Identification of miR-20b-5p as an inhibitory regulator in cardiac differentiation via TET2 and DNA hydroxymethylation.

BACKGROUND: Congenital heart disease (CHD) is a prevalent congenital cardiac malformation, which lacks effective early biological diagnosis and intervention. MicroRNAs, as epigenetic regulators of cardiac development, provide potential biomarkers for the diagnosis and treatment of CHD. However, the mechanisms underlying miRNAs-mediated regulation of cardiac development and CHD malformation remain to be further elucidated. This study aimed to explore the function of microRNA-20b-5p (miR-20b-5p) in cardiac development and CHD pathogenesis. METHODS AND RESULTS: miRNA expression profiling identified that miR-20b-5p was significantly downregulated during a 12-day cardiac differentiation of human embryonic stem cells (hESCs), whereas it was markedly upregulated in plasma samples of atrial septal defect (ASD) patients. Our results further revealed that miR-20b-5p suppressed hESCs-derived cardiac differentiation by targeting tet methylcytosine dioxygenase 2 (TET2) and 5-hydroxymethylcytosine, leading to a reduction in key cardiac transcription factors including GATA4, NKX2.5, TBX5, MYH6 and cTnT. Additionally, knockdown of TET2 significantly inhibited cardiac differentiation, which could be partially restored by miR-20b-5p inhibition. CONCLUSIONS: Collectively, this study provides compelling evidence that miR-20b-5p functions as an inhibitory regulator in hESCs-derived cardiac differentiation by targeting TET2, highlighting its potential as a biomarker for ASD.

Molecular mechanisms of Biyu decoction as treatment for psoriasis: A network pharmacology and molecular docking study.

BACKGROUND: The therapeutic effects of a combination of Chinese medicines called Biyu decoction have been clinically verified, although its molecular targets in psoriasis remain unknown. AIM: To explore the molecular mechanisms of Biyu decoction for psoriasis treatment. METHODS: In this network pharmacology and molecular docking study, the Traditional Chinese Medicine Systems Pharmacology database was searched for Biyu decoction active ingredients. GeneCards, Online Mendelian Inheritance in Man, PharmGkb, Therapeutic Target Database, and DrugBank databases were searched for psoriasis-related genes. The genes targeted by the decoction's active ingredient and disease genes were intersected to obtain predictive targets of the drug during psoriasis treatment. Cytoscape 3.8.0 was used to construct a drug component/ target disease network. The The functional protein association networks database and Cytoscape were used to construct a protein-protein interaction network and streamline the core network. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used for pathway enrichment analysis. Molecular docking technology was used to verify the drug component/target disease network. RESULTS: We screened 117 major active ingredients, including quercetin, kaempferol, naringenin, and acetyl-shikonin, and identified 213 gene targets, such as MAPK3, JUN, FOS, MYC, MAPK8, STAT3, and NFKBIA. Using a molecular docking analysis, the main active ingredients demonstrated good binding to the core targets. The Gene Ontology analysis showed that these ingredients were significantly associated with biological activities, such as transcription factor DNA binding, RNA polymerase II-specific DNA binding of transcription factors, and cytokine receptor binding; responses to lipopolysaccharides, molecules of bacterial origin, and oxidative stress; and were mainly distributed in membrane rafts, microdomains, and regions. The Kyoto Encyclopedia of Genes and Genomes analysis showed that decoction ingredients act on Th17 cell differentiation, tumor necrosis factor and mitogen-activated protein signaling pathways, the interleukin-17 signaling pathway, and the PI3K-Akt signaling pathway. CONCLUSION: Biyu decoction may be effective against psoriasis through multi-component, multi-target, and multi-channel synergy.

[Screening of Differential Expression Autophagy Genes Related to the Prognosis of Diffuse Large B-Cell Lymphoma and Establishment of an Autophagy Model].

