Predicting non-small cell lung cancer-related genes by a new network-based machine learning method.

Lung cancer is the leading cause of cancer death globally, killing 1.8 million people yearly. Over 85% of lung cancer cases are non-small cell lung cancer (NSCLC). Lung cancer running in families has shown that some genes are linked to lung cancer. Genes associated with NSCLC have been found by next-generation sequencing (NGS) and genome-wide association studies (GWAS). Many papers, however, neglected the complex information about interactions between gene pairs. Along with its high cost, GWAS analysis has an obvious drawback of false-positive results. Based on the above problem, computational techniques are used to offer researchers alternative and complementary low-cost disease-gene association findings. To help find NSCLC-related genes, we proposed a new network-based machine learning method, named deepRW, to predict genes linked to NSCLC. We first constructed a gene interaction network consisting of genes that are related and irrelevant to NSCLC disease and used deep walk and graph convolutional network (GCN) method to learn gene-disease interactions. Finally, deep neural network (DNN) was utilized as the prediction module to decide which genes are related to NSCLC. To evaluate the performance of deepRW, we ran tests with 10-fold cross-validation. The experimental results showed that our method greatly exceeded the existing methods. In addition, the effectiveness of each module in deepRW was demonstrated in comparative experiments.

The mechanism of radiotherapy for lung adenocarcinoma in promoting protein SIRT6-mediated deacetylation of RBBP8 to enhance the sensitivity of targeted therapy.

BACKGROUND: Lung cancer has the fastest increase in morbidity and mortality, and is one of the most threatening malignant tumors to human health and life. Both radiotherapy and targeted therapy are typical treatments after lung cancer surgery. Radiotherapy is a means of locally killing cancer lesions, and it plays an important role in the entire management of lung cancer. Gefitinib is one of the most commonly used targeted therapy drugs in the treatment of lung cancer. The purpose of this project is to explore the mechanism by which deacetylation of RBBP8 mediated by radiotherapy-promoting protein SIRT6 in lung adenocarcinoma enhances the sensitivity of targeted therapy. METHODS: In both the cell experiments and the animal experiments, the samples were divided into five groups: Model group, RT group, CT group, RT+CT group, and RT+CT+inhibitor group. The CCK8 method was used to detect the viability of each group of cells. The flow cytometry experiment was used to analyze the apoptotic characteristics of each group of cells. The scratch test was used to detect the migration ability of each group of cells. Transwell invasion test was used to determine the invasion ability of each group of cells. The lung tumor tissues of each group of mice were collected to analyze the tumor size, volume, and metastasis characteristics. The TUNEL experiment was used to detect the apoptosis characteristics of the cells in the lung cancer tissues of each group mice. Immunohistochemistry experiments were used to analyze the distribution and relative expression characteristics of protein SIRT6 in mouse lung cancer tissues. The colorimetric experiments were used to detect the activity of Caspase 3 and Caspase 8 in each group. Western blot method was used to detect the expression of SIRT6, RBBP8, and MYC in each group. RESULTS: In each experiment, the results of the experiment have mutually proven consistency, and there is no contradiction. In addition to the Model group, the other 4 groups used different treatment methods. The better the curative effect, the lower the cell viability of cancer cells and the higher the apoptotic ratio. This is reflected in the CCK8 test, flow cytometry analysis, cell scratch test, Transwell cell migration test, and TUNEL detection. At the same time, colorimetric detection and Western blot analysis also analyzed the levels of SIRT6, RBBP8 and other cancer-related proteins in each group at the molecular level, implying the importance of SIRT6 protein in the treatment process. CONCLUSION: Our project has proved that radiotherapy can promote the protein SIRT6 to deacetylate RBBP8 proteins, and ultimately enhance targeted therapy drug sensitivity.

The efficacy and safety of Zengxiao Jiandu decoction combined with definitive concurrent chemoradiotherapy for unresectable locally advanced non-small cell lung cancer: a randomized, double-blind, placebo-controlled clinical trial.

