairment after IS. The SERPINB9P1 rs375556 polymorphism was associated with susceptibility to female IS, and SERPINB9P1 polymorphisms may influence the metabolism of blood glucose and regulation of coagulation function in patients with IS.

Application of machine learning in diagnostic value of mRNAs for bipolar disorder.

PURPOSE: Bipolar disorder (BD) is a type of severe mental illness with symptoms of mania or depression, it is necessary to find out effective diagnostic biomarkers for BD due to diagnosing BD is based on clinical interviews without objective indicators. MATERIALS AND METHODS: The mRNA expression levels of genes included PIK3R1, FYN, TP53, PRKCZ, PRKCB, and YWHAB in the peripheral blood of 43 patients with bipolar disorder and 47 healthy controls were detected. Machine learning methods included Artificial Neural Networks, Extreme Gradient Boosting, Random Forest, and Support Vector Machine were adopted to fit different gene combinations to evaluate diagnostic value for bipolar disorder. RESULTS: The combination 'PIK3R1 + FYN' in the SVM model showed the best diagnostic value, with AUC, sensitivity, and specificity values of 0.951, 0.928, and 0.937, respectively. CONCLUSIONS: The diagnostic efficiency for bipolar disorder was significantly improved by fitting PIK3R1 and FYN through the Support Vector Machine model.

Ligand based 3D-QSAR model, pharmacophore, molecular docking and ADME to identify potential fibroblast growth factor receptor 1 inhibitors.

The FGF/FGFR system may affect tumor cells and stromal microenvironment through autocrine and paracrine stimulation, thereby significantly promoting oncogene transformation and tumor growth. Abnormal expression of FGFR1 in cells is considered to be the main cause of tumorigenesis and a potential target for the treatment of cancer. In this study, a combination of structure-based drug carriers and molecular docking-based virtual screening was used to screen new potential FGFR1 inhibitors. Forty eight known inhibitors were collected to establish 3 D-QSAR models and pharmacophore models, investigate the relationship between the activity and conformation of compounds, and verify the efficiency of pharmacophore. In Accelrys Discovery Studio 2016, the ZINC database was filtered by Lipinski's Rule of Five and SMART's filtration. Then, Hypo01 was used for virtual screening of ZINC database. Compounds with predicted activity values less than 1 µM were molecularly docked with FGFR1 protein crystals, the docking results were observed, and the interaction between compounds and targets was studied. The absorption, distribution, metabolism and excretion (ADME) and toxicity of potential inhibitors were studied, and a compound with new structural scaffolds were obtained. It could be further studied to explore their better therapeutic effects. Communicated by Ramaswamy H. Sarma.

Evaluation of a strawberry fermented beverage with potential health benefits.

BACKGROUND: Functional fermented beverages are popular worldwide due to their potential to promote health. Starter culture is the main determinant of the final quality and flavor of fermented beverages. The co-cultivation of lactic acid bacteria (LAB) and yeast makes a significant contribution to the safe flavor of fermented beverages. However, the research on the potential of antioxidant, antimicrobial, and anti-biofilm formation of strawberry fermented beverage obtained by combining the LAB and yeast as starter cultures has not been well explored. METHODS: In this study, LAB and yeast were combined as starter culture to obtain strawberry fermented beverage. Fourier transform infrared (FTIR ) spectroscopy was used for the qualitative analysis of the fresh strawberry juice and fermented beverage. From the changes in antioxidant content, free radical scavenging ability, total superoxide dismutase (T-SOD) activity and total antioxidant capacity (T-AOC) to evaluate the antioxidant capacity of fermented beverage in vitro. The antibacterial ability was tested by the Oxford cup method. The biofilms of Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 6538 under fermented beverages treatment was observed by Fluorescence microscope. In addition, sensory analysis was conducted in this study. RESULTS: In this study, the absorption peaks of Fourier transform infrared between 1,542 cm-1 and 976 cm-1, suggest the existence of organic acids, sugars and ethanol. The total phenols and total flavonoids content decreased by 91.1% and 97.5%, respectively. T-SOD activity increased by 33.33%.The scavenging ability of fermented beverage on superoxide anion free radicals was enhanced, and the scavenging ability on DPPH free radicals, hydroxyl free radicals, and ABTS free radicals was weakened. However, the T-AOC increased from 4.15 ± 0.81 to 8.43 ± 0.27 U/mL. Fermented beverage shows antibacterial activity against four pathogens. The minimum inhibitory concentration (MIC) values of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538 were 0.05 mL/mL and 0.025 mL/mL, respectively, and the minimum bactericidal concentration (MBC) were both 0.2 mL/mL. It was observed by fluorescence microscope that the green fluorescence area of the two biofilms is greatly reduced after being treated with fermented beverage. Sensory analysis results show that the average scores of fermented beverage in color, appearance and taste were increased. The overall impression and flavor were decreased. CONCLUSION: These results demonstrated that strawberry fermented beverage has potential benefits such as an antioxidant, antibacterial, and anti-biofilm formation, providing the potential for the fermented beverage to become promising candidates for natural antioxidants, antibacterial agents and anti-biofilm agents.

