A risk score based on polyamine metabolism and chemotherapy-related genes predicts prognosis and immune cells infiltration of lung adenocarcinoma.

We aimed to explore whether the genes associated with both platinum-based therapy and polyamine metabolism could predict the prognosis of LUAD. We searched for the differential expression genes (DEGs) associated with platinum-based therapy, then we interacted them with polyamine metabolism-related genes to obtain hub genes. Subsequently, we analysed the main immune cell populations in LUAD using the scRNA-seq data, and evaluated the activity of polyamine metabolism of different cell subpopulations. The DEGs between high and low activity groups were screened to identify key DEGs to establish prognostic risk score model. We further elucidated the landscape of immune cells, mutation and drug sensitivity analysis in different risk groups. Finally, we got 10 hub genes associated with both platinum-based chemotherapy and polyamine metabolism, and found that these hub genes mainly affected signalling transduction pathways. B cells and mast cells with highest polyamine metabolism activity, while NK cells were found with lowest polyamine metabolism activity based on scRNA-seq data. DEGs between high and low polyamine metabolism activity groups were identified, then 6 key genes were screened out to build risk score, which showed a good predictive power. The risk score showed a universal negative correlation with immunotherapy checkpoint genes and the cytotoxic T cells infiltration. The mutation rates of EGFR in low-risk group was significantly higher than that of high-risk group. In conclusion, we developed a risk score based on key genes associated with platinum-based therapy and polyamine metabolism, which provide a new perspective for prognosis prediction of LUAD.

miR-185-5p May Modulate the Chemosensitivity of LUSC to Cisplatin via Targeting PCDHA11: Multi-omics Analysis and Experimental Validation.

Drug resistance is the major difficulty in treatment of lung squamous cell carcinoma (LUSC). This study aims to explore drug response-related miRNAs (DRmiRNAs) based on multi-omics research. We identified DRmiRNAs of LUSC with a multi-omics integrated system that combines expression data of microRNA, lncRNA, mRNA, methylation levels, somatic mutations. After identifying DRmiRNAs, we screened and validated of the target mRNAs of DRmiRNAs through Targetscan and the miRDB database. Then, Real-time PCR and Western blot assays were used to estimate the expression of DRmiRNAs and target protein, and the dual-luciferase assays were used to confirm the interaction of DRmiRNAs and target mRNA. Furthermore, CCK-8 (Cell Counting Kit-8) assays were used to evaluate cell proliferation and drug sensitivity. After integrated analysis, hsa-miR-185-5p was identified as DRmiRNA based on multi-omics data. Through Targetscan and miRDB database, the possible target mRNAs were obtained and PCDHA11 was validated as a target mRNA of miR-185-5p by real-time PCR, Western blot assays and dual-luciferase assays. CCK-8 assays and clone formation assays showed that the proliferation of miR-185-5p mimics was significantly slower than that of miR-185-5p inhibitors, which means overexpression of miR-185-5p enhanced the anticancer effects of cisplatin, whereas the downregulation of miR-185-5p reduced the effects. Furthermore, the proliferation of silencing PCDHA11 was significantly slower than that of overexpression of PCDHA11, which means PCDHA11 overexpression weakened the anticancer effects of cisplatin, and silencing PCDHA11 enhanced the effects. This study demonstrated that miR-185-5p was involved in chemoresistance of LUSC cells to cisplatin partly via down-regulating PCDHA11, which may promote understanding the underlying molecular mechanisms of drug response.

RASAL3 predicts overall survival and CD8+ T lymphocyte infiltration in lung adenocarcinoma.

RAS-activating protein-like 3 (RASAL3) is a synaptic Ras GTPase-activating protein (SynGAP) and a potential novel biomarker of CD8+ T cell infiltration in lung adenocarcinoma (LUAD). This study explored RASAL3 expression in LUAD, the prognostic impact of RASAL3 and the relationship with immune cell infiltration. RASAL3 expression in LUAD tissues was considerably low, with high RASAL3 expression associated with better overall survival, whereas the low expression was linked to advanced T, N, M classifications, TNM stage and lower grade. Furthermore, RASAL3 expression positively correlated with CD8+ T lymphocyte infiltration. In conclusion, RASAL3 expression is a potential prognostic and immunological biomarker of LUAD.

Two closely spaced missense COL3A1 variants in cis cause vascular Ehlers-Danlos syndrome in one large Chinese family.

