Antibody-based gene expression profiling of peripheral blood from patients with idiopathic inflammatory myopathy / 中华风湿病学杂志

Objective:To elucidate the pathophysiological mechanisms of idiopathic inflammatory myopathy subtypes by analyzing the gene expression profiles of peripheral blood mononuclear cells (PBMCs) from anti-MDA5 antibody-positive and anti-Jo-1 antibody-positive myositis patients.Methods:Gene expression profiling screening and analysis of PBMCs from 12 anti-MDA5 positive, 16 anti-Jo-1 positive myositis patients and 43 healthy controls were performed using Illumina HT-12 v4 expression profiling microarrays. Applying the unpaired t test with Benjamini-Hochberg correction, the genes with the absolute value of fold change (FC) in gene expression signal ≥2 and adjusted P<0.05 were selected as differentially expressed genes. Differential gene sets were subjected to Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, with P<0.05 as the threshold for being significantly enriched. Validation of differentially expressed genes by real time-PCR. The Kolmogorov-Smirnov test was used to test the normality of continuous variables. If the distribution was normal and the variance was homogeneous, analysis of variance (one-way ANOVA) was used.If the distribution was not normal, Kruskal-Wallis test was used, and P<0.05 was regarded as statistically significant difference. Results:Analysis of gene expression profiles of PBMCs from patients with positive anti-MDA5 and anti-Jo-1 antibody revealed significant differences in gene expression of PBMCs from patients with the two myositis subtypes. The number of differentially expressed genes that specifically up-regulated in anti-MDA5 antibody positive patients was 407, and the GO functional enrichment analysis was mainly enriched in biological processes such as innate immune response ( P<0.001), response to virus ( P<0.001) and type Ⅰ interferon signaling pathway ( P<0.001), and the KEGG pathway enrichment analysis was mainly enriched in the viral infection-associated pathway ( P<0.001), RIG-Ⅰ like receptor signaling pathway ( P<0.001) and Toll-like receptor signaling pathway ( P=0.002), etc. The 259 differential genes specifically down-regulated in the anti-MDA5 antibody positive group were mainly enriched in biological processes such as immune response ( P=0.006), TGF-β receptor signaling pathway ( P=0.010) and natural killer cell mediated immunity ( P=0.015) in GO functional enrichment analysis. There were 162 differentially expressed genes up-regulated specifically in anti-Jo-1 antibody positive patients, and GO functional enrichment analysis was mainly enriched in biological processes such as nucleosome assembly ( P<0.001), negative regulation of cell growth ( P=0.001), negative regulation of apoptotic process P=0.004), and innate immune response in mucosa ( P=0.012), and the KEGG pathway enrichment analysis mainly enriched in metabolic-related signaling pathways ( P<0.001) and immune-related pathways ( P<0.001), etc. Real-time PCR confirmed that IFIH1 ( P=0.037), ISG15 ( P=0.003), and DDX58 ( P=0.032) in the RIG-Ⅰ-like receptor pathway as well as chemokines MCP-1 ( P=0.003), MCP-2 ( P<0.001), and transcription factor BATF2 ( P=0.002), and inflammatory signaling pathway-associated MYD88 ( P<0.001) were highly expressed in PBMCs from anti-MDA5 antibody-positive myositis patients. Conclusion:The gene expression profile of PBMCs in anti-MDA5 antibody-positive patients suggests that the pathogenesis of patients with anti-MDA 5 antibody positive is closely related to biological processes such as innate immune response, viral infection, and interferon response.

Study of genetic profiles and haematological phenotypes of δ-thalassemia in Guangdong population / 中华检验医学杂志

Objective:To investigate genetic variation profiles of δ-globin (HBD gene) and hematological phenotypes in Guangdong population.Methods:Retrospective case analysis was performed in this study. Blood samples of 11 616 couples who participated in free thalassemia screening in Guangzhou from July 2020 to December 2022 were collected which underwent blood routine tests and hemoglobin (Hb) capillary electrophoresis. According to the results, 154 samples were enrolled in this study: (1)group of 35 cases with HbA 2 <2.0% but no HbF band; (2)group of 64 cases with HbA 2 < 2.0% and HbF band; (3)group of 25 cases with HbA 2 <2.0% and suspected HbA 2 variants; (4) group of 25 cases with HbA 2 ≥2.0% and <3.5% and HbF band, as well as abnormal blood routine report [mean corpuscular volume (MCV) <82 fl and/or mean corpuscular hemoglobin (MCH) <27 pg]; (5)group of 5 cases with HbA 2 ≥2.0% and <3.0% accompanied with β thalassemia gene carriers Sanger sequencing was used to detect single nucleotide variants of δ-globin. Results:(1) A total of 22 genetic variations were detected, including 6 de novo variations, and the top 3 genetic variations were respectively c.-127T>C (57.02%, 65/114), c.-80T>C (9.65%, 11/114), c.349C>T (7.89%, 9/114). (2) In group of patients with HbA 2 <2.0% but no HbF band, 22 cases (62.85%, 22/35) had HBD gene variation, including 7 cases with MCV and MCH lower than reference values, 4 cases with α thalassemia; 13 cases had no HBD gene variation, including 12 cases with lower MCV and MCH. Among 19 cases with abnormal blood routine test results, levels of HbA 2 in patients (7 cases) with HBD gene variation were lower compared with those without HBD gene variation (12 cases) ( P<0.01%). (3)In group of patients with HbA 2<2.0% with HbF band, 59 cases (92.18%, 59/64) had HBD gene variations whose mutations all occurred in promoter region, and the HbF were all lower than 5.0%; 5 cases with HbF >5.0% had no HBD gene variation. (4) In group of patients with HbA 2 <2.0% and suspected HbA 2 variants, the detection rate was 100% (25/25) and δ-globin variants <1.0%. (5) In group of patients with HbA 2 ≥2.0% and <3.5% and HbF band accompanied with abnormal blood routine results, no HBD gene variation was found. (6) In group of 5 patients with HbA 2 ≥2.0% and <3.0% with β thalassemia gene carriers, HBD gene variation were found in all cases, and the level of HbA 2 was (2.62±0.17)% and HbF was (3.62±2.22)%. Conclusions:There are various genotypes of HBD gene variation, among which HBD: c.-127T>C is the most common in Guangdong population in China. Mutations in the promoter region may cause decrease in HbA 2 and increase in HbF which is mostly less than 5% but exceeds 5.0% when combined with β thalassemia. Our study enriched the gene mutation profiles of HBD gene in Guangdong population.