Biofilm characteristics and transcriptomic analysis of Haemophilus parasuis.

Haemophilus parasuis (H. parasuis) is a conditional pathogen with the ability to form biofilms which can lead to ineffective drug treatment and severe chronic infections resulting in significant economic losses to the pig industry. Currently, knowledge of biofilm formation by H. parasuis is not well developed. The objective of this study was to investigate the three-dimensional morphology of biofilms and perform transcriptomic analysis on H. parasuis cells in biofilm versus planktonic forms. The results showed that proteins and DNA accounted for a large proportion of the H. parasuis biofilm extracellular matrix. Here, we have traced the entire biofilm formation process of H. parasuis from beginning to end for the first time. These biofilms grew rapidly in the first 48 h and became stable at 60 h. According to GO and KEGG analysis, the differentially expressed genes (DEG) artM, artQ, ssrS, pflA and HutX were implicated as being involved in bacterial colonisation and adhesion; these are the most likely genes to affect biofilm formation. Most functional gene enrichments were of those involved in metabolic pathways, biosynthesis of secondary metabolites, ATP-binding cassette (ABC) transporters, and starch and sucrose metabolism. Thus, in the present pilot study, the composition and characteristics of these biofilms were explored, and the genes related to biofilm formation were screened for. This research lays the foundation for further studies on mechanisms regulating biofilm formation, in order to find new drug targets and develop new therapeutic drugs against H. parasuis.

Machine Learning Analysis of MicroRNA Expression Data Reveals Novel Diagnostic Biomarker for Ischemic Stroke.

OBJECTIVES: Ischemic stroke (IS) is one of the leading causes of morbidity and mortality worldwide. Circulating microRNAs have a potential as minimally invasive biomarkers for disease prediction, diagnosis, and prognosis. In this study, we sought to use different machine learning algorithms to identify an optimal model of microRNA by integrating the expression data of pre-selected microRNAs for discriminating patients with IS from controls. METHODS: The expression level of microRNAs in the peripheral blood of 50 patients with IS and 50 matched controls were assessed through real-time polymerase chain reaction (qRT-PCR). Machine learning algorithms, including artificial neural network, random forest, extreme gradient boosting, and support vector machine (SVM) were employed via R 3.6.3 software to establish diagnostic models for IS. RESULTS: The IS group had significantly increased expression levels of miR-19a (P < 0.001), miR-148a (P < 0.001), miR-320d (P = 0.003), and miR-342-3p (P < 0.001) compared with the control group. MiR-148a, miR-342-3p, miR-19a, and miR-320d yielded areas under the receiver operating characteristic curve (AUC) of 0.872, 0.844, 0.721, and 0.673, respectively, with 0.740, 0.940, 0.740, and 0.840 sensitivity and 0.920, 0.640, 0.600, and 0.440 specificity, respectively. Model miR-148a + miR-342-3p + miR-19a had the best predictive value when analyzed via SVM algorithm with AUC, sensitivity, and specificity values of 0.958, 0.937, and 0.889, respectively. CONCLUSION: The diagnostic value of the combination of miR-148a, miR-342-3p, and miR-19a through SVM algorithm has the potential to serve as a feasible approach to promote the diagnosis of IS.

Optimal extraction, purification and antioxidant activity of total flavonoids from endophytic fungi of Conyza blinii H. Lév.