Background: Traditional Chinese medicine (TCM) makes a synergistic and attenuative effect when combined with chemoradiotherapy. However, strong evidence-based studies are lacking. The study sought to investigate whether Zengxiao Jiandu decoction as an adjunctive therapy is superior to definitive concurrent chemoradiotherapy (DCCRT) alone in unresectable, locally advanced (LA), stage III non-small cell lung cancer (NSCLC). Methods: Patients with unresectable LA-NSCLC were randomly assigned to receive DCCRT either combined with Zengxiao Jiandu decoction (TCM arm) or placebo therapy (Control arm), by computer-generated random assignment lists using a central randomization system. The patients were routinely followed-up every 3 months for the first 2 years after the therapy, and every 6 months for the subsequent 3 years, or earlier if clinically indicated. The primary endpoint was grade ≥3 chemoradiotherapy-related toxicities, while secondary endpoints included the completion rate of chemoradiotherapy, the clinical objective response rate (ORR), and survival. The placebo achieved full consistency in color, aroma, taste and appearance with the Zengxiao Jiandu decoction. Results: From February 2019 to December 2020, 163 patients were randomly allocated to TCM arm (n=82) or Control arm (n=81). Fifty-nine (72.0%) patients in TCM arm finished chemoradiotherapy per protocol and 79 (96.3%) received protocol-specified Zengxiao Jiandu decoction. Forty-two patients in Control arm finished chemoradiotherapy per protocol. The incidence of grade ≥3 chemoradiotherapy-related toxicities was higher in Control arm than TCM arm (44.4% vs. 31.7%, P=0.094). Grade ≥3 radiation pneumonitis occurred more frequently in Control arm than TCM arm (13.6% vs. 3.7%, P=0.024). The completion rate of the protocol-specified chemotherapy was significantly higher in TCM arm than Control arm (79.3% vs. 64.2%, P=0.033), but the completion rates of the definitive-dose radiotherapy were similar. There were no significant differences in ORR between the 2 arms. The progression-free survival (PFS) of TCM arm was significantly better than Control arm (median PFS, 12.0 vs. 9.0 months, P=0.035). However, Zengxiao Jiandu decoction was not found to produce any significant benefit in overall survival. Conclusions: The Zengxiao Jiandu decoction adjunctive therapy, as compared to DCCRT alone, reduced grade ≥3 radiation pneumonitis, improved the completion rate of DCCRT, and prolonged PFS for unresectable LA-NSCLC. Trial Registration: Chinese Clinical Trial Registry ChiCTR2000031667.

A propensity-matched analysis of stereotactic body radiotherapy and sublobar resection for stage I non-small cell lung cancer in patients at high risk for lobectomy: the results in a Chinese population.

BACKGROUND: To investigate the comparative effectiveness of stereotactic body radiotherapy (SBRT) and sublobar resection (SLR) in patients with stage I non-small cell lung cancer (NSCLC) considered to be high-risk lobectomy patients. METHODS: From January 2012 to December 2015, patients who underwent SBRT or SLR for clinical stage I NSCLC were examined retrospectively. Propensity score matching (PSM) was performed to reduce selection bias in SBRT and SLR patients. RESULTS: Data from 86 SBRT and 79 SLR patients was collected. Median follow-up periods of the SBRT and SLR groups were 32 and 37 months, respectively. Patients treated with SBRT exhibited significantly higher age, higher likelihood of being male, larger tumor diameter, lower forced expiratory volume in 1 second (FEV1), and poorer performance status compared with SLR patients. There were no significant differences between SBRT and SLR patients for 3-year overall survival (OS) (80.3% and 82.3%, P=0.405), cause-specific survival (CSS) (81.3% and 83.4%, P=0.383), and local control (LC) (89.7% and 86.0%, P=0.501). Forty-nine patients were identified from each group after performing PSM. After patients were matched for age, gender, performance status, tumor characteristics and pulmonary function, no significant differences were observed in 3-year OS (85.4% and 73.3%, P=0.649), CSS (87.2% and 74.9%, P=0.637) and LC (95.6% and 82.1%, P=0.055). Prevalence of significant adverse events (grade 3 or worse) was 0% and 10.2% in the matched SBRT and SLR groups (P=0.056), respectively. CONCLUSIONS: Disease control and survival in the SBRT patients was equivalent to that seen in SLR patients with stage I NSCLC considered high-risk lobectomy candidates. SBRT could therefore be an alternative option to SLR in treating patients with a high operative risk.

