Establishment of optimal regulatory network of colorectal cancer based on p42.3 protein

Objective: to establish regulatory network of colorectal cancer involving p42.3 protein and to provide theoretical evidence for deep functional exploration of p42.3 protein in the onset and development of colorectal cancer. Methods: with protein similarity algorithm, reference protein set of p42.3 cell apoptosis was built according to structural features of p42.3. GO and KEGG databases were used to establish regulatory network of tumor cell apoptosis involving p42.3; meanwhile, the largest possible working pathway that involves p42.3 protein was screened out based on Bayesian network theory. Besides, GO and KEGG were used to build regulatory network on early diagnosis gene markers for colorectal cancer including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, at the same time, a regulatory network of colorectal cancer cell apoptosis which involves p42.3 was established. Results: cell apoptotic regulatory network that p42.3 participates in primarily consists of Bcl-2 family genes and the largest possible pathway is p42.3 → FKBP → Bcl-2 centered as FKBP protein. Combined with colorectal cancer regulatory network that involves early diagnosis gene markers, it can be predicted that p42.3 is most likely to regulate the colorectal cancer cell apoptosis through FKBP → Bcl-2 → Bax → caspase-9 → caspase-3 pathway. Conclusion: the colorectal cancer apoptosis network based on p42.3 established in the study provides theoretical evidence for deep exploration of p42.3 regulatory mechanism and molecular targeting treatment of colorectal cancer.     

NIRF constitutes a nodal point in the cell cycle network and is a candidate tumor suppressor

In biological networks, a small number of “hub” proteins play critical roles in the network integrity and functions. The cell cycle network orchestrates versatile cellular functions through interactions between many signaling modules, whose defects impair diverse cellular processes, often leading to cancer. However, the network architecture and molecular basis that ensure proper coordination between distinct modules are unclear. Here, we show that the ubiquitin ligase NIRF (also known as UHRF2), which induces G₁ arrest, interacts with multiple cell cycle proteins including cyclins (A2, B1, D1 and E1), p53 and pRB, and ubiquitinates cyclins D1 and E1. Consistent with its versatility, a bioinformatic network analysis demonstrated that NIRF is an intermodular hub protein that is responsible for the coordination of multiple network modules. Notably, intermodular hubs are frequently associated with oncogenesis. Indeed, we detected loss of heterozygosity of the NIRF gene in several kinds of tumors. When a cancer outlier profile analysis was applied to the Oncomine database, loss of the NIRF gene was found at statistically significant levels in diverse tumors. Importantly, a recurrent microdeletion targeting NIRF was observed in non-small cell lung carcinoma. Furthermore, NIRF is immediately adjacent to the single nucleotide polymorphism rs719725, which is reportedly associated with the risk of colorectal cancer. These observations suggest that NIRF occupies a prominent position within the cell cycle network, and is a strong candidate for a tumor suppressor whose aberration contributes to the pathogenesis of diverse malignancies.Key words: NIRF, UHRF2, cell cycle network, systems biology, ubiquitin ligase, COPA, tumor suppressor, glioblastoma, non-small cell lung carcinoma, rs719725     

The N-terminus region of Drp1, a Rint1 family protein is essential for cell survival and its interaction with Rad50 protein in fission yeast S.pombe

BackgroundDefects in DNA repair pathway can lead to double-strand breaks leading to genomic instability. Earlier we have shown that S.pombe Drp1, a Rint1/Tip1 family protein is required for the recovery from DNA damage.MethodsVarious truncations of Drp1 protein were constructed and their role in DNA damage response and interaction with Rad50 protein has been studied by co-immunoprecipitation and pull-down assays.ResultsThe structural and functional analysis of Drp1 protein revealed that the N-terminus region of Drp1 is indispensable for the survival. The C-terminus truncation mutants, drp1C1Δ and drp1C2Δ exhibit temperature sensitive phenotype and are hypersensitive against DNA damaging agents with elevated level of Rad52-YFP foci at non-permissive temperature indicating the impairment for DNA damage repair pathway. The essential N-terminus region of Drp1 interacts with the C-terminus region of Rad50 and might be involved in influencing the MRN/X function. Small-angle X-ray (SAXS) analysis revealed three-domain like shapes in Drp1 protein while the C-terminus region of Rad50 exhibit unusual bulges. Computational docking studies revealed the amino acid residues at the C-terminus region of Rad50 that are involved in the interaction with the residues present at the N-terminal region of Drp1 indicating the importance of the N-terminal region of Drp1 protein.ConclusionsWe have identified the region of Drp1 and Rad50 proteins that are involved in the interaction and their role in the DNA damage response pathway has been analyzed.General significanceThe functional and structural aspects of fission yeast Drp1 protein and its interaction with Rad50 have been elucidated.     