OBJECTIVE: To screen the differential expression of diffuse large B-cell lymphoma (DLBCL) autophagy-related gene (ARG), explore the mechanism of differential expression of autophagy gene (DEARG) in the occurrence and development of DLBCL and establish a prognostic model. METHODS: Using the NCICCR database containing clinical information and gene expression profile data of 481 patients with DLBCL and the HADb database containing 232 ARGs, the differential expression of ARG in DLBCL was determined by R language, the relationship between ARG and the occurrence and development of DLBCL was analyzed by GO and KEGG, the polygene prognostic model was established by Cox regression algorithm, the survival curve was drawn by Kaplan-Meier method, and the reliability of the prognostic model was evaluated by ROC curve. RESULTS: A total of 122 DEARGs were extracted from lymph node samples of 481 patients with DLBCL and 5 normal lymph nodes, including 4 up-regulated genes and 118 down-regulated genes. GO enrichment mainly focused on ontological annotations such as mitochondrial autophagy, autophagy regulation, and cell response to external stimuli. KEGG enrichment was mainly concentrated in cell senescence, NOD-like receptor signal pathway, PI3K-Akt signal pathway, and PD-1/PD-L1 signal pathway. Survival analysis was performed on 230 samples with complete clinical information. Univariate Cox analysis showed that 20 ARGs were significantly correlated with overall survival of DLBCL patients. Nine prognostic ARGs (HIF1A, CAPN1, ITPR1, PRKCQ, TRAIL, HDAC1, TSC2, NRG3, and MAPK3) were screened by multivariate Cox regression to establish DLBCL ARG prognostic model. Kaplan-Meier survival curve analysis showed that there was significant difference in survival rate between high risk group and low risk group (P<0.001). Multivariate Cox regression analysis showed that international prognostic index and risk value were independent prognostic indicators of DLBCL patients (P<0.05), the area under ROC curve was 0.762 and 0.747, respectively. CONCLUSION: DLBCL ARG prognostic model can be used to predict the prognosis of patients, but it still needs to be confirmed by a large sample of clinical studies.

[Bioinformatics Analysis of the Influence of Coronavirus Infection on Hematopoietic System and Potential Intervention Drugs and Their Significance for COVID-19].

OBJECTIVE: To analyze and predict the effect of coronavirus infection on hematopoietic system and potential intervention drugs, and explore their significance for coronavirus disease 2019 (COVID-19). METHODS: The gene expression omnibus (GEO) database was used to screen the whole genome expression data related with coronavirus infection. The R language package was used for differential expression analysis and KEGG/GO enrichment analysis. The core genes were screened by PPI network analysis using STRING online analysis website. Then the self-developed apparent precision therapy prediction platform (EpiMed) was used to analyze diseases, drugs and related target genes. RESULTS: A database in accordance with the criteria was found, which was derived from SARS coronavirus. A total of 3606 differential genes were screened, including 2148 expression up-regulated genes and 1458 expression down-regulated genes. GO enrichment mainly related with viral infection, hematopoietic regulation, cell chemotaxis, platelet granule content secretion, immune activation, acute inflammation, etc. KEGG enrichment mainly related with hematopoietic function, coagulation cascade reaction, acute inflammation, immune reaction, etc. Ten core genes such as PTPRC, ICAM1, TIMP1, CXCR5, IL-1B, MYC, CR2, FSTL1, SOX1 and COL3A1 were screened by protein interaction network analysis. Ten drugs with potential intervention effects, including glucocorticoid, TNF-α inhibitor, salvia miltiorrhiza, sirolimus, licorice, red peony, famciclovir, cyclosporine A, houttuynia cordata, fluvastatin, etc. were screened by EpiMed plotform. CONCLUSION: SARS coronavirus infection can affect the hematopoietic system by changing the expression of a series of genes. The potential intervention drugs screened on these grounds are of useful reference significance for the basic and clinical research of COVID-19.

No-nonspecific recognition-based amplification strategy for endonuclease activity screening with dual-color DNA nano-clew.