AZIN1-AS1, A Novel Oncogenic LncRNA, Promotes the Progression of Non-Small Cell Lung Cancer by Regulating MiR-513b-5p and DUSP11.

BACKGROUND: Emerging researches have demonstrated that aberrantly expressed long non-coding RNAs (lncRNAs) have great significance in non-small cell lung cancer (NSCLC) progression. The aim of this study was to explore the role of lncRNA AZIN1 antisense RNA 1 (AZIN1-AS1) in NSCLC and the related mechanism. METHODS: Expressions of AZIN1-AS1 and miR-513b-5p in NSCLC samples were detected by qRT-PCR. NSCLC cell lines (H1299 and HCC827) were used in vitro assays. CCK-8 assay, EdU assay, wound healing test and Transwell assay were carried out to test the biological influence of AZIN1-AS1 on NSCLC cells. Subcutaneous xenotransplanted tumor model and tail vein injection model were established to test the role of AZIN1-AS1 in vivo. Interactions between AZIN1-AS1 and miR-513b-5p, miR-513b-5p and dual-specificity phosphatase 11 (DUSP11) were determined by bioinformatic analysis, qRT-PCR, Western blot, and luciferase reporter assay. RESULTS: AZIN1-AS1 was up-regulated in NSCLC cells and tissues, while miR-513b-5p was significantly down-regulated. Silencing of AZIN1-AS1 or overexpression of miR-513b-5p markedly inhibited proliferation, migration and invasion of NSCLC cells, while overexpression of AZIN1-AS1 or inhibition of miR-513b-5p functioned oppositely. Importantly, AZIN1-AS1 mediated the promotion of malignancy of NSCLC cells was reversed by miR-513b-5p mimics. What's more, AZIN1-AS1 could down-regulate miR-513b-5p via sponging it, and there existed a negative correlation between AZIN1-AS1 expression and miR-513b-5p expression in NSCLC samples. AZIN1-AS1 also enhanced the expression levels of DUSP11, which was proved as a target gene of miR-513b-5p. Further in vivo experiments showed that silencing of AZIN1-AS1 decreased tumor growth and metastasis, which was accompanied by overexpression of miR-513b-5p and inhibition of DUSP11 in tumor tissues. CONCLUSION: AZIN1-AS1 acts as a tumor promoter in NSCLC, which is ascribed to the regulation of miR-513b-5p and DUSP11.

Pulmonary emphysema is a risk factor for radiation pneumonitis in NSCLC patients with squamous cell carcinoma after thoracic radiation therapy.

Pulmonary emphysema (PE) has been demonstrated to have a high prevalence in patients with locally advanced non-small cell lung cancer (NSCLC). A total of 153 patients with locally advanced NSCLC were enrolled in this study to investigate the association between PE and radiation pneumonitis (RP) after definitive thoracic radiation therapy (TRT). The incidence of RP in Grade 2, 3 and 5 were 11.1%, 9.8% and 0.7%, respectively. Univariate analysis revealed that age, PE, forced vital capacity (FVC), arterial partial pressure of oxygen (PO2) and mean lung dose (MLD) were significantly associated with the risk of Grade ≥2 or Grade ≥3 RP in patients with squamous cell carcinoma (SCC, P < 0.05). Logistic analysis demonstrated that PE was an independent risk factor of RP in SCC (P < 0.05). Receiver operating characteristics (ROC) analysis revealed that the combination of age, PE, FVC, PO2 and MLD had a higher value to predict RP in SCC (AUC = 0.856 in Grade ≥2 RP and 0.882 in Grade ≥3 RP, respectively). Kaplan-Meier analysis revealed that the more severe the PE, the higher the incidence of RP in SCC. Our results revealed that PE was a high risk factor for locally advanced NSCLC patients followed definitive TRT, especially for SCC patients.