LncRNA Erbb4-IR promotes esophageal squamous cell carcinoma (ESCC) by downregulating miR-145

Erbb4-IR is a recently identified lncRNA with pivotal functions in renal injury. The present study investigated the roles of Erbb4-IR in esophageal squamous cell carcinoma (ESCC). It was observed that Erbb4-IR was upregulated in tumor tissues of patients with ESCC. Plasma levels of Erbb4-IR in patients with ESCC were positively correlated with expression levels of Erbb4-IR in tumor tissues. MicroRNA-145 (miR-145) was downregulated in tumor tissues and inversely correlated with Erbb4-IR only in tumor tissues. Erbb4-IR overexpression led to downregulated miR-145, and increased rates of ECSS cell proliferation and decreased rates of ECSS cell apoptosis. Overexpression of miR-145 showed no significant effects on Erbb4-IR expression, but played an opposite role on cancer cell proliferation and apoptosis. In addition, miR-145 overexpression attenuated the effects of Erbb4-IR overexpression. Therefore, lncRNA Erbb4-IR may promote ESCC by downregulating miR-145.     

Study of lung cancer regulatory network that involves erbB4 and tumor marker gene

Our purpose is to screen out serum tumor markers closely correlated to the nature of solitary pulmonary nodule (SPN) and to draw a regulatory network containing genes correlated to lung cancer. Two hundred and sixty cases of SPN patients confirmed through pathological diagnosis were collected as subjects, factors closely correlated to the nature of SPN were screened out from eight tumor markers through Fisher discriminant method, and functional annotation and pathway analysis were conducted on erbB4 as well as its tumor marker genes by GO and KEGG databases. Four key tumor markers: CYFRA21-1, CA125, SCC-Ag and CA153 were successfully screened out and the first three proteins’ corresponding gene were KRT19, MUC16 and SERPINB3 while that of CA153 was not found. GO analysis on erbB4, KRT19, MUC16 and SERPINB3 showed that they covered three domains, cell components, molecular function and biological process; meanwhile, combined with KEGG database and based on signal pathway of erbB4, a regulatory network of lung cancer cells escaping from apoptosis was successfully made. This study indicates that serum tumor marker genes play an important role in the occurrence and development of lung cancer, besides, this study primarily discussed the molecular mechanism of these tumor markers in predicting tumor, which provides a basis for in-depth information about lung cancer.     

miR-204通过抑制OGT的表达调控非小细胞肺癌细胞的增殖和迁移

目的:探究miR-204和O-连接N-乙酰氨基葡萄糖转移酶(O link N-acetylglucosamine transferase,OGT)对非小细胞肺癌(Non-small cell lung cancer,NSCLC)细胞增殖和转移的影响,并深入分析其可能机制。方法:采用Oncomine及KM-Ploter数据库分析OGT在肺癌组织中的表达及与肺癌患者预后的关系;采用慢病毒转染人非小细胞肺癌A549及永生化人肺支气管上皮细胞BEAS-2B,分别构建OGT稳定下调和过表达的细胞系,利用CCK-8、平板克隆和裸鼠皮下成瘤实验检测细胞增殖的情况,划痕实验、Transwell实验和裸鼠尾静脉注射肺转移模型检测细胞转移的情况。利用数据库分析可能参与OGT调控的microRNA,并用双荧光素酶报告基因验证。利用TCGA数据库分析miR-204在肺癌中的表达情况,并在30例肺癌组织及其对应癌旁组织中分析miR-204与OGT之间的相关性。结果:OGT在肺癌组织中呈高表达,且与患者的不良预后相关(HR=1.22,P 0.01);OGT的表达上调肺癌细胞的增殖和转移;miR-204可以负向调控OGT的表达,且miR-204在肺癌组织中表达水平显著低于癌旁组织,在肺癌组织中miR-204的水平与OGT的表达水平呈负相关(R~2=-0.4729,P 0.01)。结论:在非小细胞肺癌中,miR-204的降低通过上调OGT的表达促进肺癌的增殖和转移。     

