Unveiling the role of hypoxic macrophage-derived exosomes in driving colorectal cancer progression.

The crosstalk between tumor cells and macrophages under hypoxic conditions has been acknowledged as a pivotal determinant in the progression of colorectal cancer (CRC). Previous research has underscored the significance of exosomes derived from hypoxic tumor cells in facilitating tumor progression through inducing the polarization of macrophages towards the M2-like phenotype. The precise influence of hypoxic macrophage-derived exosomes (HMDEs) on the progression of CRC has not yet been fully elucidated. The objective of this study was to investigate the role of HMDEs in the progression of CRC. We discovered that there was an elevated release of exosomes derived from macrophages in hypoxic conditions. Additionally, the hypoxia-induced macrophage-derived exosomes played a crucial role in promoting the progression of CRC. We have also demonstrated that HMDEs have the ability to induce cell cycle transition and inhibit cell apoptosis, thereby promoting the growth of CRC cells. Furthermore, the underlying molecular mechanisms of these effects have been identified. The overexpression of Hif-1α results in its direct interaction with distinct regions (-521- -516 bp and -401- -391 bp) of the Hsp90 promoter during hypoxic circumstances. This binding event led to the overexpression of Hsp90 and the subsequent elevation of Hsp90 protein levels within HMDEs. Importantly, the crucial interaction between Hsp90 and Lats1 resulted in the deactivation of Lats1 and the inhibition of Yap phosphorylation. Ultimately, this series of events lead to the deactivation of the Hippo signaling pathway. Our in vivo and in vitro studies presented compelling evidence for the crucial role of hypoxic macrophage-derived exosomal Hsp90 in promoting CRC progression through the inhibition of the Hippo signaling pathway. These findings represented a significant advancement in our comprehension of the complex interplay between macrophages and CRC cells under hypoxic conditions.

GPCR signaling contributes to immune characteristics of microenvironment and process of EBV-induced lymphomagenesis.

Epstein-Barr virus (EBV) is the oncogenic driver of multiple cancers. However, the underlying mechanism of virus-cancer immunological interaction during disease pathogenesis remains largely elusive. Here we reported the first comprehensive proteogenomic characterization of natural killer/T-cell lymphoma (NKTCL), a representative disease model to study EBV-induced lymphomagenesis, incorporating genomic, transcriptomic, and in-depth proteomic data. Our multi-omics analysis of NKTCL revealed that EBV gene pattern correlated with immune-related oncogenic signaling. Single-cell transcriptome further delineated the tumor microenvironment as immune-inflamed, -deficient, and -desert phenotypes, in association with different setpoints of cancer-immunity cycle. EBV interacted with transcriptional factors to provoke GPCR interactome (GPCRome) reprogramming. Enhanced expression of chemokine receptor-1 (CCR1) on malignant and immunosuppressive cells modulated virus-cancer interaction on microenvironment. Therapeutic targeting CCR1 showed promising efficacy with EBV eradication, T-cell activation, and lymphoma cell killing in NKTCL organoid. Collectively, our study identified a previously unknown GPCR-mediated malignant progression and translated sensors of viral molecules into EBV-specific anti-cancer therapeutics.

Long-term, real-time and label-free live cell image processing and analysis based on a combined algorithm of CellPose and watershed segmentation.

Developing a rapid and quantitative method to accurately evaluate the physiological abilities of living cells is critical for tumor control. Many experiments have been conducted in the field of biology in an attempt to measure the proliferation and movement abilities of cells, but existing methods cannot provide real-time and objective data for label-free cells. The quantitative imaging technique, including an automatic segmentation algorithm for individual label-free cells, has been a breakthrough in this regard. In this study, we develop a combined automatic image processing algorithm of CellPose and watershed segmentation for the long-term and real-time imaging of label-free cells. This method shows strong reliability in cell identification regardless of cell densities, allowing us to obtain accurate information about the number and proliferation ability of the target cells. Additionally, our results also suggest that this method is a reliable way to assess real-time data on drug cytotoxicity, cell morphology, and cell movement ability.

A nuclear NKRF interacting long noncoding RNA controls EBV eradication and suppresses tumor progression in natural killer/T-cell lymphoma.