BACKGROUND: Flavonoids are widely used in the market because of their antibacterial, antiviral, and antioxidant activities. But the production speed of flavonoids is limited by the growth of plants. CBL9 (Chaetomium cruentum) is a flavonoid-producing endophytic fungi from Conyza blinii H. Lév, which has potential to produce flavonoids. METHODS: In this study, we isolated total flavonoids from endophytic fungus CBL9 of Conyza blinii H. Lév using macroporous resin D101. The process was optimized by response surface and the best extraction process was obtained. The antioxidant activities of total flavonoids were analyzed in vitro. RESULTS: It was found that the best parameters were 25 °C pH 2.80, 1.85 h, and the adsorption ratio reached (64.14 ± 0.04)%. A total of 60% ethanol was the best elution solvent. The elution ratio of total flavonoid reached to (81.54 ± 0.03)%, and the purity was 7.13%, which was increased by 14.55 times compared with the original fermentation broth. Moreover its purity could rise to 13.69% after precipitated by ethanol, which is very close to 14.10% prepared by ethyl acetate extraction. In the antioxidant research, the clearance ratio of L9F-M on DPPH, ABTS, •OH, •O2-, (96.44 ± 0.04)% and (75.33 ± 0.03)%, (73.79 ± 0.02)%, (31.14 ± 0.01)% at maximum mass concentration, was higher than L9F. CONCLUSION: The result indicated using macroporous resin in the extraction of total flavonoid from endophytic fungus is better than organic solvents with higher extraction ratio, safety and lower cost. In vitro testing indicated that the flavonoid extracted by macroporous resin have good antioxidant activity, providing more evidence for the production of flavonoid by biological fermentation method.

Expression of antimicrobial peptide Cecropin P1 in Saccharomyces cerevisiae and its antibacterial and antiviral activity in vitro

BACKGROUND: Cecropin P1, acting as an antimicrobial, has a broad-spectrum antibacterial activity with some antiviral and antifungal properties. It is a promising natural alternative to antibiotics which is originally isolated from the pig intestinal parasitic nematode Ascaris suum. Many studies have shown that Cecropin P1 is helpful for the prevention or treatment of clinical diseases. Therefore, it is very necessary to establish a safe, nontoxic, and efficient expression method of Cecropin P1. RESULTS: The results indicated that the recombinant protein was about 5.5 kDa showed by Tricine­SDS­ PAGE and Western blot. And Cecropin P1 was efficiently secreted and expressed after 12 h of induction, with an increasing yield over the course of the induction. Its maximum concentration was 7.83 mg/L after concentration and purification. In addition, in vitro experiments demonstrated that Cecropin P1 not only exerted a strong inhibitory effect on Escherichia coli, Salmonella sp., Shigella sp., and Pasteurella sp., but also displayed an antiviral activity against PRRSV NADC30-Like strain. CONCLUSIONS: Collectively, the strategy of expressing Cecropin P1 in Saccharomyces cerevisiae is harmless, efficient, and safe for cells. In addition, the expressed Cecropin P1 has antiviral and antibacterial properties concurrently.

The machine learning algorithm for the diagnosis of schizophrenia on the basis of gene expression in peripheral blood.

BACKGROUND: Schizophrenia (SCZ) is a highly heritable mental disorder with a substantial disease burden. Machine learning (ML) method can be used to identify individuals with SCZ on the basis of blood gene expression data with high accuracy. METHODS: This study aimed to differentiate patients with SCZ from healthy individuals by using the messenger RNA expression level in peripheral blood of 48 patients with SCZ and 50 controls via ML algorithms, namely, artificial neural networks, extreme gradient boosting, support vector machine (SVM), decision tree, and random forest. The expression of six mRNAs was detected using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS: The relative expression levels of GNAI1 (P < 0.001), PRKCA (P < 0.001), and PRKCB (P = 0.021) increased in the SCZ group, whereas those of FYN (P < 0.001), LYN (P = 0.022), and YWHAZ (P < 0.001) decreased in the SCZ group. We generated models with various combinations of genes based on five ML algorithms. The SVM model with six factors (GNAI1, FYN, PRKCA, YWHAZ, PRKCB, and LYN genes) was the best model for distinguishing patients with SCZ from healthy individuals (AUC = 0.993, sensitivity = 1.000, specificity = 0.895, and Youden index = 0.895). CONCLUSIONS: This study suggested that the combination of genes using the ML method is better than the use of a single gene to discriminate patients with SCZ from healthy individuals. The combination of GNAI1, FYN, PRKCA, YWHAZ, PRKCB, and LYN under the SVM model can be used as a diagnostic biomarker for SCZ.