Oncomine数据库在肿瘤研究中的应用

Oncomine 是目前世界上最大的癌基因芯片数据库和综合数据挖掘平台之一,该数据库整合了GEO、TCGA和已发表文献来源的RNA和DNA-seq数据。数据库目前含有715个基因表达数据集（datasheet）、86 733个人体肿瘤组织和正常组织样本的信息,且有新的数据不断更新。Oncomine 数据库囊括的肿瘤类型有19种,包括：膀胱癌、脑/中枢神经系统肿瘤、乳腺癌、宫颈癌、结直肠癌、食管癌、胃癌、头/颈肿瘤、肾癌、白血病、肝癌、肺癌、淋巴瘤、黑色素瘤、骨髓瘤、卵巢癌、胰腺癌、前列腺癌、肉瘤。本文就如何利用Oncomine数据库,进行肿瘤组织中癌基因表达差异性分析以及基因共表达分析、癌基因在肿瘤组织中的表达及拷贝数分析、多组研究数据集的荟萃分析（meta analysis）、以及癌基因表达与患者生存率关系等进行分析。通过该数据库可以对肿瘤癌基因进行研究前的筛查,有利于发现新的肿瘤生物标记物或治疗靶点,为临床科学研究奠定一定的理论基础。     

Involvement of erbB4 and tumor marker genes in renal carcinoma regulatory network

BackgroundRenal carcinoma is a common urologic tumor, and there is no ideal tumor marker for clinical diagnosis except for imaging diagnosis. This study aims to screen the serum tumor markers closely related with the benign and malignant of renal carcinoma out and chart out the regulatory network that involves renal carcinoma-related genes.MethodsBased on 96 pathologically diagnosed renal cancer patients, factors strongly linked to renal carcinoma character were selected using Fisher discriminant analysis. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to manipulate function annotation of erbB4 and the selected genes and pathway analysis.ResultsFour essential tumor markers CYFRA21-1, CA125, VHL and HIF-1β were successfully screened out. Using GO and KEGG databases, the regulatory network of renal cancer cell escaping apoptosis was charted out on the basis of erbB4 signaling pathway.ConclusionSerum tumor marker genes play a certain part in the genesis and development of renal carcinoma. We preliminarily illustrated the molecular mechanism of these markers to predict tumor, laying a foundation for further exploration in renal carcinoma.     

p42.3 gene expression in gastric cancer cell and its protein regulatory network analysis

Background

To analyze the p42.3 gene expression in gastric cancer (GC) cell, find the relationship between protein structure and function, establish the regulatory network of p42.3 protein molecule and then to obtain the optimal regulatory pathway.

Methods

The expression of p42.3 gene was analyzed by RT-PCR, Western Blot and other biotechnologies. The relationship between the spatial conformation of p42.3 protein molecule and its function was analyzed using bioinformatics, MATLAB and related knowledge about protein structure and function. Furthermore, based on similarity algorithm of spatial layered spherical coordinate, we compared p42.3 molecule with several similar structured proteins which are known for the function, screened the characteristic nodes related to tumorigenesis and development, and established the multi variable relational model between p42.3 protein expression, cell cycle regulation and biological characteristics in the level of molecular regulatory networks. Finally, the optimal regulatory network was found by using Bayesian network.

Results

(1) The expression amount of p42.3 in G1 and M phase was higher than that in S and G2 phase; (2) The space coordinate systems of different structural domains of p42.3 protein were established in Matlab7.0 software; (3) The optimal pathway of p42.3 gene in protein regulatory network in gastric cancer is Ras protein, Raf-1 protein, MEK, MAPK kinase, MAPK, tubulin, spindle protein, centromere protein and tumor.