Long intergenic noncoding RNAs (lincRNAs) are differentially expressed in EBV-infected cells and play an essential role in tumor progression. Molecular pathogenesis of lincRNAs in EBV-driven natural killer T cell lymphoma (NKTCL) remains unclear. Here we investigated the ncRNA profile using high-throughput RNA sequencing data of 439 lymphoma samples and screened out LINC00486, whose downregulation was further validated by quantitative real-time polymerase chain reaction in EBV-encoded RNA (EBER)-positive lymphoma, particularly NKTCL. Both in vitro and in vivo studies revealed the tumor suppressive function of LINC00486 through inhibiting tumor cell growth and inducing G0/G1 cell cycle arrest. As mechanism of action, LINC00486 specifically interacted with NKRF to abrogate its binding with phosphorylated p65, activated NF-κB/TNF-α signaling and subsequently enhanced EBV eradication. Solute carrier family 1 member 1 (SLC1A1), upregulated and mediated the glutamine-addiction and tumor progression in NKTCL, was negatively correlated with the expression of NKRF. NKRF specifically bound to the promoter and transcriptionally downregulated the expression of SLC1A1, as evidenced by Chromatin Immunoprecipitation (ChIP) and luciferase assay. Collectively, LINC00486 functioned as a tumor suppressor and counteracted EBV infection in NKTCL. Our study improved the knowledge of EBV-driven oncogenesis in NKTCL and provided the clinical rationale of EBV eradication in anti-cancer treatment.

Euclidean distance-based Raman spectroscopy (EDRS) for the prognosis analysis of gastric cancer: A solution to tumor heterogeneity.

The prognosis analysis of gastric cancer is critical for selection of treatments and development of advanced therapeutic methods. A prognosis approach that is accurate, fast, convenient, and of low cost for gastric cancers is in high demand. Raman spectroscopy is a label-free and non-destructive technique to provide molecular fingerprints of biological samples, holding promises for cancer prognosis. However, the major challenge of gastric cancer prognosis lies in the widely existing tumor heterogeneity, which leads to unexpected spectral variations within one type of samples. In this work, we have developed the Euclidean distance (ED)-based Raman spectroscopy (EDRS) method for the prognosis analysis of gastric cancer to eliminate the influence of tumor heterogeneity. Raman spectra were first collected on the slices of paraffin-preserved tumor tissues from gastric cancer patients. A standard spectrum to represent the 'worst prognostic tumor cells' was then established. The similarity between each spectrum of tissues and the standard spectrum was assessed by ED, to provide a direct assessment on the prognosis status. We have successfully classified the patients into poor and favorable prognosis groups, either based on the averaged regional ED values (sensitivity of 75 %, specificity of 96.8 %), or based on the minimal ED values at the patient level (sensitivity of 90 %, specificity of 100 %). EDRS was also investigated for survival analysis (AUC = 0.955), much better than the commonly applied post-neoadjuvant therapy (ypTNM) category (AUC = 0.718). Our work highlights EDRS as a rapid, accurate, low-cost and robust tool for heterogeneous cancer-related prognosis assessment and survival prediction, providing new insights for spectroscopic tumor analysis.

Analysis of ceRNA networks during mechanical tension-induced osteogenic differentiation of periodontal ligament stem cells.

The molecular mechanisms underlying osteogenic differentiation of periodontal ligament stem cells (PDLSCs) under mechanical tension remain unclear. This study aimed to identify a potential long non-coding ribonucleic acids (lncRNAs)/circular RNAs (circRNAs)-microRNAs (miRNAs)-messenger RNAs (mRNAs) network in mechanical tension-induced osteogenic differentiation of PDLSCs. PDLSCs were isolated from the healthy human periodontal ligament, identified, cultured, and exposed to tensile force. The expression of osteogenic markers was examined, and whole transcriptome sequencing was performed to identify the expression patterns of lncRNA, circRNA, miRNAs, and mRNAs. Enrichment analyses were also performed. Candidate targets of differentially expressed non-coding RNAs (ncRNAs) were predicted, and potential competitive endogenous RNA (ceRNA) networks were constructed by Cytoscape. We found that the osteogenic differentiation of PDLSCs was significantly enhanced under dynamic tension (magnitude: 12%, frequency: 0.7 Hz). Overall, 344 lncRNAs, 57 miRNAs, 41 circRNAs, and 70 mRNAs were differentially expressed in the tension group and the control group. Functional enrichment analysis showed that differentially expressed mRNAs were mainly enriched in osteogenesis-related and mechanical stress-related biological processes and signal transduction pathways (e.g., tumor necrosis factor [TNF] and Hippo signaling pathways). The lncRNA/circRNA-miRNA-mRNA networks were depicted, and potential key ceRNA networks were identified. Our findings may help to further explore the underlying regulatory mechanism of osteogenic differentiation of PDLSCs under mechanical tensile stress.