Role of glutathione transferase in nonalcoholic fatty liver disease: An analysis based on gene expression profile / 临床肝胆病杂志

Objective To investigate the role of glutathione transferase in nonalcoholic fatty liver disease (NAFLD) induced by high-fat diet using the RNA-Seq technique in combination with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes. Methods A total of 14 male C57BL/6J mice were divided into control group with 6 mice and model group with 8 mice by random sampling. The mice in the control group were fed with normal diet, and those in the model group were fed with high-fat diet for 7 consecutive weeks to establish a model of NAFLD. Kits were used to measure the activities of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and the level of triglyceride (TG), and HE staining and oil red staining were used to observe liver pathology and deposition of lipid droplets. Liver tissue RNA was extracted for RNA-Seq, and genes with a fold change of ≥2.0 and a P value of 0.05). Compared with the control group, the model group had a significantly higher serum level of TG (2.02±0.50 mmol/L vs 1.00±0.29 mmol/L, t =-4.45, P =0.001). HE staining showed diffuse steatosis and ballooning degeneration in the model group, and oil red staining showed that the model group had a significant increase in orange-red lipid droplets in the cytoplasm of hepatocytes and a significantly higher grade of hepatocyte steatosis than the control group (1.88±0.64 vs 1.00±0.00, t =-3.86, P =0.006). RNA-seq results showed a total of 1367 differentially expressed genes between the two groups, among which there were 608 upregulated genes and 759 downregulated genes, and there were 17 differentially expressed GST genes between the two groups. The top 10 GST genes in terms of fold change were validated, and compared with the control group, the model group had downregulated expression of GSTa2, GSTa3, GSTa4, GSTm1, GSTm2, GSTm3, GSTm4, GSTp1, and GSTo1 and upregulated expression of GSTk1. The results of qRT-PCR were consistent with the results of sequencing. Conclusion GST affects lipid metabolism by participating in various biological processes such as steroid metabolism, fatty acid metabolism, and cholesterol metabolism and is closely associated with the pathogenesis of NAFLD.

Clinicopathologic characteristics and prognostic analysis of testicular diffuse large B-cell lymphoma / 中华血液学杂志

Objective: To analyze the clinicopathologic characteristics and prognosis of testicular diffuse large B-cell lymphoma (DLBCL) . Methods: A retrospective analysis was performed on 68 patients with testicular DLBCL admitted to Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine from October 2001 to April 2020. The gene mutation profile was evaluated by targeted sequencing (55 lymphoma-related genes) , and prognostic factors were analyzed. Results: A total of 68 patients were included, of whom 45 (66.2% ) had primary testicular DLBCL and 23 (33.8% ) had secondary testicular DLBCL. The proportion of secondary testicular DLBCL patients with Ann Arbor stage Ⅲ-Ⅳ (P<0.001) , elevated LDH (P<0.001) , ECOG score ≥ 2 points (P=0.005) , and IPI score 3-5 points (P<0.001) is higher than that of primary testicular DLBCL patients. Sixty-two (91% ) patients received rituximab in combination with cyclophosphamide, adriamycin, vincristine, and prednisone (R-CHOP) -based first-line regimen, whereas 54 cases (79% ) underwent orchiectomy prior to chemotherapy. Patients with secondary testicular DLBCL had a lower estimated 5-year progression-free survival (PFS) rate (16.5% vs 68.1% , P<0.001) and 5-year overall survival (OS) rate (63.4% vs 74.9% , P=0.008) than those with primary testicular DLBCL, and their complete remission rate (57% vs 91% , P=0.003) was also lower than that of primary testicular DLBCL. The ECOG scores of ≥2 (PFS: P=0.018; OS: P<0.001) , Ann Arbor stages Ⅲ-Ⅳ (PFS: P<0.001; OS: P=0.018) , increased LDH levels (PFS: P=0.015; OS: P=0.006) , and multiple extra-nodal involvements (PFS: P<0.001; OS: P=0.013) were poor prognostic factors in testicular DLBCL. Targeted sequencing data in 20 patients with testicular DLBCL showed that the mutation frequencies of ≥20% were PIM1 (12 cases, 60% ) , MYD88 (11 cases, 55% ) , CD79B (9 cases, 45% ) , CREBBP (5 cases, 25% ) , KMT2D (5 cases, 25% ) , ATM (4 cases, 20% ) , and BTG2 (4 cases, 20% ) . The frequency of mutations in KMT2D in patients with secondary testicular DLBCL was higher than that in patients with primary testicular DLBCL (66.7% vs 7.1% , P=0.014) and was associated with a lower 5-year PFS rate in patients with testicular DLBCL (P=0.019) . Conclusion: Patients with secondary testicular DLBCL had worse PFS and OS than those with primary testicular DLBCL. The ECOG scores of ≥2, Ann Arbor stages Ⅲ-Ⅳ, increased LDH levels, and multiple extra-nodal involvements were poor prognostic factors in testicular DLBCL. PIM1, MYD88, CD79B, CREBBP, KMT2D, ATM, and BTG2 were commonly mutated genes in testicular DLBCL, and the prognosis of patients with KMT2D mutations was poor.