The inevitable nonspecific recognition severely restricted widely used nucleic acid amplification strategies, which has become an urgent problem in current scientific research. Herein, we developed a novel no-nonspecific recognition-based amplification strategy to construct dual-color dye loaded nano-clew as ultrabright illuminant for screening endonuclease activity with Escherichia coliRY13 I (EcoR I) as a model, which overcame some major drawbacks such as nonspecific recognition and photobleaching. Typically, the target endonuclease induces cleavage of the customized dumbbell-shape substrate (DSS) to generate two same triggers that can initiate the rolling circle amplification (RCA) to prepare long single-strand DNA (lssDNA), which could self-assemble into irregular DNA nano-clew based on the electrostatic interactions with Mg2+ to furtherly capture the donor and accepter fluorophore proximately, constructing the dye loaded nano-clew with dual-color fluorescence (FL) emission to resist photobleaching. Importantly, in absence of EcoR I, even if the DSS could combine with circular template a little, the reaction system performed hardly RCA reaction due to no cohesive terminus, resulting an extremely low background fluorescence signal because of the prevention of nonspecific RCA reaction. As expected, the proposed sensing platform with a low limit of detection (LOD) of 3.4 × 10-7 U/µL was demonstrated to work well for endonuclease inhibitors screening also. Furthermore, the proposed no-nonspecific recognition strategy could be readily extended to various DNA or RNA enzymes such as DNA methyltransferase, DNA repair-related enzymes and polynucleotide kinase just by simply changing the recognition sequence in the DNA substrate, performing great potential of endonucleases-related clinical diagnosis and drugs discovery.

Hydrophobic-Driven Electrochemiluminescence Enhancement via Target-Induced Self-Enrichment for Ultrasensitive Bioassay.

Considering the central challenge of the simple and efficient strategy to generate sensitive analysis technology, herein, we proposed a novel electrochemiluminescence (ECL) strategy based on target-induced self-enrichment via hydrophobic interaction to generate significant ECL enhancement for untrasensitive detection of clinical biomarkers with cardiac troponin I (cTnI) for early diagnosis of acute myocardial infarction (AMI) as a model. Typically, the first antibody of cTnI (fAb) was immobilized onto the as-prepared electrode surface with the titanium dioxide nanoflower and gold nanoclusters When there was target cTnI, it could be captured onto the electrode surface based on the specific antigen-antibody interaction to furtherly capture cholesterol-modified second antibody of cTnI to increase the hydrophobicity of the electrode surface, which could be employed for the self-enrichment of hydrophobic ECL luminophore, tris(2,2'-bipyridyl-4,4'-dicarboxylato) ruthenium(II), and coreactant, tripropylamine in the detection solution. Thus, an increased ECL emission could be achieved due to the increased concentration of ECL luminophore and coreactant, which was quantitatively related with the concentration of target cTnI. As expected, a higher sensitivity was obtained with a detection limit of 0.04 pg/mL based on simplest operations of the proposed strategy with target-induced self-enrichment via hydrophobic interaction. Importantly, this hydrophobic interaction-based ECL strategy could be easily expanded to the bioassay of various biomarkers, providing an efficient tool for early clinical diagnosis of AMI and some other diseases.

[Bioinformatics analysis of genes related to poor prognosis of human hepatocellular carcinoma and its clinical significance].

OBJECTIVE: To screen genes associated with poor prognosis of hepatocellular carcinoma (HCC) and to explore the clinical significance of these genes. METHODS: The proper expression profile data of HCC was obtained from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by differential expression analysis. The DAVID and String database were used for function enrichment analysis and to construct the protein-protein interaction (PPI) network respectively. The Cancer Genome Atlas (TCGA) database and the Cox Proportional Hazard Model were used for prognosis analysis of the DEGs. RESULTS: A eligible human HCC data set (GSE84402) met the requirements. A total of 1141 differentially expressed genes were identified, including 720 up-regulated and 421 down-regulated genes. The results of function enrichment analysis and PPI network performed that CDK1、CDC6、CCNA2、CHEK1、CENPE 、PIK3R1、RACGAP1、BIRC5、KIF11 and CYP2B6 were prognosis key genes. And the prognosis analysis showed that the expressions of CDC6、PIK3R1、KIF11 and RACGAP1 were increased, and the expression of CENPE was decreased, which was closely related to prognosis of HCC. CONCLUSION: CDC6、CENPE、PIK3R1、KIF11 and RACGAP1 may be closely related to poor prognosis of HCC, and can be used as molecular biomarkers for future research of HCC prognosis.