Phosphoinositide-3-kinase regulatory subunit 1 gene polymorphisms are associated with schizophrenia and bipolar disorder in the Han Chinese population.

Schizophrenia (SCZ) and bipolar disorder (BD) are severe psychiatric disorders that share many genetic risk factors. This study aimed to investigate the association of phosphoinositide-3-kinase regulatory subunit1 (PIK3R1) gene rs3756668 and rs3730089 polymorphisms with SCZ and BD risks and determine the expression levels of PIK3R1. A total of 548 SCZ cases, 512 BD cases, and 598 healthy controls were included in this study. Single nucleotide polymorphisms (SNPs) were genotyped using the Sequenom MassARRAY platform, and quantitative reverse transcription polymerase chain reaction was conducted to examine the mRNA expression of PIK3R1. The genotypic distribution of rs3756668 in the BD group was significantly different from that in the healthy controls (P = 0.038). After adjustment for gender and age was made, rs3730089 was significantly associated with the risk of SCZ [AA/(AG + GG): OR = 2.25, Padj = 0.040; AA/GG: OR = 2.27, Padj = 0.038]. The SNP rs3756668 was associated with the susceptibility of BD (AA+GG/AG: OR = 0.73, P = 0.011) and the association remained after adjusting for gender and age. The mRNA level of PIK3R1 was significantly upregulated in patients with BD compared with that in the control group (P < 0.001). In terms of the diagnostic value of PIK3R1 for BD, the receiver operating characteristic curve analysis showed an area under the curve of 0.809 with 74.0% sensitivity and 73.9% specificity. PIK3R1 may be the shared susceptibility gene of SCZ and BD and may be a potential diagnostic biomarker for BD.

TP53 Polymorphism Contributes to the Susceptibility to Bipolar Disorder but Not to Schizophrenia in the Chinese Han Population.

TP53 has been reported to be involved in diverse neurological processes related to the pathogenesis of psychosis. In this study, we aim to determine the association of TP53 polymorphisms, rs1042522 and rs17879353, with the susceptibility to schizophrenia (SCZ) or bipolar disorder (BD) in Chinese Han population. A total of 548 SCZ patients, 512 BD patients, and 598 healthy controls were recruited. Genotyping was conducted through Sequenom MassARRAY technology platform. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect TP53 expression level. Results revealed that the allele frequency and genotype distribution of rs1042522 within BD patients were significantly different from those of the controls. Rs1042522 was significantly associated with BD risk under diverse genetic models. However, no significant association was found for rs17879353 and BD risk and for rs1042522 and rs17879353 and SCZ risk. TP53 expression was significantly increased in SCZ patients and BD patients compared with that in the controls but was significantly decreased in BD patients with CC genotype of rs1042522 compared with that in other BD patients with either CG or GG genotype. In summary, we observed for the first time that rs1042522 is significantly associated with BD risk in the Chinese Han population. The increased TP53 expression might affect the occurrence of BD and SCZ, and rs1042522 might affect the progress of BD by disturbing gene expression.

Influence of CTNNB1 rs2953 polymorphism on schizophrenia susceptibility in Chinese Han population through modifying miR-485 binding to CTNNB1.

Schizophrenia (SCZ) and bipolar disorder (BD) are two major neuropsychiatric diseases that are the most substantial causes of disability and mortality worldwide. CTNNB1 encodes beta-catenin, an important protein in canonical Wnt signaling. We aimed to investigate the association between the rs2953 of CTNNB1 and the risk of SCZ and BD and to further explore the function of rs2953. A total of 1658 samples (548 SCZ cases, 512 BD cases, and 598 controls) were examined in terms of the genotype of CTNNB1 rs2953. The mRNA expression level of CTNNB1 significantly increased in the SCZ and BD groups compared with that in the control group. Significant association remained between CTNNB1 3'-untranslated region (UTR) variant rs2953 and SCZ susceptibility (additive and dominant model) after gender and age were adjusted. rs2953 disrupted the binding of CTNNB1 and miR-485. miR-485 significantly suppressed the luciferase activity of CTNNB1-T vector by binding to the CTNNB1 3'-UTR containing the T allele of rs2953. The mRNA expression of CTNNB1 can be used as a biomarker for the diagnosis of SCZ and BD. The 3'-UTR variant rs2953 in CTNNB1 influences the risk of SCZ in the Han Chinese population and modifies the binding of miR-485 to CTNNB1.