Multifunctional theranostic nanoparticles for multi-modal imaging-guided CAR-T immunotherapy and chemo-photothermal combinational therapy of non-Hodgkin's lymphoma.

Accurate and effective tumor diagnosis, detection, and treatment are key for improving the survival rates of patients. Chimeric antigen receptor T (CAR-T) cell therapy has shown remarkable clinical success in eradicating hematologic malignancies. However, the hostile microenvironment in solid tumors severely prevents CAR-T cells from migrating and from infiltrating and killing malignant cells. Tumor microenvironment modulation strategies have attracted much attention in the field of cancer immunotherapy. Multifunctional nanoplatforms that integrate the advantages of different therapeutic techniques can allow for the multimodal synergistic treatment of tumors. In this study, a biocompatible, tumor-targeting, on-demand approach combining CAR-T cell immunotherapy and a chemo-photothermal therapy nanoplatform (FA-Gd-GERTs@Ibrutinib) based on gadolinium-loaded gap-enhanced Raman tags (Gd-GERTs) has been developed for multimodal imaging, and it provides a reliable treatment strategy for solid tumor immunotherapy via microenvironment reconstruction. In our study, folate (FA) receptor targeted molecules are used to improve the accuracy and sensitivity of computed tomography/magnetic resonance/Raman multimodal tumor imaging. The photothermal effect of the nanoprobe can promote the angiogenesis of lymphoma tissue, destroy the extracellular matrix, loosen compact tissue, stimulate chemokine secretion, and effectively enhance the infiltration ability in the case of non-Hodgkin's lymphoma, without dampening the CD19 CAR-T cell activity. The treatment results in tumor-bearing mice proved the existence of excellent synergistic therapy; photothermal therapy improves the accumulation and effector function of CAR-T cells within solid tumors. It is believed that multifunctional nanomaterials with targeted multi-modal imaging capabilities that support combination therapy can provide an efficient route for accurate diagnosis and efficient treatment.

FAM3B Serves as a Biomarker for the Development and Malignancy of Oral Lichen Planus.

PURPOSE: Oral lichen planus (OLP) is a potentially malignant condition with unclear etiology. This study aimed to identify potential biomarkers and mechanisms for OLP progression through bioinformatics analyses. METHODS: Gene Expression Omnibus (GEO) datasets were screened to identify differentially expressed genes (DEGs) between OLP patients and healthy individuals. The functions and enriched pathways of the DEGs were identified. Sequencing dataset GSE70665 was then used to analyze the role of DEGs in the development of OLP to oral squamous cell carcinoma (OSCC). Oncomine and The Cancer Genome Atlas (TCGA) databases were utilized to evaluate clinicopathological characters of OSCC. Univariate and multivariate Cox regression models were used to identify independent prognostic factors. RESULTS: A total of 24 DEGs were identified between OLP and normal samples. FAM3B was under-expressed in OLP compared with normal samples and was further significantly downregulated in OSCC compared with OLP. Under-expression of FAM3B was significantly correlated with tumor stage and disease-specific survival (DSS), progression-free interval (PFI) and overall survival (OS) of OSCC patients. With univariate and multivariate Cox regression analysis, FAM3B was an independent prognostic factor. CONCLUSION: Under-expression of FAM3B was associated with the development and malignancy of OLP. FAM3B may serve as a potential prognostic biomarker for OLP.

Dysregulated MDR1 by PRDM1/Blimp1 Is Involved in the Doxorubicin Resistance of Non-Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma.