Recent progress in the development of white spot syndrome virus vaccines for protecting shrimp against viral infection.

White spot syndrome virus (WSSV) has been extensively investigated since the white spot disease outbreak in shrimp in 1990. These investigations have mainly focused on determining the function of viral structural proteins, and on utilizing the envelope proteins as subunit vaccines to protect the host. These studies have shown that a WSSV vaccine can be a practical and effective approach for controlling WSSV infection. The development of such a vaccine has become an intense focus of research in the field. This research has resulted in significant progress in the development of WSSV vaccines. However, because of the progress of this work, periodic summaries are needed to facilitate further research on the development of effective WSSV vaccines. This paper provides a comprehensive summary on the status of WSSV vaccines with regard to the following aspects: subunit vaccines, inactivated whole virus vaccines, DNA vaccines, protective antibodies, and the application of RNAi technology. Current limitations in this area of research are also described, as well as prospects for the development and application of improved WSSV vaccines in the future, and for investigating other important aquatic diseases.

Quantitative assessment of the relationship between RASSF1A gene promoter methylation and bladder cancer (PRISMA).

BACKGROUND: Methylation of the Ras-association domain family 1 isoform A (RASSF1A) gene promoter region is thought to participate in the initiation and development of many different cancers. However, in bladder cancer the role of RASSF1A methylation was unclear. To evaluate the relationship between RASSF1A methylation and bladder cancer, a quantitative assessment of an independent meta-analysis was performed. In addition, a DNA methylation microarray database from the cancer genome atlas (TCGA) project was used to validate the results of the meta-analysis. METHODS: We searched published articles from computerized databases, and DNA methylation data were extracted from TCGA project. All data were analyzed by R software. RESULTS: The results of the meta-analysis indicated that the frequency of RASSF1A gene methylation in bladder cancer patients is significantly higher than in healthy controls. The hazard ratio (HR) was 2.24 (95% CI = [1.45; 3.48], P = 0.0003) for overall survival (OS), and the RASSF1A gene promoter methylation status was strongly associated with the TNM stage and differentiation grade of the tumor. The similar results were also found by the data from TCGA project. CONCLUSION: There was a significant relationship between the methylation of the RASSF1A gene promoter and bladder cancer. Therefore, RASSF1A gene promoter methylation will be a potential biomarker for the clinical diagnosis of bladder cancer.

Efficacy of pemetrexed in a patient with brain metastases during crizotinib treatment.

ALK-positive patients with non-small-cell lung cancer (NSCLC) exhibit more aggressive clinical progression, a poorer response to chemotherapy, and less favorable survival outcomes in comparison with ALK-negative patients. Although crizotinib has proved effective in treating ALK-positive NSCLC, this agent penetrates the blood-brain barrier poorly and CNS progression is common. As pemetrexed, a multitargeted antifolate chemotherapeutic agent, has demonstrated benefit in the control of brain metastases in patients with NSCLC, treatment with pemetrexed was added to crizotinib in a young male patient with ALK-positive NSCLC who had developed brain metastases during crizotinib therapy. After four cycles of pemetrexed chemotherapy, the patient's brain lesions were significantly reduced in size and a chest CT scan showed that the lung lesions had stabilized.

[Construction of RGD10-NGR9 dual-targeting superparamagnetic iron oxide and its magnetic resonance imaging features in nude mice].