Conclusion

It is of vital significance for mechanism research to find out the action pathway of p42.3 in protein regulatory network, since p42.3 protein plays an important role in the generation and development of GC.

     

Identification of KIF4A and its effect on the progression of lung adenocarcinoma based on the bioinformatics analysis

Background: Lung adenocarcinoma (LUAD) is the most frequent histological type of lung cancer, and its incidence has displayed an upward trend in recent years. Nevertheless, little is known regarding effective biomarkers for LUAD.Methods: The robust rank aggregation method was used to mine differentially expressed genes (DEGs) from the gene expression omnibus (GEO) datasets. The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to extract hub genes from the protein–protein interaction (PPI) network. The expression of the hub genes was validated using expression profiles from TCGA and Oncomine databases and was verified by real-time quantitative PCR (qRT-PCR). The module and survival analyses of the hub genes were determined using Cytoscape and Kaplan–Meier curves. The function of KIF4A as a hub gene was investigated in LUAD cell lines.Results: The PPI analysis identified seven DEGs including BIRC5, DLGAP5, CENPF, KIF4A, TOP2A, AURKA, and CCNA2, which were significantly upregulated in Oncomine and TCGA LUAD datasets, and were verified by qRT-PCR in our clinical samples. We determined the overall and disease-free survival analysis of the seven hub genes using GEPIA. We further found that CENPF, DLGAP5, and KIF4A expressions were positively correlated with clinical stage. In LUAD cell lines, proliferation and migration were inhibited and apoptosis was promoted by knocking down KIF4A expression.Conclusion: We have identified new DEGs and functional pathways involved in LUAD. KIF4A, as a hub gene, promoted the progression of LUAD and might represent a potential therapeutic target for molecular cancer therapy.     

Establishment of axon regeneration regulatory network and the role of low intensity pulsed ultrasound in the network

ObjectiveTo establish an axon regeneration regulatory network for optimal selection, and explore the role of low intensity pulsed ultrasound in the network.MethodsThe axon regeneration regulatory network involving axon regeneration-related proteins NGF, BDNF and PirB was constructed by using GO and KEGG. The maximum possible pathway acting on axon regeneration was screened by Bayesian network theory. The node of low - intensity pulsed ultrasound in NGF - involved axon regeneration network was complemented by combining literature methods.ResultsThe NGF, BDNF and PirB-involved axonal regeneration regulatory pathway was successfully constructed. The low intensity pulsed ultrasound played a role in axon regeneration by acting on ERK1/2-CREB pathway and GSK-3β. NGF-TrKA-Rap1-ERK1/2-CREB-Bcl-2 was optimized as optimal pathway by Bayesian theory.ConclusionThe regulatory pathway of axon regeneration involving nerve growth related factors and low intensity pulsed ultrasound was initially established, which provided a theoretical basis for further study of axon regeneration, and also new ideas for action of low intensity pulsed ultrasound on axon regeneration regulatory pathway.     

Astaxanthin prevents pulmonary fibrosis by promoting myofibroblast apoptosis dependent on Drp1‐mediated mitochondrial fission

Promotion of myofibroblast apoptosis is a potential therapeutic strategy for pulmonary fibrosis. This study investigated the antifibrotic effect of astaxanthin on the promotion of myofibroblast apoptosis based on dynamin‐related protein‐1 (Drp1)‐mediated mitochondrial fission in vivo and in vitro. Results showed that astaxanthin can inhibit lung parenchymal distortion and collagen deposition, as well as promote myofibroblast apoptosis. Astaxanthin demonstrated pro‐apoptotic function in myofibroblasts by contributing to mitochondrial fission, thereby leading to apoptosis by increasing the Drp1 expression and enhancing Drp1 translocation into the mitochondria. Two specific siRNAs were used to demonstrate that Drp1 is necessary to promote astaxanthin‐induced mitochondrial fission and apoptosis in myofibroblasts. Drp1‐associated genes, such as Bcl‐2‐associated X protein, cytochrome c, tumour suppressor gene p53 and p53‐up‐regulated modulator of apoptosis, were highly up‐regulated in the astaxanthin group compared with those in the sham group. This study revealed that astaxanthin can prevent pulmonary fibrosis by promoting myofibroblast apoptosis through a Drp1‐dependent molecular pathway. Furthermore, astaxanthin provides a potential therapeutic value in pulmonary fibrosis treatment.     