INTRODUCTION: The chemoresistance mechanism of diffuse large B-cell lymphoma (DLBCL) is still poorly understood, and patient prognosis remains unsatisfactory. This study aimed to investigate drug resistance mechanisms in non-germinal center B-cell-like (non-GCB) DLBCL. METHODS: Doxorubicin (DOX)-resistant OCI-Ly3 cells were generated through long-term incubation of cells in a medium with gradually increasing DOX concentrations. The expression levels of genes related to drug metabolism were determined using a functional gene grouping polymerase chain reaction (PCR) array. Drug-resistant proteins were identified using bioinformatics, and molecular association networks were subsequently generated. The association and mechanism of key genes were determined using a dual-luciferase reporter assay System and chromatin immunoprecipitation (ChIP). The expression of drug-resistant genes and target genes was then measured using Western blotting and immunohistochemistry. The correlation between gene expressions was analyzed using Spearman's rank correlation coefficient. RESULTS: Using the PCR array, MDR1 was identified as the key gene that regulates DOX resistance in OCI-Ly3/DOX-A100, a non-GCB DLBCL cell line. The dual-luciferase reporter assay system demonstrated that MDR1 transcription could be inhibited by PRDM1. ChIP results showed that PRDM1 had the ability to bind to the promoter region (-1,132 to -996) of MDR1. In OCI-Ly3/DOX cells, NF-κB activity and PRDM1 expression decreased with an increase in drug-resistant index, whereas MDR1 expression increased with enhanced drug resistance. Immunohistochemical analysis revealed that relative MDR1 expression was higher than that of PRDM1 in human DLBCL tissue samples. A negative correlation was observed between MDR1 and PRDM1. CONCLUSION: In non-GCB DLBCL cells, NF-κB downregulates PRDM1 and thereby promotes MDR1 transcription by terminating PRDM1-induced transcriptional inhibition of MDR1. Such a mechanism may explain the reason for disease recurrence in non-GCB DLBCL after R-CHOP or combined CHOP with bortezomib treatment. Our findings may provide a potential therapeutic strategy for reducing drug resistance in patients with DLBCL.

An Analysis of the Correlation Between Clinical Indexes and Pathological Classifications in 202 Patients with Lupus Nephritis.

OBJECTIVE: To investigate the correlation between clinical indexes and pathological classifications in 202 patients with lupus nephritis (LN). METHODS: A total of 202 LN cases were retrospectively analyzed. All these patients met the four diagnostic criteria for systemic lupus erythematosus (SLE) of the American College of Rheumatology revised in 1997. The pathological diagnostic criteria of LN were in accordance with the pathological LN classification revised by the International Society of Nephrology and the Society of Kidney Pathology in 2003. The patients were scored according to the improved SLE Disease Activity Index 2000 (SLEDAI-2K), and their basic data, clinical data, laboratory data, and pathological data were collected. RESULTS: Among the 202 patients, the ratio of male to female was 1:5.73, and type IV was the most common pathological LN classification. There were differences in the urine analysis, hypertension incidence, blood cell analysis, blood lipids, renal function, plasma albumin, immunological indexes, renal pathological score among the different pathological types (P < 0.05). In the early finding of renal function damage of the patients, cystatin C sensitivity was significantly higher than that of serum creatinine and blood urea nitrogen. Multiple linear regression analysis show that there are strong correlations between AI and SLEDAI, 24hU-Pr, serum C3, serum ALB, BUN, creatinine, UA and PLT (P < 0.001); and there are correlations between AI and serum IgM, IgA, C4, TC and LDL-C (P < 0.05). CONCLUSION: There is a clear correlation between pathological classifications and clinical indexes of LN. TRIAL REGISTRATION: Shen-PJ-2018-40, Study on Clinical and Molecular Mechanism of SLE.

A dual-role of SARS-CoV-2 nucleocapsid protein in regulating innate immune response.

The recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of ongoing global pandemic of COVID-19, may trigger immunosuppression in the early stage and overactive immune response in the late stage of infection; However, the underlying mechanisms are not well understood. Here we demonstrated that the SARS-CoV-2 nucleocapsid (N) protein dually regulated innate immune responses, i.e., the low-dose N protein suppressed type I interferon (IFN-I) signaling and inflammatory cytokines, whereas high-dose N protein promoted IFN-I signaling and inflammatory cytokines. Mechanistically, the SARS-CoV-2 N protein dually regulated the phosphorylation and nuclear translocation of IRF3, STAT1, and STAT2. Additionally, low-dose N protein combined with TRIM25 could suppress the ubiquitination and activation of retinoic acid-inducible gene I (RIG-I). Our findings revealed a regulatory mechanism of innate immune responses by the SARS-CoV-2 N protein, which would contribute to understanding the pathogenesis of SARS-CoV-2 and other SARS-like coronaviruses, and development of more effective strategies for controlling COVID-19.