[Analysis of Unfavorable Prognosis Gene Markers in Patients with Acute Myeloid Leukemia by Multiomics].

OBJECTIVE: To analyze the molecular markers associated with occurrence, development and poor prognosis of acute myeloid leukemia (AML) by using the data of GEO and TCGA database, as well as multiomics analysis. METHODS: The transcriptome data meeting requirements were down-loaded from GEO database, the differentially expressed genes were screened by using the R language limma package, and the GO function enrichment analysis and KEGG pathway analysis were performed for differentially expressed genes, at the same time, the protein interaction network was contracted by using STRING database and cytoscape software to screen out the hub gene, then the prognosis analysis was carried out for hub gene by combination with the clinical information affected in TCGA database. RESULTS: 620 differentially expressed genes were screened out, among which 162 differentially expressed genes were up-regulated, and 458 differentially expressed genes were down-regulated. Based on the results of GO functional enrichment, the KEGG pathway enrichment and protein interaction network, CXCL4, CXCR4, CXCR1, CXCR2, CCL5 and JUN were selected as hub genes. The survival analysis showed that the high expression of CXCL4, CXCR1, and CCL5 was a risk factor for poor prognosis of patiants. CONCLUSION: CXCL4, CXCR1 and CCL5 can be used as biomarkers for the occurrence and development of AML, which relateds with the unfavorable prognosis and can provide a basis for further study.

[Prognosis-related miRNA bioinformatics screening of lung adenocarcinoma and its clinical significance].

OBJECTIVE: To investigate the prognosis-related miRNA histological features and clinical significance of lung adenocarcinoma. METHODS: Using The Cancer Genome Atlas (TCGA) data, the miRNA expression profile data of human lung adenocarcinoma were searched for differential analysis, and the prognosis-related miRNAs were screened by Cox risk regression model. The targeted miRNAs were predicted by mirwalk analysis platform, KEGG functional enrichment analysis, and finally, predict the function of prognosis-related miRNAs. RESULTS: A total of 46 differential miRNAs in lung adenocarcinoma were screened, including 19 up-regulated and 27 down-regulated. Six prognostic-related miRNAs were screened by Cox survival analysis, namely hsa-mir-21, hsa-mir-142, hsa-mir-200a high expression, hsa-mir-101, hsa-let-7c, hsa-mir-378e low expression, hsa-mir-21 and hsa-mir-378e were associated with poor prognosis in patients with lung adenocarcinoma, and the survival time was shortened significantly (P<0.05, AUC=0.618). KEGG analysis showed that the above prognosis-related miRNA targeting regulatory genes were related with immune response pathways, miRNA and cancer pathways, metabolic pathways and so on. CONCLUSIONS: Hsa-mir-21 and hsa-mir-378e are associated with poor prognosis of lung adenocarcinoma, and may be used as a molecular marker for prognosis of lung adenocarcinoma after further clinical verification.

The relationship between apolipoprotein E gene ε2/ε3/ε4 polymorphism and breast cancer risk: a systematic review and meta-analysis.

