iSUMO-RsFPN: A predictor for identifying lysine SUMOylation sites based on multi-features and feature pyramid networks.

SUMOylation is a protein post-translational modification that plays an essential role in cellular functions. For predicting SUMO sites, numerous researchers have proposed advanced methods based on ordinary machine learning algorithms. These reported methods have shown excellent predictive performance, but there is room for improvement. In this study, we constructed a novel deep neural network Residual Pyramid Network (RsFPN), and developed an ensemble deep learning predictor called iSUMO-RsFPN. Initially, three feature extraction methods were employed to extract features from samples. Following this, weak classifiers were trained based on RsFPN for each feature type. Ultimately, the weak classifiers were integrated to construct the final classifier. Moreover, the predictor underwent systematically testing on an independent test dataset, where the results demonstrated a significant improvement over the existing state-of-the-art predictors. The code of iSUMO-RsFPN is free and available at https://github.com/454170054/iSUMO-RsFPN.

iCancer-Pred: A tool for identifying cancer and its type using DNA methylation.

DNA methylation is an important epigenetics, which occurs in the early stages of tumor formation. And it also is of great significance to find the relationship between DNA methylation and cancer. This paper proposes a novel model, iCancer-Pred, to identify cancer and classify its types further. The datasets of DNA methylation information of 7 cancer types have been collected from The Cancer Genome Atlas (TCGA). The coefficient of variation firstly is used to reduce the number of features, and then the elastic network is applied to select important features. Finally, a fully connected neural network is constructed with these selected features. In predicting seven types of cancers, iCancer-Pred has achieved an overall accuracy of over 97% accuracy with 5-fold cross-validation. For the convenience of the application, a user-friendly web server: http://bioinfo.jcu.edu.cn/cancer or http://121.36.221.79/cancer/ is available. And the source codes are freely available for download at https://github.com/Huerhu/iCancer-Pred.

Circular RNA circ-RNF121 contributes to cisplatin (DDP) resistance of non-small-cell lung cancer cells by regulating the miR-646/SOX4 axis.

Chemo-resistance is considered a major obstacle in the clinical treatment of non-small-cell lung cancer (NSCLC). Circular RNA (circRNA) circ-RNF121 (hsa_circ_0023404) has been identified to be related to the cisplatin (DDP) resistance. However, the role and mechanism of circ-RNF121 in the DDP resistance in NSCLC are still unknown. Real-time quantitative PCR (RT-qPCR) was applied to detect the levels of circ-RNF121, microRNA-646 (miR-646) and SRY-related HMG box transcription factor 4 (SOX4). Cell viability, proliferation, apoptosis, migration, invasion and cell cycle progression were assessed by 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT), colony formation, flow cytometry, wound-healing, transwell and flow cytometry assays, severally. The binding relationship between miR-646 and circ-RNF121 or SOX4 was predicted by the circular RNA interactome or Target Scan Human7.2 and then verified by a dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. SOX4 protein level was measured by western blot assay. The biological role of circ-RNF121 on NSCLC tumor growth and drug resistance was examined by the xenograft tumor model in vivo. Circ-RNF121 and SOX4 were increased, and miR-646 was declined in DDP-resistant NSCLC tissues and cells. Furthermore, the circ-RNF121 deficiency could enhance DDP sensitivity by inhibiting cell proliferation, migration, invasion, cell cycle progression and promoting apoptosis in DDP-resistant NSCLC cells in vitro. Mechanically, circ-RNF121 served as a sponge of miR-646 to increase SOX4 expression. Circ-RNF121 knockdown improved the drug sensitivity of NSCLC in vivo. Circ-RNF121 silencing could reduce the DDP resistance of NSCLC cells by regulating SOX4 expression via miR-646. These findings hinted at a promising therapeutic target for NSCLC treatment.

Expression of miR-92a, miR-224 and miR-25 in non-small cell lung cancer and their correlation with clinical characteristics.

OBJECTIVE: To analyze the correlation of the expression of microRNA-92a (miR-92a), microRNA-224 (miR-224), and microRNA-25 (miR-25) in non-small cell lung cancer with its clinical characteristics. METHODS: This prospective study was performed in 125 non-small cell lung cancer patients admitted to our hospital between January 2019 and January 2020. All patients' cancer and adjacent tissue were collected and the expression of miR-92a, miR-224, and miR-25 were detected using real-time fluorescence quantitative RT-PCR. Data were analyzed using SPSS statistical software (version 20.0). Correlation analysis was conducted using Pearson correlation coefficient. RESULTS: Compared with adjacent tissue, the relative expression of miR-92a, miR-224, and miR-25 in cancer tissue were increased (all P<0.001). There was no correlation between the expression of miR-92a, miR-224, and miR-25 and baseline data like gender, age, smoking history, and tumor size (all P>0.05). The relative expression of miR-92a, miR-224 and miR-25 in differentiated cancer patients were higher than those in highly and moderately differentiated cancer patients (all P<0.05). The relative expression of miR-92a, miR-224 and miR-25 in patients with lymph node metastasis (LNM) were increased when compared with those had no LNM (all P<0.001). Compared with stage I and II patients, the relative expression of miR-92a, miR-224 and miR-25 in stage III and IV patients were increased (all P<0.001). The relative expression of miR-92a, miR-224, and miR-25 were positively correlated to each other (all P<0.01). CONCLUSION: miR-92a, miR-224, and miR-25 are overexpressed in non-small cell lung cancer and the expressions are related to the degree of differentiation, presence or absence of LNM, and TNM staging. In addition, the expression of miR-92a, miR-224 and miR-25 are positively correlated to each other. This suggests that miR-92a, miR-224, and miR-25 cooperatively participated in the occurrence and development of non-small cell lung cancer.

