A tricarboxylic acid cycle-based machine learning model to select effective drug targets for the treatment of esophageal squamous cell carcinoma

Background: The tricarboxylic acid cycle (TCA cycle) is an important metabolic pathway and closely related to tumor development. However, its role in the development of esophageal squamous cell carcinoma (ESCC) has not been fully investigated.Methods: The RNA expression profiles of ESCC samples were retrieved from the TCGA database, and the GSE53624 dataset was additionally downloaded from the GEO database as the validation cohort. Furthermore, the single cell sequencing dataset GSE160269 was downloaded. TCA cycle-related genes were obtained from the MSigDB database. A risk score model for ESCC based on the key genes of the TCA cycle was built, and its predictive performance was evaluated. The association of the model with immune infiltration and chemoresistance were analyzed using the TIMER database, the R package “oncoPredict” score, TIDE score and so on. Finally, the role of the key gene CTTN was validated through gene knockdown and functional assays.Results: A total of 38 clusters of 8 cell types were identified using the single-cell sequencing data. The cells were divided into two groups according to the TCA cycle score, and 617 genes were identified that were most likely to influence the TCA cycle. By intersecting 976 key genes of the TCA cycle with the results of WGCNA, 57 genes significantly associated with the TCA cycle were further identified, of which 8 were screened through Cox regression and Lasso regression to construct the risk score model. The risk score was a good predictor of prognosis across subgroups of age, N, M classification and TNM stage. Furthermore, BI-2536, camptothecin and NU7441 were identified as possible drug candidates in the high-risk group. The high-risk score was associated with decreased immune infiltration in ESCC, and the low-risk group had better immunogenicity. In addition, we also evaluated the relationship between risk scores and immunotherapy response rates. Functional assays showed that CTTN may affect the proliferation and invasion of ESCC cells through the EMT pathway.Conclusion: We constructed a predictive model for ESCC based on TCA cycle-associated genes, which achieved good prognostic stratification. The model are likely associated with the regulation of tumor immunity in ESCC

Effects of VATS Lobectomy, VATS Anatomic Segmentectomy, and Open Thoracotomy on Pulmonary Function of Patients with Non-small Cell Lung Cancer

Background and objective Lung cancer is a malignancy with high morbidity and mortality rates worldwide. Surgery is the preferred treatment for non-small cell lung cancer. This study aims to investigate the effects of video-assisted thoracoscopic surgery (VATS) lobectomy, VATS segmentectomy, and open thoracotomy on pulmonary function in the early postoperative stage and compare the difference among three groups. Methods Pulmonary function data of patients were collected from September 2015 to February 2016 in Department of Thoracic Surgical Oncology, Cancer Hospital Chinese Academy of Medical Sciences. The patients were categorized according to operation methods into three groups, namely, VATS segmentectomy, VATS lobectomy, and open thoracotomy groups. Pulmonary function was assessed 1 day before the surgery, 3 days after the surgery, and 3 months after the surgery. Statistical analysis was performed with SPSS 20.0 through single-factor analysis of variance. Results Pulmonary function 3 days after the surgery was compared among the three groups. There was a significant difference in forced vital capacity (FVC), FVC%, forced expiratory volume in one second (FEV1), FEV1%, peak expiratory flow (PEF), maximal voluntary ventilation (MVV), transfer factor for carbon monoxide of lung (TLCO) and TLCO% (P values were as follows: 0.033, 0.042, 0.029, 0.045, 0.039, 0.021, 0.018, 0.024). The comparison of pulmonary function of 3 groups at the time of 3 months after operation showed that there was a significant difference among three groups in FVC, FVC%, FEV1, FEV1%, PEF, MVV, TLCO, TLCO% (P values were as follows: 0.019, 0.024, 0.044, 0.021, 0.037, 0.029, 0.045, 0.017). Conclusion No matter in the early stage after surgery or at the time of 3 months after surgery, the patients’ pulmonary function in VATS segmentectomy is better than the data of VATS lobectomy group, and the pulmonary function data of VATS lobectomy patients recovered better than the open thoracotomy group

BRD7 Acts as a Tumor Suppressor Gene in Lung Adenocarcinoma.

Lung cancer is one of the most malignant tumors and the leading cause of cancer-related deaths worldwide. Among lung cancers, 40% are diagnosed as adenocarcinoma. Bromodomain containing 7 (BRD7) is a member of bromodomain-containing protein family. It was proved to be downregulated in various cancers. However, the role of BRD7 in lung adenocarcinoma is still unknown. Western blot and qRT-PCR was performed to measure the BRD7 expression in lung adenocarcinoma tissues and cells. CCK8 and migration assay was done to detect the functional role of BRD7 in lung adenocarcinoma. In this study, we showed that the expression of BRD7 was downregulated in lung adenocarcinoma tissues and cells. The lower of BRD7 levels in patients with lung adenocarcinoma was associated with shortened disease-free survival. Furthermore, overexpression of BRD7 inhibited lung adenocarcinoma cell proliferation and migration. Inhibition of BRD7 expression promoted cell proliferation and migration by activating ERK phosphorylation. Overexpression of BRD7 inhibited cyclin D and myc expression. Our findings are consistent with a tumor suppressor role for BRD7 in lung adenocarcinoma tumorigenesis

Overexpression of BRD7 inhibited lung adenocarcinoma cell proliferation and migration.

<p>(A) The protein expression level of BRD7 was measured by using Western blot. (B) The mRNA expression level of BRD7 was measured by using qRT-PCR. (C) Overexpression of BRD7 inhibited lung adenocarcinoma cell line A549 proliferation. (D) Overexpression of BRD7 inhibited lung adenocarcinoma cell line A549 migration. (E) Relative ratio of wound closure per field is shown. *p<0.05 and ***p<0.001.</p

Inhibition of BRD7 promoted ERK phosphorylation in lung adenocarcinoma.

<p>(A) The protein expression level of BRD7 was measured by using Western blot. (B) The mRNA expression level of BRD7 was measured by using qRT-PCR. (C) Inhibition of BRD7 promoted the ERK phosphorylation in the A549 cells. (D) CCK8 analysis was used to measure the A549 cell proliferation. (E) Overexpression of BRD7 suppressed the ERK phosphorylation in the A549 cells. (F) Wound-healing assay was performed to measure the A549 cell migration. (G) Relative ratio of wound closure per field is shown. *p<0.05 and ***p<0.001.</p

The expression level of BRD7 was downregulated in lung adenocarcinoma cell lines.

<p>(A) The protein expression level of BRD7 in four lung adenocarcinoma cell lines (H1299, H23, SPC-A1 and A549) and one lung adenocarcinoma tissues and adjacent no-tumor tissue was measured by Western blot. (B) The signal in each lane was quantified using ImageJ software and the ratio of BRD7 to GAPDH was determined. (C)The mRNA expression level of BRD7 in four lung adenocarcinoma cell lines (H1299, H23, SPC-A1 and A549) and one lung adenocarcinoma tissues and adjacent no-tumor tissue was measured by qRT-PCR.</p

The protein expression level of BRD7 was downregulated in lung adenocarcinoma tissues.

<p>(A) Lower of BRD7 levels in patients with lung adenocarcinoma was associated with shortened disease-free survival (hazards ratio = 0.36). (B) The protein expression level of BRD7 was measured in lung adenocarcinoma tissues and their corresponding adjacent normal tissues using Western blot.</p