Transcriptomic analyses in hippocampus based on RNA-seq and construction of a competing endogenous RNA regulatory network in mice with sepsis-associated encephalopathy / 中华麻醉学杂志

Objective:To identify the differentially expressed long-chain non-coding RNA(lncRNA) and mRNA using ribonucleic acid sequencing(RNA-seq), and construct a competing endogenous RNA(ceRNA) regulatory network in mice with sepsis-associated encephalopathy.Methods:Ten clean-grade healthy male C57BL/6 mice, aged 6-8 weeks, weighing 20-25 g, were divided into 2 groups( n=5 each) using a random number table method: sham operation group(group Sham) and sepsis group(group Sepsis). Sepsis was induced by cecal ligation and puncture(CLP) in group Sepsis, while group Sham only underwent laparotomy without CLP. Morris water maze test and contextual fear conditioning test were performed to detect the cognitive function on 1 day before CLP and 3 days after CLP. Three mice were randomly sacrificed in group Sham, and 3 mice with the worst results in the cognitive function test were sacrificed in group Sepsis. The hippocampal tissues were obtained for RNA-seq via the BGISEQ-500 platform, and the differentially expressed mRNA and lncRNA were identified. The differentially expressed mRNAs and lncRNAs were visualized and analyzed by Dr. Tom platform provided by Shenzhen BGI Technology Service Co., Ltd., and the ceRNA regulatory network was constructed using the online visualization tool Cytoscape software. Results:Compared with group Sham, the escape latency was significantly prolonged, and the percentage of time of staying at the target quadrants and percentage of time spent freezing were decreased in group Sepsis( P<0.05). A total of 62 differentially expressed lncRNAs were obtained from RNA-seq, of which the expression of 45 lncRNAs was up-regulated and the expression of 17 lncRNAs was down-regulated.There were 282 differentially expressed mRNAs identified from RNA-seq, of which the expression of 173 mRNAs was up-regulated, and the expression of 109 mRNAs was down-regulated.Gene Ontology enrichment analysis revealed that the differentially expressed mRNAs were involved in biological processes such as memory, learning or memory, inflammatory responses, regulation of aging-related behavioral decline, and regulation of synaptic plasticity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that differentially expressed mRNAs were enriched in IL-17 signaling pathway, TNF signaling pathway, NF-κB signaling pathway and etc. KDA analysis was performed on the differentially expressed mRNAs to identify the key driver genes, and the results showed that Ch25h, Il6ra, Lcn2, Sgk1, Nr4a3, Osm, Saa3, Ccl7, Sqle, Dhcr24 were the key SAE genes.A competing endogenous RNA regulatory network was successfully constructed based on 9 lncRNAs, 28 mRNAs and 134 miRNAs in the hippocampus of mice with SAE. Conclusions:The results of RNA-seq find that 10 mRNAs including Ch25h, Il6ra, Lcn2, Sgk1, Nr4a3, Osm, Saa3, Ccl7, Sqle, Dhcr24 and lncRNAs such as Rian, Gm35874 and Gm34347 are key genes regulating SAE in mice. Meanwhile, a ceRNA regulatory network based on lncRNA-miRNA-mRNA is successfully constructed in the hippocampus of mice with SAE.

Infiltration of tumor-associated macrophages and its association with prognosis of patients with diffuse large B-cell lymphoma based on gene expression profile data / 白血病·淋巴瘤

Objective:To analyze the infiltration of tumor-associated macrophages and their subtypes, and to investigate their association with prognosis of patients with diffuse large B-cell lymphoma (DLBCL) based on the gene chip expression database.Methods:The data were retrieved from microarray (Affymetrix U133 plus 2.0) database (No:GSE10846) of DLBCL patients in PubMed gene expression omnibus (GEO). The database included 414 DLBCL patients, among which 306 cases had complete clinical, cell of origin phenotype (COO subtyping), treatment and follow-up information. The data analysis was performed on the online computer program which could identify the cell-type (CIBERSORT) by estimating relative percentage of RNA transcripts. From the returned result file, the percentage of immune cells including macrophages subtypes of all cases in all identifiable immune cells in the microenvironment was identified in GSE10846 database. Taking the median percentage of macrophages subsets in all types of immune cells as cut-off value; ≥ cut-off value was high infiltration and < cut-off value was low infiltration. The median value of gene RNA expression level of myc, bcl-2, programmed death ligand-1 (PD-L1) and programmed death ligand-2 (PD-L2) of 414 DLBCL patients in the GSE10846 database was treated as the cut-off value; ≥ cut-off value was the high expression and < cut-off value was the low expression. The correlation of the expression levels of all subsets and total macrophages with clinical factors, gene expression, survival was analyzed; Cox proportional hazard model was used to make multivariate analysis of the prognosis for DLBCL patients. surv_cutpoint function of surv_miner package in R 4.0.4 software was used for the optimal cut-off value of the percentage of macrophages subsets in all immune cells in the microenvironment; the result less than the optimal cut-off value was statistically low infiltration and the result greater than or equal to the optimal cut-off value was statistically high infiltration.Results:CIBERSORT analysis showed that M0 macrophages [15.00% (0-44.41%)], M1 macrophages [7.46% (0-23.00%)] and M2 macrophages [6.28% (0-43.35%)] in the tumor microenvironment were identified in all 414 DLBCL cases. Among 306 patients with complete clinical and follow-up data, there were 155 cases (50.7%), 152 cases (49.7%), 156 cases (51.0%), 152 cases (49.7%), respectively in high infiltration patients with M0, M1, M2 and total macrophages; the high infiltration of M0 macrophages was correlated with COO subtyping germinal center B-cell (GCB) type and the high expression of PD-L1 gene, the absence of myc and bcl-2 double high expression at RNA level (R-DEL) (all P < 0.05); the high infiltration of M1 macrophages was correlated with female, the high expression of PD-L1 gene and PD-L2 gene (all P < 0.05); the high infiltration of M2 macrophages was correlated with COO subtyping GCB type, the high expression of PD-L2 gene (all P < 0.05); the high infiltration of total macrophages was correlated with female, COO subtyping GCB type, the high expression of PD-L1 gene and PD-L2 gene, the absence of R-DEL (all P < 0.05).The high expression of PD-L1 gene was associated with high infiltration of M0, M1 and total macrophages (all P < 0.01), and high PD-L2 gene expression was correlated with high infiltration of M1, M2 and total macrophages (all P < 0.01). The overall survival (OS) of M0 macrophage high infiltration group was better than that of the lower infiltration group ( P = 0.002); the OS of M2 macrophage low infiltration group was better than that of the high infiltration group ( P = 0.019). The OS of R-DEL group was worse than that of R-DEL absent group ( P = 0.001). The patients with low international prognostic index (IPI) score (0-2), COO subtyping GCB type, and treatment with rituximab had better OS (all P < 0.01). Multivariate Cox regression analysis showed that 60 years or above, COO subtyping non-GCB type, treatment without rituximab, M0 macrophage low infiltration, M2 macrophage high infiltration were all independent adverse prognostic factors for OS of DLBCL patients (all P < 0.05). The optimal cut-off value for M0 macrophages was 4.3%, and the optimal cut-off value for M2 macrophages was 4.8%, and the OS in the group with statistically low infiltration of M0 macrophage was worse ( P < 0.001), and so was the OS in the group with statistically high infiltration of M2 macrophage ( P = 0.001). Conclusions:Tumor-associated macrophage is confirmed as the most abundant immune cells in the tumor microenvironment of DLBCL. Patients with high infiltration of M2 macrophage have poor prognosis, while high infiltration of M0 macrophage indicates a better prognosis.