MMP-16 as a New Biomarker for Predicting Prognosis and Chemosensitivity of Serous Ovarian Cancer: A Study Based on Bioinformatics Analysis.

OBJECTIVE: To explore the prognostic value of MMP-16 expression in patients with serous ovarian cancer and the usefulness of MMP-16 expression to predict sensitivity to chemoradiotherapy. METHODS: The relationship between MMP-16 expression and clinicopathological parameters of serous ovarian cancer was evaluated in The Cancer Genome Atlas (TCGA) database. Cox proportional hazard regression analysis was performed to measure the prognostic significance of MMP-16 in serous ovarian cancer. Dataset GSE51373 was applied to estimate the difference of MMP-16 expression between chemotherapy-sensitive group and resistant group of serous ovarian cancer. Receiver operating characteristic (ROC) curve was also drawn. In addition, the online tool Kaplan-Meier Plotter was used to assess the prognostic value of MMP-16 in patients with serous ovarian cancer. RESULTS: A total of 235 patients with serous ovarian cancer were included in the TCGA database. Cox regression univariate analysis showed that high expression of MMP-16 was not conducive to the overall survival of patients with serous ovarian cancer (hazard ratio [HR] = 1.47, 95% CI: 1.03~2.08; P < 0.05). The results of Cox regression multivariate analysis also demonstrated that there was a statistically significant difference. The results of the online database Kaplan-Meier Plotter analysis showed that the high expression of MMP-16 was not conducive to the progression-free survival (PFS) of patients with serous ovarian cancer (HR = 1.26, 95% CI: 1.06~1.29; P < 0.05). The expression of MMP-16 in the chemotherapy-sensitive group was notably lower than that in the chemotherapy-resistant group, which had a moderate predictive value in predicting the chemosensitivity of serous ovarian cancer (AUC = 0.7187). CONCLUSION: High expression of MMP-16 is not conducive to chemotherapy sensitivity and survival of patients with serous ovarian cancer, and has predictive value for chemotherapy resistance and prognosis.

Seven-year follow-up of a patient with hereditary gingival fibromatosis treated with a multidisciplinary approach: case report.

BACKGROUND: Hereditary gingival fibromatosis (HGF) is rare in clinical practice, and the long-term results of the combined orthodontic-periodontal treatment of HGF are rarely reported. CASE PRESENTATION: This study reports for the first time the results of seven years of follow-up in a seven-year-old girl with HGF. The diagnosis was confirmed by clinical signs, family history and histopathological examination. First, periodontal scaling and oral hygiene reinforcement were performed regularly in the mixed dentition stage. Next, gingivoplasty was performed on the permanent dentition. Two months after the surgery, treatment with fixed orthodontic appliances was conducted. The teeth were polished on a monthly basis, and oral hygiene was reinforced to control gingival enlargement. Gingival hypertrophy recurred slightly, and gingivectomies were performed in the months following the start of orthodontic treatment. Follow-up was performed for 24 months with orthodontic retention, and gingival enlargement remained stable after the combined treatment. CONCLUSIONS: The risk of gingival hyperplasia recurrence during and after orthodontic treatment is high, but satisfying long-term outcomes can be achieved with gingivectomy, malocclusion correction, and regular follow-up maintenance.

SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Production Through Ubiquitin-Mediated Degradation of TBK1.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative pathogen of current COVID-19 pandemic, and insufficient production of type I interferon (IFN-I) is associated with the severe forms of the disease. Membrane (M) protein of SARS-CoV-2 has been reported to suppress host IFN-I production, but the underlying mechanism is not completely understood. In this study, SARS-CoV-2 M protein was confirmed to suppress the expression of IFNß and interferon-stimulated genes induced by RIG-I, MDA5, IKKϵ, and TBK1, and to inhibit IRF3 phosphorylation and dimerization caused by TBK1. SARS-CoV-2 M could interact with MDA5, TRAF3, IKKϵ, and TBK1, and induce TBK1 degradation via K48-linked ubiquitination. The reduced TBK1 further impaired the formation of TRAF3-TANK-TBK1-IKKε complex that leads to inhibition of IFN-I production. Our study revealed a novel mechanism of SARS-CoV-2 M for negative regulation of IFN-I production, which would provide deeper insight into the innate immunosuppression and pathogenicity of SARS-CoV-2.