OBJECTIVE: To construct angiogenesis-specific RGD10-NGR9 dual-targeting superparamagnetic iron oxide nanoparticles, and to evaluate its magnetic resonamce imaging (MRI) features in nude mice and potential diagnostic value in tumor MRI. METHODS: Dual-targeting peptides RGD10-NGR9 were designed and synthesized. Ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles were synthesized by chemical co-precipitation method and the surface was modified to be hydrophilic by coating with dextran. The dual-targeting peptides RGD10-NGR9 were conjugated to USPIO. Cell binding affinity and up-taking ability of the dual-targeting USPIO nanoparticles to integrin ανß3-APN positive cells were subsequently tested by Prussian blue staining and phenanthroline colorimetry in vitro. The RGD10-NGR9 conjugated with USPIO was injected intravenously into xenograft mice, which were scanned by MRI at predetermined time points. The MRI and contrast-to-noise ratio (CNR) values were calculated to evaluate the ability of dual-targeting USPIO as a potential contrast agent in nude mice. RESULTS: P-CLN-Dextran-USPIO nanoparticles with stable physical properties were successfully constructed. The average diameter of Fe3O4 nanoparticles was 8-10 nm, that of Dextran-USPIO was about 20 nm and P-CLN-Dextran-USPIO had an average diameter about 30 nm. The in vitro studies showed a better specificity of dual-targeting USPIO nanoparticles on proliferating human umbilical vein endothelia cells (HUVEC). In vivo, RGD10-NGR9-USPIO showed a significantly reduced contrast in signal intensity and 2.83-times increased the CNR in the tumor MRI in xenograft mice. CONCLUSION: This novel synthesized RGD10-NGR9 dual-targeting USPIO is with better specific affinity in vitro and in vivo, and might be used as a molecular contrast agent for tumor angiogenesis MRI.

[Analysis of prognostic factors in NSCLC patients with brain metastases 
diagnosed by constrast-enhanced MRI after whole brain radiotherapy].

BACKGROUND AND OBJECTIVE: Brain metastases are a common complication of lung cancer, occurring in 20%-40% of patients. The aim of this study is to explore prognostic factors in non-small cell lung cancer (NSCLC) in patients with brain metastases diagnosed by constrast-enhanced MRI after whole brain radiotherapy. METHODS: TA retrospective review of clinical data from 241 NSCLC patients with brain metastases received whole brain radiotherapy from April 2007 to October 2008 was performed. A number of potential factors that might affect prognosis after irradiation were evaluated. The significance of prognostic variables in the survival resulted from univariate analysis by Kaplan-Meier combining with Log-rank test, and the multivariate analysis was obtained by Cox regression model. RESULTS: Median follow-up time for the survivors was 19.1 months. For all patients, the median survival time (MST) was 8.7 months. By univariate analysis, female patients with KPS>70, no symptom when diagnosed with brain metastases, tumor controlled in the chest, and received more than 3 cycles of chemotherapy and combined target therapy were the important factors for overall survival. By multivariate analysis, female, tumors controlled in the chest, and combined target therapy were independent prognostic factors for NSCLC patients with brain metastases. Tumor controlled in the chest was the most important independent prognostic factor. CONCLUSIONS: Gender, local tumor controlled, and combined target therapy significantly influenced NSCLC brain metastases diagnosed by constrast-enchanced MRI survival after whole brain radiotherapy.eciated patient subsets and is a useful method for dissecting complex clinical situations. Moreover, CART can be used to identify homogeneous patient populations in clinical practice and future clinical trials.

[Clinical trial of concurrent low-dose chemotherapy plus radiation vs sequential chemoradiotherapy for unresectable stage III non-small cell lung cancer].