Values of Ki-67 expression level and 4 molecular types for risk classification of prognosis in medulloblastoma / 肿瘤研究与临床

Objective:To investigate the values of Ki-67 expression level and 4 molecular types for risk classification of prognosis in patients with medulloblastoma (MB).Methods:A retrospective study of 92 MB patients who underwent surgery and were confirmed by postoperative pathology in the First Affiliated Hospital of Zhengzhou University from January 2009 to January 2018 was performed. The clinical data and survival data of the patients were collected and sorted out. The overall survival (OS) and progression-free survival (PFS) were analyzed by Kaplan-Meier method, and the log-rank test was performed. Risk stratification of prognosis of patients was performed according to the Ki-67 expression level combined with molecular typing, the low-risk group had Ki-67 positive index ≤50% and WNT or SHH subtype, the medium-risk group had Ki-67 positive index ≤50% and GROUP 3 or GROUP 4 subtype, or Ki-67 positive index >50% and WNT or SHH subtype), and the high-risk group had Ki-67 positive index >50% and GROUP 3 or GROUP 4 subtype. The differences in OS and PFS among different risk groups were compared. A multivariate Cox proportional hazards model was used to assess factors affecting the survival of patients.Results:There were 50 cases (54.3%) with Ki-67 positive index ≤50% and 42 cases (45.7%) with Ki-67 positive index >50%. The 5-year PFS rate and OS rate of patients with Ki-67 positive index ≤50% were 46.9% and 63.1%, and patients with Ki-67 positive index >50% were 28.5% and 32.0%, there were statistical differences in PFS and OS between the two groups ( P values were 0.020 and 0.028). There were 16 cases (17.4%) of WNT subtype, 14 cases (15.2%) of SHH subtype, 40 cases (43.5%) of GROUP 3 subtype and 22 cases (23.9%) of GROUP 4 subtype, their 5-year PFS rates were 78.0%, 76.0%, 19.2% and 19.9%, respectively, and their 5-year OS rates were 82.1%, 76.0%, 40.2% and 0, respectively. MB patients with GROUP 3 or GROUP 4 subtype had poorer PFS and OS than patients with WNT or SHH subtype ( P values were 0.003 and 0.039). Ki-67 expression level and molecular typing were combined to carry out risk classification of prognosis. There were 12 cases (13.0%) in the low-risk group, 56 cases (60.9%) in the medium-risk group, and 24 cases (26.1%) in the high-risk group . There were statistical differences in PFS and OS among MB patients in low-, medium- and high-risk groups (both P < 0.001). Multivariate Cox regression analysis showed that radiotherapy and risk classification of prognosis as medium risk and low risk were independent protective factors for PFS (radiotherapy vs. no radiotherapy: OR = 0.263, 95% CI 0.124-0.556, P < 0.001; medium-risk group vs. high-risk group: OR = 0.069, 95% CI 0.008-0.581, P = 0.014; low-risk group vs. high-risk group: OR = 0.260, 95% CI 0.131-0.514, P < 0.001); radiotherapy and risk classification of prognosis as low risk were independent protective factors for OS (radiotherapy vs. no radiotherapy: OR = 0.221, 95% CI 0.097-0.503, P < 0.001; low-risk group vs. high-risk group: OR = 0.328, 95% CI 0.150-0.717, P = 0.005). Conclusions:The expression level of Ki-67 and 4 molecular types are related to the prognosis of MB patients. The combination of the two can be used to classify the prognosis risk of MB patients, which has reference significance for the prediction of prognosis of patients and the selection of individualized treatment plans.