Development and Validation of a Novel Prognostic Model for Acute Myeloid Leukemia Based on Immune-Related Genes.

The prognosis of acute myeloid leukemia (AML) is closely related to immune response changes. Further exploration of the pathobiology of AML focusing on immune-related genes would contribute to the development of more advanced evaluation and treatment strategies. In this study, we established a novel immune-17 signature based on transcriptome data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) databases. We found that immune biology processes and transcriptional dysregulations are critical factors in the development of AML through enrichment analyses. We also formulated a prognostic model to predict the overall survival of AML patients by using LASSO (Least Absolute Shrinkage and Selection Operator) regression analysis. Furthermore, we incorporated the immune-17 signature to improve the prognostic accuracy of the ELN2017 risk stratification system. We concluded that the immune-17 signature represents a novel useful model for evaluating AML survival outcomes and may be implemented to optimize treatment selection in the next future.

FOXC1 Negatively Regulates DKK1 Expression to Promote Gastric Cancer Cell Proliferation Through Activation of Wnt Signaling Pathway.

Gastric cancer (GC), characterized by uncontrolled growth, is a common malignant tumor of the digestive system. The Wnt signaling pathway plays an important role in the tumorigenesis and proliferation of GC. Many studies on this signaling pathway have focused on its intracellular regulatory mechanism, whereas little attention has been given to extracellular regulatory factors. Dickkopf-1 (Dkk1) is a secretory glycoprotein, and it can bind inhibit activation of the Wnt pathway. However, the regulation and mechanism of DKK1 in the proliferation of GC remain unclear. FOXC1 plays an important role in organ development and tumor growth, but its role in GC tumor growth remains unknown. In this study, we found that the FOXC1 is highly expressed in patients with GC and high expression of FOXC1 correlates to poor prognosis. In addition, we found that the Wnt signaling pathway in GC cells with high FOXC1 expression was strongly activated. FOXC1 negatively regulates DKK1 expression by binding to its promoter region, thereby promoting the activation of Wnt pathway. FOXC1 can also form a complex with unphosphorylated ß-catenin protein in the cytoplasm and then dissociates from ß-catenin in the nucleus, thereby promoting the entry of ß-catenin into the nucleus and regulating expression of c-MYC, which promotes the proliferation of GC cells. Our study not only reveals the function and mechanism of FOXC1 in GC, but also provides a potential target for clinic GC treatment.

[Effect of MiR-96 on Cell Invasion and Apoptosis in Pediatric Acute Myeloid Leukemia via Regulating MYB].

OBJECTIVE: To analyze the relationship of the expression of transcription factor MYB targeted regulation by miR-96 to cell invasion and apoptosis in pediatric acute myeloid leukemia (AML). METHODS: A total of 65 children with AML in The 928 Hospital of PLA Joint Logistics Support Forces from January 2017 to November 2019 were selected, including 35 cases diagnosed as primary AML and 30 cases as complete remission AML. Thirty children with immune thrombocytopenia were selected as control group. The clinical characteristics were analyzed and compared between the two groups. The levels of miR-96 and MYB in peripheral blood samples were detected by qRT-PCR and compared between the two groups. The miR-96 mimics and its negative control (NC), inhibitor-miR-96 and its NC transfected HL60 cells induced by liposome (Lipofectamine 2000), respectively, Then the expression levels of MYB were detected with Western blot and compared among four HL60 cell groups. The invasion ability of four HL60 cell groups were detected with Transwell assay. The cell proliferation ability of four HL60 cell groups were detected with MTT at 24 h, 48 h, and 72 h, respectively. The apoptosis rates of four HL60 cell groups were detected with flow cytometry. RESULTS: Compared with control group, the level of miR-96 in AML children were higher, but MYB lower (P<0.05). Compared with complete remission AML, the level of miR-96 in primary AML was higher, but MYB lower (P<0.05). Western blot analysis showed that, the expression level of MYB in the four HL60 cell groups was different (P<0.05), the lowest was in miR-96 mimics group, followed by miR-96 NC group and inhibitor-miR-96 NC group, and the highest in inhibitor-miR-96 group (P<0.05), while there was no difference between miR-96 NC group and inhibitor-miR-96 NC group (P>0.05). The promotion of over-expression level of miR-96 on the invasion ability of HL 60 cells was confirmed by Transwell assay. MTT assay showed that miR-96 could promote the proliferation of HL60 cells, inhibit the apoptosis of HL60 cells, and the effect was time-dependent manner (r=0.804). The inhibition of miR-96 on HL60 cells apoptosis was also confirmed with flow cytometry. CONCLUSION: MiR-96 has significant negative effect on invasion and apoptosis of AML cells by targeting regulation MYB, and it might be a potential novel strategy for pediatric AML treatment.