MiRNA‐30a inhibits AECs‐II apoptosis by blocking mitochondrial fission dependent on Drp‐1

Apoptosis of type II alveolar epithelial cells (AECs‐II) is a key determinant of initiation and progression of lung fibrosis. However, the mechanism of miR‐30a participation in the regulation of AECs‐II apoptosis is ambiguous. In this study, we investigated whether miR‐30a could block AECs‐II apoptosis by repressing mitochondrial fission dependent on dynamin‐related protein‐1 (Drp‐1). The levels of miR‐30a in vivo and in vitro were determined through quantitative real‐time PCR (qRT‐PCR). The inhibition of miR‐30a in AECs‐II apoptosis, mitochondrial fission and its dependence on Drp‐1, and Drp‐1 expression and translocation were detected using miR‐30a mimic, inhibitor‐transfection method (gain‐ and loss‐of‐function), or Drp‐1 siRNA technology. Results showed that miR‐30a decreased in lung fibrosis. Gain‐ and loss‐of‐function studies revealed that the up‐regulation of miR‐30a could decrease AECs‐II apoptosis, inhibit mitochondrial fission, and reduce Drp‐1 expression and translocation. MiR‐30a mimic/inhibitor and Drp‐1 siRNA co‐transfection showed that miR‐30a could inhibit the mitochondrial fission dependent on Drp‐1. This study demonstrated that miR‐30a inhibited AECs‐II apoptosis by repressing the mitochondrial fission dependent on Drp‐1, and could function as a novel therapeutic target for lung fibrosis.     

Network pharmacology and molecular docking analyses on Lianhua Qingwen capsule indicate Akt1 is a potential target to treat and prevent COVID‐19

ObjectivesCoronavirus disease 2019 (COVID‐19) is rapidly spreading worldwide. Lianhua Qingwen capsule (LQC) has shown therapeutic effects in patients with COVID‐19. This study is aimed to discover its molecular mechanism and provide potential drug targets.Materials and MethodsAn LQC target and COVID‐19–related gene set was established using the Traditional Chinese Medicine Systems Pharmacology database and seven disease‐gene databases. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein‐protein interaction (PPI) network were performed to discover the potential mechanism. Molecular docking was performed to visualize the patterns of interactions between the effective molecule and targeted protein.ResultsA gene set of 65 genes was generated. We then constructed a compound‐target network that contained 234 nodes of active compounds and 916 edges of compound‐target pairs. The GO and KEGG indicated that LQC can act by regulating immune response, apoptosis and virus infection. PPI network and subnetworks identified nine hub genes. The molecular docking was conducted on the most significant gene Akt1, which is involved in lung injury, lung fibrogenesis and virus infection. Six active compounds of LQC can enter the active pocket of Akt1, namely beta‐carotene, kaempferol, luteolin, naringenin, quercetin and wogonin, thereby exerting potential therapeutic effects in COVID‐19.ConclusionsThe network pharmacological strategy integrates molecular docking to unravel the molecular mechanism of LQC. Akt1 is a promising drug target to reduce tissue damage and help eliminate virus infection.     

Fission yeast Drp1 is an essential protein required for recovery from DNA damage and chromosome segregation

DNA double strand breaks (DSBs) are the most critical types of DNA damage that can leads to chromosomal aberrations, genomic instability and cancer. Several genetic disorders such as Xeroderma pigmentosum are linked with defects in DNA repair. Human Rint1, a TIP1 domain containing protein is involved in membrane trafficking but its role in DNA damage response is elusive. In this study we characterized the role of Drp1 (damage responsive protein 1), a Rint1 family protein during DNA damage response in fission yeast. We identified that Drp1 is an essential protein and indispensable for survival and growth. Using in vitro random mutagenesis approach we isolated a temperature sensitive mutant allele of drp1 gene (drp1-654) that exhibits sensitivity to DNA damaging agents, in particular to alkylation damage and UV associated DNA damage. The drp1-654 mutant cells are also sensitive to double strand break inducing agent bleomycin. Genetic interaction studies identified that Rad50 and Drp1 act in the same pathway during DNA damage response and the physical interaction of Drp1 with Rad50 was unaffected in drp1-654 mutant at permissive as well as non permissive temperature. Furthermore Drp1 was found to be required for the recovery from MMS induced DNA damage. We also demonstrated that the Drp1 protein localized to nucleus and was required to maintain the chromosome stability.     