Screening and a preliminary study of specific microRNA for hepatic alveolar echinococcosis / 临床肝胆病杂志

ObjectiveTo investigate new biomarkers for hepatic alveolar echinococcosis by screening out differentially expressed microRNAs (miRNAs) in the tissues and plasma of patients with hepatic alveolar echinococcosis, since hepatic alveolar echinococcosis is caused by the infection of multilocular hydatid cyst. MethodsPatients with hepatic alveolar echinococcosis diagnosed in Qinghai University Affilrated Hospital from June 2016 to May 2018 were in cluded. Two marginal tissue samples and three adjacent normal tissue samples were collected from patients with hepatic alveolar echinococcosis, and plasma samples were collected from three patients with hepatic alveolar echinococcosis and three healthy controls. Agilent Human miRNA microarray was used to obtain the miRNA expression profile in tissue and plasma, and differentially expressed miRNAs were screened out based on fold change (FC＞1.2) and P value (P＜0.05). Plasma miRNAs and tissue miRNAs associated with liver diseases were selected based on target gene prediction of differentially expressed miRNAs and literature reports, and quantitative real-time PCR (qRT-PCR) was used for validation. The t-test was used for comparison of continuous data between two groups. A spearman analysis was used to investigate correlcction. ResultsThere was a significant difference in microRNA expression profile between the patients with hepatic alveolar echinococcosis and the health individuals, and qRT-PCR found that three miRNAs (hsa-miR-4644, hsa-miR-136-5p, hsa-miR-483-3p) were significantly differentially expressed in patients with hepatic alveolar echinococcosis (P＜0.05), among which hsa-miR-4644 and hsa-miR-483-3p were significantly upregulated (P＜0.05) and hsa-miR-136-5p was significantly downregulated (P＜0.05) in patients with hepatic alveolar echinococcosis. Target gene prediction was performed for miRNAs based on TargetScan, PITA, and microRNAorg databases, and the intersection of the target genes predicted by these three databases showed that 137 genes were targeted with miRNAs. The differentially expressed miRNA hsa-miR-483-3p was involved in the target regulation of the genes (IL17A, IL5, CD40LG, TAP2, and TNF) associated with immune response and liver diseases. Gene ontology and Kyoto Encyclopedia of Genes and Genome analyses showed that the target genes of hsa-miR-483-3p played an important role in the primary immunodeficiency signaling pathway, the IL-17 signaling pathway, and the TNF signaling pathway. ConclusionHepatic alveolar echinococcosis has a unique microRNA expression profile, among which hsa-miR-483-3p can be used as a new biomarker for hepatic alveolar echinococcosis, and the target genes regulated by this miRNA are mainly involved in the primary immunodeficiency signaling pathway, the IL-17 signaling pathway, and the TNF signaling pathway. However, further studies are needed to verify the regulatory relationship between these miRNAs and hepatic alveolar echinococcosis.

Screening of differentially expressed genes in CD4 + T cells in peripheral blood of 45 leprosy patients / 中华皮肤科杂志

Objective:To detect the mRNA expression profile of CD4 + T cells in the peripheral blood of leprosy patients, and to screen and identify genes that may be closely related to the pathogenesis of leprosy. Methods:From July 2018 to May 2020, 45 leprosy patients were collected from Hunan Province, and 45 healthy volunteers from Health Examination Center of Changsha Central Hospital. CD4 + T cells were isolated from peripheral blood samples by using magnetic beads, and then RNA was extracted. Solexa sequencing was performed to screen differentially expressed genes between 6 patients and 6 healthy controls, who were randomly selected from the above subjects. Differentially expressed genes were defined as those with a fold change greater than 2 and a P value below 0.05, and then Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis was performed. Real-time fluorescence-based quantitative PCR was conducted to verify the gene expression. Results:Genetic screening revealed 4 831 newly-discovered transcripts with protein-coding potential. Eight differentially expressed genes were screened out between the two groups. Among them, the mRNA expression of CXCL8, PPBP, RPS18 and IL-1β genes was up-regulated, while the mRNA expression of RNH1, RPL39, RPL15 and AMBRA1 genes was down-regulated. Verification results of real-time fluorescence-based quantitative PCR were consistent with the above-mentioned genetic screening results. KEGG analysis showed that the differentially expressed genes between leprosy patients and healthy controls were mainly enriched in mitochondrial autophagy, autophagy-related pathways and human papillomavirus infection pathways.Conclusion:Down-regulated mRNA expression of AMBRA1 and RNH1 genes and up-regulated mRNA expression of CXCL8, PPBP and IL-1β genes were identified in patients with leprosy, which may be involved in the pathogenesis of leprosy through the mitochondrial autophagy pathway and chemokine-mediated signaling pathway, respectively.

Analysis for potential targeting genes of TPF regimen induction chemotherapy in hypopharyngeal squamous cell carcinoma / 中华耳鼻咽喉头颈外科杂志

Objective@#To analyze the differentially expressed genes related to the chemosensitivity with the TPF regimen for hypopharyngeal squamous cell carcinoma and to measure potential functional targeting genes expressions.@*Methods@#Twenty-nine patients with primary hypopharyngeal cancer who underwent induction chemotherapy with TPF from January 2013 to December 2017 in Beijing Tongren Hospital were enrolled for microarray analysis, including 28 males and 1 female, aged from 43 to 73 years old. Among them, 16 patients were sensitive to chemotherapy while 13 patients were non-sensitive. Illumina Human HT-12 Bead Chip was applied to analyze the gene expressions and online bioinformatics analysis was used to analyze the differentially expressed genes. Reverse transcription and quantitative real-time PCR (RT-qPCR) was used to measure the mRNA expression of potential functional genes of TPF induction chemotherapy in 43 samples, 29 from original patients and 14 from additional patients. Graphpad prism 7.0 software was used for statistical analysis.@*Results@#A total of 1 381 significantly differentially expressed genes were screened out. By GO analysis, up-regulated genes included sequestering in extracellular matrix, chemokine receptor binding and potassium channel regulator activity; down-regulated genes included regulation of angiogenesis, calcium ion binding and natural killer cell activation involved in immune response. With KEGG database analysis, down-regulated pathways included ECM-receptor interaction and peroxisome and up-regulated pathways included Glutathione metabolism and PPAR signaling pathway. The expressions of CD44 and IL-6R were significantly different and appeared biologically significant. CD44 was significantly upregulated in insensitive tissues (0.54±0.06) compared with sensitive tissues (0.33±0.04)(P<0.01). IL-6R was significantly downregulated in insensitive tissues (0.44±0.03) compared with sensitive tissues. (0.68±0.03) (P<0.01).@*Conclusion@#CD44 and IL-6R may be potentially functional genes of TPF induction chemotherapy in hypopharyngeal squamous cell carcinoma.