BACKGROUND: Concurrent chemotherapy plus radiotherapy is a trend in treatment of non-small cell lung cancer (NSCLC), but the treatment program is rather complicated and the toxicity is more severe than chemotherapy or radiotherapy alone. The aim of this study is to evaluate the early response and toxicity of concurrent chemoradiotherapy. METHODS: Eighty unresectable stage IIIA-IIIB NSCLC patients pathologically proved were randomly divided into 2 groups. Group A: patients were treated with concurrent chemotherapy of vinorelbine (12.5mg/m², on days 1, 8, 29, 36) and cisplatin (40mg/m², on days 1, 8, 29, 36) (NP regimen) plus conventional radiotherapy. Patients were irradiated at 1.8-2.0Gy/Fx daily, 5 days per week. The total dose was 60Gy/30-33 Fx. After the radiation, 3 cycles of NP regimen were performed, but the dose of vinorelbine was 25mg/m². Group B: patients received sequential chemoradiotherapy. At first radiation was performed as same as group A. Then chemotherapy of NP (NVB 25mg/m², on days 1 and 8, DDP 80mg/m², on day 1) was followed for 4-5 cycles. RESULTS: The overall response rate in concurrent and sequential groups was 80.0% and 57.5% respectively (Chi-Square=4.71, P < 0.05). Incidences of grade III-IV acute radiation esophagitis and leukopenia were 47.5% and 65.0% in group A, and 25.0% and 42.5% in group B respectively (P < 0.05). The acute radiation pneumonitis rate was 32.5% in group A and 20.0% in group B (P > 0.1). CONCLUSIONS: Concurrent chemoradiotherapy is well tolerated in most unresectable stage IIIA-IIIB NSCLC patients. Its early response is better than sequential chemoradiotherapy.

[Escalated hyperfractionated accelerated radiation therapy combined with chemotherapy for stage IIIB non-small cell lung cancer].

BACKGROUND: To evaluate the therapeutic effect and acute side-effect of escalated hyperfractionated accelerated radiation therapy (EHART) combined with chemotherapy for stage IIIB non-small cell lung cancer (NSCLC). METHODS: From Aug. 1998 to Aug. 2001, a prospective trial for NSCLC was carried out in 112 patients with stage IIIB. These patients were nonrandomly divided into 2 groups: conventional fractionated radiation therapy group (CFRT 65 cases) and EHART group (47 cases). The CFRT patients were treated by 1.8-2 Gy/fraction per day, 5 treatment days per week; the total doses received in center of tumor were 54-70 Gy /27-40 fractions/37-85 days, the median was 60 Gy/30 factions/43 days. The EHART patients were treated by escalated doses: In the first and second weeks, 1.2 Gy/fraction twice a day was given, then 1.3 Gy , 1.4 Gy , and 1.5 Gy from third to fifth weeks respectively, twice fractions a day (over 6 hours interval), 5 treatment days each week, the total doses were 60-66 Gy/46-50 fractions/30-45 days, the median was 66 Gy /50 fractions/34 days. Radiation fields just covered the tumor mass which were determined by thoracic CT with 1.5 cm margins. A total of 4-6 cycles chemotherapy with MVP regimen mostly was delivered before (1-2 cycles) and after (3-5 cycles) radiotherapy. Each patient was followed up for 1 year. RESULTS: Seven cases were excluded from EHART, twelve from CFRT. There were 93 patients to be evaluated. The immediate response rate of tumor by EHART and CFRT was 72.5% and 64.2% respectively (Chi-square=1.02, P=0.346). The 1-year survival rate was 60.0% and 47.2% respectively (Chi-square=2.56, P=0.107), and the local control rate was 67.5% and 52.8% respectively (Chi-square=3.01, P=0.085). The incidence and degree of acute radiation esophagitis in EHART were more severe than that in CFRT (Chi-square=5.02, P=0.025). CONCLUSIONS: The treatment effect by EHART for stage IIIB NSCLC is encouraging and its toxicities could be tolerated by most of patients. It is worthy of further study on survival rate and late complications in long term.