Application of Bayesian phylogenetic inference modelling for evolutionary genetic analysis and dynamic changes in 2019-nCoV.

The novel coronavirus (2019-nCoV) has recently caused a large-scale outbreak of viral pneumonia both in China and worldwide. In this study, we obtained the entire genome sequence of 777 new coronavirus strains as of 29 February 2020 from a public gene bank. Bioinformatics analysis of these strains indicated that the mutation rate of these new coronaviruses is not high at present, similar to the mutation rate of the severe acute respiratory syndrome (SARS) virus. The similarities of 2019-nCoV and SARS virus suggested that the S and ORF6 proteins shared a low similarity, while the E protein shared the higher similarity. The 2019-nCoV sequence has similar potential phosphorylation sites and glycosylation sites on the surface protein and the ORF1ab polyprotein as the SARS virus; however, there are differences in potential modification sites between the Chinese strain and some American strains. At the same time, we proposed two possible recombination sites for 2019-nCoV. Based on the results of the skyline, we speculate that the activity of the gene population of 2019-nCoV may be before the end of 2019. As the scope of the 2019-nCoV infection further expands, it may produce different adaptive evolutions due to different environments. Finally, evolutionary genetic analysis can be a useful resource for studying the spread and virulence of 2019-nCoV, which are essential aspects of preventive and precise medicine.

High-Throughput Screen for Cell Wall Synthesis Network Module in Mycobacterium tuberculosis Based on Integrated Bioinformatics Strategy.

BACKGROUND: Mycobacterium tuberculosis is one of the deadliest pathogens in humans. Co-infection of M. tuberculosis with HIV and the emergence of multi-drug-resistant tuberculosis (TB) constitute a serious global threat. However, no effective anti-TB drugs are available, with the exception of first-line drugs such as isoniazid. The cell wall of M. tuberculosis, which is primarily responsible for the lack of effective anti-TB drugs and the escape of the bacteria from host immunity, is an important drug target. The core components of the cell wall of M. tuberculosis are peptidoglycan, arabinogalactan, and mycotic acid. However, the functional genome and metabolic regulation pathways for the M. tuberculosis cell wall are still unknown. In this study, we used the biclustering algorithm integrated into cMonkey, sequence alignment, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other bioinformatics methods to scan the whole genome of M. tuberculosis as well as to identify and statistically analyze the genes related to the synthesis of the M. tuberculosis cell wall. METHOD: We performed high-throughput genome-wide screening for M. tuberculosis using Biocarta, KEGG, National Cancer Institute Pathway Interaction Database (NCI-PID), HumanCyc, and Reactome. We then used the Database of Origin and Registration (DOOR) established in our laboratory to classify the collection of operons for M. tuberculosis cell wall synthetic genes. We used the cMonkey double clustering algorithm to perform clustering analysis on the gene expression profile of M. tuberculosis for cell wall synthesis. Finally, we visualized the results using Cytoscape. RESULT AND CONCLUSION: Through bioinformatics and statistical analyses, we identified 893 M. tuberculosis H37Rv cell wall synthesis genes, distributed in 20 pathways, involved in 46 different functions related to cell wall synthesis, and clustered in 386 modules. We identified important pivotal genes and proteins in the cell wall synthesis pathway such as murA, a class of operons containing genes involved in cell wall synthesis such as ID6951, and a class of operons indispensable for the survival of the bacteria. In addition, we found 41 co-regulatory modules for cell wall synthesis and five co-expression networks of molecular complexes involved in peptidoglycan biosynthesis, membrane transporter synthesis, and other cell wall processes.