Advances in Philadelphia chromosome-like acute lymphoblastic leukemia / 上海交通大学学报（医学版）

Philadelphia chromosome-like acute lymphoblastic leukemia (BCR-ABL1-like ALL) is a newly defined ALL subtype in 2009. It is Philadelphia chromosome (Ph)/BCR-ABL1-negative and characterized by a set of gene expression profile which is highly similar to that of Ph/BCR-ABL1-positive ALL. However, there is no definitive unified diagnostic criteria yet. BCR-ABL1-like ALL is generally resistant to chemotherapy, with a high relapsed rate and poor prognosis. It harbors a diverse range of genetic alterations that affect cytokine receptor and/or signal transduction pathway of tyrosine kinase. Overexpression of CRLF2, JAK-STAT pathway abnormalities and ABL-class gene rearrangements are the most common. These genetic aberrations could be therapeutic targets. Both in vitro and in vivo experiments and clinical data support the efficacy of targeted therapy. Beside conventional multi-drug chemotherapy, the combination of targeted therapy, cellular immunotherapy and allogeneic hematopoietic stem cell transplantation is promising to improve the prognosis of BCR-ABL1-like ALL. In this paper, the research status of BCR-ABL1-like ALL is described from five aspects: definition, diagnosis, clinical characteristics, molecular biological characteristics and treatment.

Interaction of genetic background and exercise training intensity on endothelial function in mouse aorta

The purpose of this study was to characterize the genetic contribution to endothelial adaptation to exercise training. Vasoreactivity was assessed in aortas from four inbred mouse strains (129S1, B6, NON, and SJL) after 4 weeks of moderate intensity continuous exercise training (MOD), high intensity interval training (HIT) or in sedentary controls (SED). Intrinsic variations in endothelium-dependent vasorelaxation (EDR) to acetylcholine (ACh) as well as vasocontractile responses were observed across SED groups. For responses to exercise training, there was a significant interaction between mouse strain and training intensity on EDR. Exercise training had no effect on EDR in aortas from 129S1 and B6 mice. In NON, EDR was improved in aortas from MOD and HIT compared with respective SED, accompanied by diminished responses to PE in those groups. Interestingly, EDR was impaired in aorta from SJL HIT compared with SED. The transcriptional activation of endothelial genes was also influenced by the interaction between mouse strain and training intensity. The number of genes altered by HIT was greater than MOD, and there was little overlap between genes altered by HIT and MOD. HIT was associated with gene pathways for inflammatory responses. NON MOD genes showed enrichment for vessel growth pathways. These findings indicate that exercise training has non-uniform effects on endothelial function and transcriptional activation of endothelial genes depending on the interaction between genetic background and training intensity.

Analysis for potential targeting genes of TPF regimen induction chemotherapy in hypopharyngeal squamous cell carcinoma / 中华耳鼻咽喉头颈外科杂志

To analyze the differentially expressed genes related to the chemosensitivity with the TPF regimen for hypopharyngeal squamous cell carcinoma and to measure potential functional targeting genes expressions. Twenty-nine patients with primary hypopharyngeal cancer who underwent induction chemotherapy with TPF from January 2013 to December 2017 in Beijing Tongren Hospital were enrolled for microarray analysis, including 28 males and 1 female, aged from 43 to 73 years old. Among them, 16 patients were sensitive to chemotherapy while 13 patients were non-sensitive. Illumina Human HT-12 Bead Chip was applied to analyze the gene expressions and online bioinformatics analysis was used to analyze the differentially expressed genes. Reverse transcription and quantitative real-time PCR (RT-qPCR) was used to measure the mRNA expression of potential functional genes of TPF induction chemotherapy in 43 samples, 29 from original patients and 14 from additional patients. Graphpad prism 7.0 software was used for statistical analysis. A total of 1 381 significantly differentially expressed genes were screened out. By GO analysis, up-regulated genes included sequestering in extracellular matrix, chemokine receptor binding and potassium channel regulator activity; down-regulated genes included regulation of angiogenesis, calcium ion binding and natural killer cell activation involved in immune response. With KEGG database analysis, down-regulated pathways included ECM-receptor interaction and peroxisome and up-regulated pathways included Glutathione metabolism and PPAR signaling pathway. The expressions of CD44 and IL-6R were significantly different and appeared biologically significant. CD44 was significantly upregulated in insensitive tissues (0.54±0.06) compared with sensitive tissues (0.33±0.04)(0.01). IL-6R was significantly downregulated in insensitive tissues (0.44±0.03) compared with sensitive tissues. (0.68±0.03) (0.01). CD44 and IL-6R may be potentially functional genes of TPF induction chemotherapy in hypopharyngeal squamous cell carcinoma.