OBJECTIVE: We conducted a systematic review and meta-analysis aiming to assess the relationship between apolipoprotein E (APOE) gene ε2/ε3/ε4 polymorphism and breast cancer risk. METHODS: Yun-Long Liu and Hao-Min Zhang independently completed literature retrieval and data collection, and statistical analyses were performed by Stata. Individual odds ratio (OR) and 95% confidence interval (CI) were pooled in a random-effects model using the DerSimonian-Laird method. Heterogeneity was evaluated by I (2) statistic at a significance level of 50%. Publication bias was assessed by Egger's test. RESULTS: Eleven articles including 2,074 breast cancer patients and 2,372 controls were summarized. Using the most common allele ε3 as a reference, the ε2 (OR =0.87, 95% CI =0.72-1.05, P=0.154, I (2)=0.0%) and ε4 (OR =1.07, 95% CI =0.80-1.42, P=0.654, I (2)=71.8%) alleles were not found to be significantly associated with breast cancer risk in the overall analyses. Subgroup analyses revealed that the comparison of allele ε4 with ε3 was significant in Asians (OR =1.58, 95% CI =1.17-6.32, P=0.003, I (2)=12.1%) and in studies that used the restriction fragment length polymorphism (RFLP) genotyping method (OR =1.27; 95% CI =1.01-1.61, P=0.045, I (2)=34.3%), and was marginally significant in hospital-based studies (OR =1.33; 95% CI =0.98-1.79, P=0.065, I (2)=30.2%), without heterogeneity. Moreover, the presence of the ε2 allele was significantly associated with breast cancer in small studies (total sample size <500) (OR =0.73, 95% CI =0.54-1.00, P=0.052, I (2)=0.0%) without heterogeneity. The Egger's test indicated low probabilities of publication bias. CONCLUSION: We observed a significant association between APOE gene ε4 allele and breast cancer risk in Asian populations. Moreover, the findings of our subgroup analyses suggest that source of controls, genotyping platform, and sample size might be the potential causes of heterogeneity.

Circulating Tumor Cells and Tumor Stem Cells Detection in the Peripheral Blood Mononuclear Cells of Breast Cancer.

BACKGROUND: Our aim was to retrospectively analyze the relationships between circulating tumor cells (CTCs) and the development of breast cancer, for elucidating the role of CTCs in breast cancer. METHODS: A total of 107 female patients with primary breast cancer and 48 matched healthy female volunteers were recruited. After blood collection, isolation of peripheral blood mononuclear cells (PBMC) was performed followed by the detection of cytokeratin 19 positive (CK19(+) ) and CD44(+) /CD24(-/low) cells, as well as estrogen receptor (ER), progesterone, and CerbB2. Data were analyzed with the SPSS 20.0 software. RESULTS: None of the 48 volunteers were detected with CK19(+) cells in their PBMC, while in 77 patients, 72% of 107 female patients with primary breast cancer, the CK19(+) cells were detected. CK19(+) could also be detected among patients in each grouping by different clinical staging and lymph node metastasis, with statistical differences (all P < 0.05). Further, among the 83 CK19(+) specimens, 32 were also detected with CD44(+) /CD24(-/low) cells. Comparisons of CK19(+) and CD44(+) /CD24(-/low) cells in patients with different clinical features (ER positive vs. ER negative, C-erbB2 positive vs. C-erbB2 negative) and molecular subtypes (triple-negative breast cancer, ER positive, and C-erbB2 positive) showed no obvious difference (all P > 0.05). CONCLUSIONS: Both CTCs and tumor stem cells (TSCs) could be detected in the PBMC of breast cancer patients; besides, positive expression rate of CTCs might be obviously associated with the clinical stage and metastasis. Positive relationship of TSCs and the clinical stage of breast cancer was also proved in this study.

[Analysis of clinical characteristics of gastrointestinal cancer in Heilongjiang province, China 1998 to 2007].