CD200: a putative therapeutic target in cancer

CD200 was recently described as a new prognosis factor in multiple myeloma and acute myeloid leukemia. CD200 is a membrane glycoprotein that imparts an immunoregulatory signal through CD200R, leading to the suppression of T-cell-mediated immune responses. We investigated the expression of CD200 in cancer using publicly available gene expression data. CD200 gene expression in normal or malignant human tissues or cell lines was obtained from the Oncomine Cancer Microarray database, Amazonia database and the ITTACA database. We found significant overexpression of CD200 in renal carcinoma, head and neck carcinoma, testicular cancer, malignant mesothelioma, colon carcinoma, MGUS/smoldering myeloma, and in chronic lymphocytic leukemia compared to their normal cells or their tissue counterparts. Moreover, we show that CD200 expression is associated with tumor progression in various cancers. Taken together, these data suggest that CD200 is a potential therapeutic target and prognostic factor for a large array of malignancies.     

PTEN overexpression promotes glioblastoma death through triggering mitochondrial division and inactivating the Akt pathway

Abstract

Objective: PTEN has been acknowledged as an anticancer factor in the progression of glioblastoma. Mitochondrial division has been found to be associated with cancer cell death.

Objective: The aim of our study is to explore whether PTEN attenuates the development of glioblastoma by modulating mitochondrial division.

Materials and methods: PTEN adenovirus was used to overexpress PTEN in U87 cells. Mitochondrial function was detected via western blot and immunofluorescence. Pathway blocker was used to inhibit the Akt activation.

Results: The results of our study demonstrated that PTEN overexpression reduced cell viability by increasing cell apoptosis. At the molecular level, PTEN overexpression activated mitochondrial apoptosis by mediating mitochondrial dysfunction. Furthermore, we found that Drp1-related mitochondrial division was required for PTEN-mediated mitochondrial dysfunction and cell death. Finally, we found that PTEN modulated Drp1-related mitochondrial division via the Akt pathway; inactivation of Akt induced cell death, and mitochondrial damage, similar to the results obtained via PTEN overexpression.

Conclusions: Taken together, our results clarify that the anticancer mechanism of PTEN in glioblastoma is dependent on the activation of Drp1-related mitochondrial division via Akt pathway modulation. This finding might provide new insight into the tumor-suppressive role played by PTEN in glioblastoma.     

Prediction of immune factors and signaling pathways in lung injury induced by LPS based on network analysis

ObjectiveTo construct a regulatory network involved in acute lung injury, so as to provide a new theoretical basis and research ideas for studying the relationship between inflammatory factors and immune proteins to collectively regulate the occurrence of acute lung injury.MethodBy using Meta-analysis, GO, KEGG and other methods notarized and constructed the regulatory network pathways of cytokine cascade and lung injury induced by LPS.ResultsThe result of Meta-analysis showed that the correlation between CD14, TNF-α, IL-6 gene and acute lung injury was statistically significant. GO analysis and KEGG analysis showed that acute lung injury contained CD14, TNF-α, IL-6 and other involved factors in the induced process of LPS, these inflammatory factors and immune proteins jointly regulate the process of disease development.ConclusionCD14 receptor is an important receptor involved in mediating LPS-activated cells, and is a high-affinity LPS receptor. LPS stimulates inflammatory effector cells to bind to LPS receptor- CD14 to activate intracellular signal cascade. Direct or indirect involvement of pathogenic factors enable cytokine caused by induction form a particularly complex network of cytokine regulatory pathways, of which the inflammatory factors TNF-α and IL-6 are simultaneously involved in LPS-mediated and CD14-mediated cytokine cascades.