Transcriptome Analysis Identifies an Attenuated Local Immune Response in Invasive Nonfunctioning Pituitary Adenomas

BACKGROUND: Invasive nonfunctioning pituitary adenomas (NFPAs) remain challenging due to their high complication rate and poor prognosis. We aimed to identify the distinctive molecular signatures of invasive NFPAs, compared with noninvasive NFPAs, using gene expression profiling by RNA sequencing. METHODS: We obtained frozen fresh tissue samples from 14 patients with NFPAs who underwent primary transsphenoidal surgery. Three non-invasive and 11 invasive NFPAs were used for RNA sequencing. The bioinformatics analysis included differential gene expression, gene ontology analysis, and pathway analysis. RESULTS: A total of 700 genes were differentially expressed (59 up-regulated and 641 down-regulated genes) between invasive and non-invasive NFPAs (false discovery rate <0.1, and |fold change| ≥2). Using the down-regulated genes in invasive NFPAs, gene ontology enrichment analyses and pathway analyses demonstrated that the local immune response was attenuated and that transforming growth factor-β (TGF-β) RII-initiated TGF-β signaling was down-regulated in invasive NFPAs. The overexpression of claudin-9 (CLDN9) and the down-regulation of insulin-like growth factor-binding protein 5 (IGFBP5), death-associated protein kinase 1 (DAPK1), and tissue inhibitor of metalloproteinase-3 (TIMP3) may be related with invasiveness in NFPAs. CONCLUSION: Invasive NFPAs harbor different gene expression profiles relative to noninvasive NFPAs. In particular, local suppression of the immune response and TGF-β signaling can make PAs prone to invasiveness.

The effect of hypoxia on gene expression and signaling pathway in 3D cultured cerebral cortex cells / 中国医师杂志

Objective To explore potential therapeutic targets for neonatal hypoxic brain injury,we analyzed the effects of hypoxia on the gene expression profiles and signaling pathway in 3D cultured cerebral cortex cells.Methods R studio software was used to analyze the differentially expressed genes of hypoxia treated cerebral cortex cell data (GSE112137) which was downloaded from GEO database.Gene Oncology and KEGG software were used to enrich the molecular function,biological process and signaling pathways of differentially expressed genes.Then String and Cytoscape software were adapted to analyzed gene interaction network between these genes.Results There were 395 increasing genes and 185 decreasing genes (Change Fold ≥2) were identified in hypoxic cerebral cells compared with the control groups.Most elevated genes were mainly related with molecular function including dioxygenase activity,isomerase activity and misfolded protein binding,while the decreasing genes were enriched in RNA polymerase Ⅱ proximal promoter sequence-specific DNA binding.Biological process enrichment analysis revealed that hypoxia up-regulated genes were associated with endoplasmic reticulum stress,oxidation-reduction process and glycolysis,while down-regulated genes were involved in the progress of neural development and cell differentiation.KEGG pathway enrichment results indicated hypoxia increasing genes were mainly related with endoplasmic reticulum protein processing,glycolysis,amino acid biosynthesis,and decreasing genes were mainly enriched in Parkinson's disease signaling pathway.Conclusions Hypoxia in human cerebral cortex cells could cause endoplasmic reticulum stress,protein misfolding and metabolic abnormalities,inhibited the development of neuron cells.Drugs targeting these process may be beneficial to alleviate cerebral hypoxia injury.

The effect of hypoxia on gene expression and signaling pathway in 3D cultured cerebral cortex cells / 中国医师杂志

Objective@#To explore potential therapeutic targets for neonatal hypoxic brain injury, we analyzed the effects of hypoxia on the gene expression profiles and signaling pathway in 3D cultured cerebral cortex cells.@*Methods@#R studio software was used to analyze the differentially expressed genes of hypoxia treated cerebral cortex cell data (GSE112137) which was downloaded from GEO database. Gene Oncology and KEGG software were used to enrich the molecular function, biological process and signaling pathways of differentially expressed genes. Then String and Cytoscape software were adapted to analyzed gene interaction network between these genes.@*Results@#There were 395 increasing genes and 185 decreasing genes (Change Fold≥2) were identified in hypoxic cerebral cells compared with the control groups. Most elevated genes were mainly related with molecular function including dioxygenase activity, isomerase activity and misfolded protein binding, while the decreasing genes were enriched in RNA polymerase Ⅱ proximal promoter sequence-specific DNA binding. Biological process enrichment analysis revealed that hypoxia up-regulated genes were associated with endoplasmic reticulum stress, oxidation-reduction process and glycolysis, while down-regulated genes were involved in the progress of neural development and cell differentiation. KEGG pathway enrichment results indicated hypoxia increasing genes were mainly related with endoplasmic reticulum protein processing, glycolysis, amino acid biosynthesis, and decreasing genes were mainly enriched in Parkinson′s disease signaling pathway.@*Conclusions@#Hypoxia in human cerebral cortex cells could cause endoplasmic reticulum stress, protein misfolding and metabolic abnormalities, inhibited the development of neuron cells. Drugs targeting these process may be beneficial to alleviate cerebral hypoxia injury.

Progress of detection techniques of Philadelphia chromosome鄄like acute lymphoblastic leukemia / 白血病·淋巴瘤

Philadelphia chromosome_like acute lymphoblastic leukemia (Ph_like ALL) characterized by a high rate of relapse and poor outcome of chemotherapy and prognosis, also known as BCR_ABL1_like ALL, is a kind of B_ALL subtypes, a pattern of gene expression profiling similar to that of BCR_ABL1 ALL positive but lacking BCR_ABL1 fusion gene. With the better understanding of gene expression profiling, the World Health Organization (WHO) (2016) has regarded Ph_like ALL as an independent subtype of B_ALL. The diagnosis highly depends on the laboratory techniques, and a wide range of diagnostic methods can be applied in clinic, which may bring a big challenge for the clinicians. This paper reviews the various laboratory techniques of Ph_like ALL and subtype group analysis, to provide a basis for target therapy and to improve the prognosis.