Effects of harmaline on cell growth of human liver cancer through the p53/p21 and Fas/FasL signaling pathways.

The effects of harmaline on the viability and apoptosis of human liver carcinoma were investigated in vitro. HepG2 cells were treated with harmaline (0-10 µM), and the proliferation and apoptosis of HepG2 cells were investigated using an MTT assay and flow cytometry, respectively. The protein expression of cellular tumor antigen p53 (p53), cyclin-dependent kinase inhibitor 1 (p21), tumor necrosis factor receptor superfamily member 6 (Fas), Fas ligand (FasL) and caspase-8 was subsequently measured using western blotting. In addition, an ELISA was used to analyze caspase-8/3 activity. Harmaline significantly increased p53, p21, Fas and FasL protein expression in HepG2 cells. Additionally, treatment with harmaline significantly increased the expression of caspase-8 and caspase-8/3 activity. The results from the present study suggest that harmaline suppresses the viability, but induces the apoptosis, of human liver carcinoma cells through upregulation of the p53/p21 and Fas/FasL signaling pathways.

Cloning of transforming growth factor-beta 1 (TGF-beta 1) and its type II receptor from zebrafish ovary and role of TGF-beta 1 in oocyte maturation.

TGF-beta is a multifunctional factor involved in regulating a variety of cellular activities. In mammals, TGF-beta is known to regulate reproduction, including ovarian functions. The role of TGF-beta in lower vertebrates, such as fish, is poorly understood. To examine the role of TGF-beta in fish reproduction, cDNAs encoding TGF-beta 1 and the type II TGF-beta receptor (T beta RII) were cloned from the zebrafish ovary using PCR- based strategies. The mature peptide region of the zebrafish TGF-beta 1 shows 70-85% identity with TGF-beta 1 from other species. The zebrafish T beta RII cDNA sequence is the first to be reported from a fish species, and it shows a high level of conservation at the kinase domain. Using RT-PCR, we have detected mRNA expression of TGF-beta 1, T beta RII, as well as its downstream signaling molecules Smad2, 3, and 4 in ovarian follicles at different stages of development. In addition, we have examined the effect of TGF-beta 1 on oocyte maturation. TGF-beta 1 significantly inhibited both gonadotropin- and 17 alpha, 20 beta-dihydroxyprogesterone-induced oocyte maturation in a dose- and time-dependent manner. These findings demonstrate, for the first time, that TGF-beta 1 plays a role in regulating oocyte maturation in fish and suggest that a TGF-beta/Smad signaling pathway is present in the zebrafish ovary.

Identification of novel isoforms of activin receptor-like kinase 7 (ALK7) generated by alternative splicing and expression of ALK7 and its ligand, Nodal, in human placenta.

Members of the transforming growth factor (TGF) beta family play critical roles in regulating placental functions. Using polymerase chain reaction (PCR)-based strategies, we have cloned four transcripts encoding full-length activin receptor-like kinase 7 (ALK7) and three novel ALK7 isoforms from the human placenta. The full-length ALK7 has 493 amino acids and exhibits all characteristics of TGFbeta type I receptors, including an activin receptor-binding domain, a transmembrane domain, a GS domain, and a serine/threonine kinase domain. The three ALK7 isoforms identified include a truncated ALK7 (tALK7) and two soluble proteins designated as soluble ALK7a (sALK7a) and soluble ALK7b (sALK7b). The tALK7 lacks the first 50 amino acids of the full-length ALK7, resulting in a truncated receptor-binding domain. Both sALK7a and sALK7b lack transmembrane and GS domains. The ALK7 gene, located on chromosome 2q24.1, is composed of at least nine exons and eight introns. The isoforms of ALK7 are generated by alternative splicing. Transcripts encoding the sALK7 isoforms differ from the full-length transcript by lacking exon III or both exons III and IV in sALK7a and sALK7b, respectively. The transcript for tALK7 uses an alternative exon located within the first intron of the full-length transcript. These results indicate that four distinct proteins are encoded by the human ALK7 gene. Both reverse transcription-PCR and Western blot analysis showed that ALK7 and its isoforms are expressed in human placentae of different stages of pregnancy and that their expression is developmentally regulated. In addition, mRNA expression of Nodal, a ligand for ALK7, was also detected in placentae of different gestational age. The role of Nodal and ALK7 in human placenta is currently under investigation.