OBJECTIVE: To provide basic information for epidemiological research of gastrointestinal (GI) malignant tumors. METHODS: Data of GI cancer diagnosed in 15 hospitals of Heilongjiang province between January 1998 and December 2007 were analyzed retrospectively. The data mainly involved the age of onset, initial symptoms, pathological types, clinical staging and types of surgical procedure. RESULTS: Gastric cancer was the most common type (45.8%) among the 33,540 GI cancer cases, then were rectal cancer (27.3%) and colon cancer (26.8%). Right colon cancer cases were more common than the left ones (1.3:1.0), particularly in people over 80 (2.1:1.0). Only 1.3% of colorectal cancer could be found in age under 30 years old. In patients aged 50 to 70, advanced gastric cancer accounted for 70.6%, advanced colon cancer 73.4% and advanced rectal cancer 72.4%. Well-moderately differentiated adenocarcinoma in early gastric cancer was 49.7%, early colon cancer 77.3% and rectal cancer 83.2%. Patients undergone radical excision in early gastric cancer accounted for 69.1%, advanced gastric cancer 79.9%, left colon cancer 91.9%, right colon cancer 83.9% and in rectal cancer for 88.3%. CONCLUSIONS: People aged 50 to 70 tend to get GI cancer in Heilongjiang province. Gastric cancer is the most common GI cancer. Radical excision is the main choice of therapy.

[Clinical analysis of primary small intestinal neoplasms in 305 cases].

OBJECTIVE: To summarive the experience in diagnosis and treatment of primary small intestinal neoplasm. METHODS: The data of 305 patients with pathologically confirmed primary small intestinal tumor collected from 6 hospitals around the Songhua River during the past 33 years were analyzed retrospectively. RESULTS: There were 42 benign and 263 malignant tumors in this series with a ratio of 1: 6.26. The 263 malignant tumors in this series consisted of 135 adenocarcinomas, 57 malignant stromal tumors, 37 malignant lymphomas, 20 carcinoids, and etc. Chronic occult bleeding, gradual of body weight loss and mild abdominal pain (three obscurities) were the common clinical features and alerting massage of intestinal tumor. Correct preoperative diagnostic rate was only 57.0% (174/305) due to difficulty in early diagnosis, which was 67.2% (92/137) in the duodenal tumors, and 51.9% (82/168) in the jejunoileal tumors. All of the 42 benign tumors were resected completely. For the 263 patients with malignant tumors, radical dissection was performed in 153, palliative resection in 34, and gut by-pass or biopsy in 76. The median survival of the patients who underwent radical resection of their malignant tumors was 92 months, which was significantly higher than that of the other groups. CONCLUSION: Early diagnosis of primary small intestinal tumors is difficult and with a preoperative misdiagnosis rate of 43.0%. Total intestinal barium swallowing, endoscopy and superior mesenteric arteriography are three critical examinations for diagnosis and location. Early surgical resection is crucial in improving the prognosis. The primary small intestinal tumor should be resected as early as possible if no distant metastasis is detected.

[Analysis of clinical manifestations and surgical treatment of Crohn disease: a report of 82 cases].

OBJECTIVE: To elucidate the clinical types of Crohn disease and evaluate its surgical treatment. METHODS: Clinical data of 82 cases with Crohn disease were retrospectively analyzed from June 1972 to June 2003. RESULTS: Among 82 cases with Crohn disease,38 cases were diagnosed before operation,and 44 cases(53.7% ) were misdiagnosed. Main clinical manifestations included abdominal pain(96.3% ),diarrhea(89.0% ) and abdominal mass(28.0% ),other clinical manifestations included fistulation,intestinal hemorrhage and extra- intestinal manifestations such as ulcerative stomatitis,mycotic stomatitis. Patients received different surgical procedures as following: partial enterectomy in 57 cases,hemicolectomy and colostomy in 4 patients,partial ileectomy and ileostomy in 2,ileocolic bypass procedure in 3 patients,partial enterectomy and colectomy and anastomosis in 3 patients because of internal fistula,repair of ileal perforation in 2,lysis of adhesion in 6,drainage of intraperitoneal abscess and ostomy in 3,radical operation in 2 due to colon cancerization. Seventy- three cases(89.0% ) were cured by operation,postoperative complications occurred in 9 patients and 2 cases died. CONCLUSION: It is the key point to achieve successful operation that the corresponding operative modes respectively for varied types of Crohn disease should be adopted.