Changes in transcriptome expression profiles and functional analysis of differentially expressed genes during mycelium-to-yeast transformation of Sporothrix schenckii / 中华皮肤科杂志

Objective To compare and analyze the differences in the transcriptomics between mycelium and early yeast phases of Sporothrix schenckii (S.schenckii),and to realize the changes in transcriptome expression profiles during mycelium-to-yeast transformation.Methods A standard strain of S.schenckii (ATCC 10268) was subjected to 96-hour culture with Sabouraud medium at 25 ℃ or 36-hour culture with brain-heart infusion medium at 37 ℃ to obtain the mycelium and yeast form of S.schenckii,and then,their transcriptomes were sequenced.Functional annotation was performed for screened unigenes by comparison using several databases (such as NR,Swiss-Prot,KEGG,COG,KOG,GO and Pfam),coding sequence prediction,and gene expression analysis in each sample.Finally,the differentially expressed genes were subjected to pattern clustering,functional annotation and enrichment analysis.Results A total of 14.76 Gb valid data (clean data) were obtained,and functional annotation results were acquired in 28 094 of 43 863 assembled unigene clusters.Compared with S.schenckii in mycelium phase,there were 10 969 up-regulated genes and 199 down-regulated genes in S.schenckii in yeast phase.These differentially expressed genes were involved in protein phosphorylation,intracellular protein transport,cellular protein modification,small guanosine triphosphate-mediated signal transduction,vesicle-mediated transport,translation,intracellular signal transduction,microtubule formation,adenosine triphosphate synthesis,coupled proton transport and so on.Sixteen genes in the mitogen-activated protein kinase (MAPK) pathway and two-component signaling pathway,which were two important signal transduction pathways involved in fungal morphogenesis,and 16 genes involved in chitin synthesis and metabolism were all confirmed to be up-regulated in S.schenckii in yeast phase.Conclusions Compared with S.schenckii in mycelium phase,great changes in gene expression profiles were observed in S.schenckii in yeast phase.These differentially expressed genes are involved in many functions,suggesting that the dimorphic transition of S.schenckii is regulated by a multi-gene network system.

Effect of STIL on the Gene Expression Profile of Gastric Cancer Cells / 中国医学科学院学报

To explore the molecular mechanism underlying gastric carcinogenesis and progression by using gene expression profiling array together with bioinformatics. Lentivirus short hairpin RNA targeting STIL(ShSTIL)and scrambled sequence RNA(ShCon)were transduced into the gastric cancer cell line SGC-7901.RNA extraction,complementary DNA synthesis,construction of biotin-labelled amplified RNA probes,and hybridization with gene expression profile were consecutively performed.We collected corresponding data and analyzed differentially expressing genes(DEGs),followed by the analysis of gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)enrichment,transcription factor regulating network,and protein-protein interacting networks. Compared with ShCon,a total of 417 and 87 genes were respectively down-regulated and up-regulated,respectively,in the ShSTIL group(1 or <-1).GO and KEGG enrichment analysis indicated that genes regulated by STIL were localized in cytoplasm,extracellular exosome,Golgi apparatus and various biomembranes,and were implicated in the ubiquitin-mediated proteolysis,P53 signaling pathway,and pathways regulating pluripotency of stem cells.Evaluation on genes enriched in KEGG pathways,regulation of transcription factors,and protein-protein interacting network demonstrated that IGF1R,STUB1,SKP2,and FOXO1 were localized at the centre of the network and played a key role in the development and progression of gastric cancer. Through the protein-protein interactions,STIL may activate E3 ubiquitin ligase STUB1 or SKP2,promote the proteolysis of FOXO1-a transcription factor,regulate the expression of IGF1R,and thus promote gastric carcinogenesis and progression.

CircuLar RNA expression profiLes in women with gestationaL diabetes meLLitus: a nested case-controL study / 中华围产医学杂志

Objective To investigate the expression of circular RNA (circRNA) in peripheral blood of gravidas with gestational diabetes mellitus (GDM) using gene chip technology, and to provide evidence for studying pathogenesis of GDM. Methods A prospective cohort-based nested case-control study was used to select 1 018 pregnant women who were examined and delivered in Guangzhou Women and Children's Medical Center from September 2014 to April 2016. The information of prenatal examination was recorded and the outcome of delivery was followed up. Six pregnant women diagnosed as GDM were selected as the GDM group. Six normal pregnant women who were collected blood samples by 1 ∶ 1 were selected as the control group. The difference of gestational week was less than 7 days, the number of previous pregnancies was less than 2 times, and the difference of previous delivery times as same as the control group. The expression of circRNA in maternal peripheral blood was analyzed by chromosome microarray technique, and the function and the regulation network forecast were analyzed by GO (http://www.geneontology.org/), KEGG PATHWAY (http://www.genome.jp/kegg/pathway.html) and CircNet(http://circnet.mbc.nctu.edu.tw/). t-test was used for data analysis. ResuLts Compared to the normal pregnant women, 2 678 circRNAs were identified to be differentially expressed >2.0 times in GDM women, among which 1 532 were up-regulated and 1 146 were down-regulated. Functional analysis showed that the up-regulated circRNA was enriched in the biological processes of insulin response, gene silencing regulation, glucagon response and cell senescence. Signal pathway analysis showed that circRNA involved in insulin pathway. Taking has_circ_0042852 and has_circ_0004001 as center, the possible GDM-related regulatory networks were predicted. ConcLusions The peripheral blood of GDM women is rich in circRNAs, which might involve in many biological processes, insulin signaling pathway and possibly induding GDM-related regulatory networks.