Vascular Ehlers-Danlos syndrome (vEDS) is a rare and severe hereditary connective tissue disease arising from a mutation in the type III collagen alpha I chain (COL3A1) gene, with a poor prognosis due to exceptional vascular ruptures and premature death. Herein, starting from a 36-year-old Chinese male patient with a complaint of upper abdominal pain, we collected clinical data of and performed a genetic analysis of a total of 20 family members. We identified two closely spaced COL3A1 missense variants in cis, p.Leu734Phe (c.2199_2200TC>AT) and p.Gly741Ser (c.2221G>A), as the cause of vEDS in this family. p.Gly741Ser, a glycine substitution mutation, has been previously reported, whereas p.Leu734Phe, a non-glycine substitution mutation, is novel. We analysed their independent and combined effects on the COL3A1 level in transfected skin fibroblast cells by means of Western blotting. We found that both variants independently led to a reduced COL3A1 level and, when combined, led to an even more reduced COL3A1 level compared to the wild type. Thus, each missense variant can be independently classified as a pathogenic variant, albeit with a synergetic effect when occurring together. Moreover, our genetic findings provide an explanation for four previous sudden deaths and identified two high-risk carriers in the family.

The increased expression and aberrant methylation of SHC1 in non-small cell lung cancer: Integrative analysis of clinical and bioinformatics databases.

Despite the previous evidence showing that SHC adaptor protein 1 (SHC1) could encode three distinct isoforms (p46SHC, p52SHC and p66SHC) that function in different activities such as regulating life span and Ras activation, the precise underlying role of SHC1 in lung cancer also remains obscure. In this study, we firstly found that SHC1 expression was up-regulated both in lung adenocarcinoma (LUAD) and in lung squamous cell carcinoma (LUSC) tissues. Furthermore, compared to patients with lower SHC1 expression, LUAD patients with higher expression of SHC1 had poorer overall survival (OS). Moreover, higher expression of SHC1 was also associated with worse OS in patients with stages 1 and 2 but not stage 3 lung cancer. Significantly, the analysis showed that SHC1 methylation level was associated with OS in lung cancer patients. It seemed that the methylation level at specific probes within SHC1 showed negative correlations with SHC1 expression both in LUAD and in LUSC tissues. The LUAD and LUSC patients with hypermethylated SHC1 at cg12473916 and cg19356022 probes had a longer OS. Therefore, it is reasonable to conclude that SHC1 has a potential clinical significance in LUAD and LUSC patients.

Postoperative Adjuvant Therapy Versus Surgery Alone for Stage IIB-III Esophageal Squamous Cell Carcinoma: A Phase III Randomized Controlled Trial.

BACKGROUND: Retrospective studies have shown that adjuvant treatment improves survival of patients with stage IIB-III esophageal squamous cell carcinoma, but there is no evidence from prospective trials so far. MATERIALS AND METHODS: Patients with pathological stage IIB-III esophageal squamous cell carcinoma were randomly assigned to receive surgery alone (SA), postoperative radiotherapy (PORT), or postoperative concurrent chemoradiotherapy (POCRT). PORT patients received 54 Gy in 27 fractions; the POCRT group received 50.4 Gy in 28 fractions, plus concurrent chemotherapy with paclitaxel (135-150 mg/m2 ) and cisplatin or nedaplatin (50-75 mg/m2 ) every 28 days. The primary endpoint was disease-free survival (DFS), and the secondary endpoint was overall survival (OS). RESULTS: A total of 172 patients were enrolled (SA, n = 54; PORT, n = 54; POCRT, n = 64). The 3-year DFS was significantly better in PORT/POCRT patients than in SA patients (53.8% vs. 36.7%; p = .020); the 3-year OS was also better in PORT/POCRT patients (63.9% vs. 48.0%; p = .025). The 3-year DFS for SA, PORT, and POCRT patients were 36.7%, 50.0%, 57.3%, respectively (p = .048). The 3-year OS for SA, PORT, and POCRT patients were 48.0%, 60.8%, 66.5%, respectively (p = .048). CONCLUSION: PORT/POCRT (especially POCRT) may significantly improve DFS and OS in stage IIB-III esophageal squamous cell carcinoma. IMPLICATIONS FOR PRACTICE: The results of this phase III study indicated that postoperative radiotherapy/postoperative concurrent chemoradiotherapy (PORT/POCRT) could significantly improve disease-free survival and overall survival in stage IIB-III esophageal squamous cell carcinoma compared with surgery alone with acceptable toxicities. In-field and out-of-field recurrences were comparable between the POCRT and PORT groups, which demonstrates the rationality and safety of the radiation field used in this study. The postoperative regimens in this trial might be accepted as standard treatment options for pathological stage IIB-III esophageal cancer. Larger sample size prospective randomized trials to identify the value are warranted.

Development and Validation of a Nomogram Prognostic Model for Resected Limited-Stage Small Cell Lung Cancer Patients.

BACKGROUND: In this study, we developed and validated nomograms for predicting the survival in surgically resected limited-stage small cell lung cancer (SCLC) patients. METHODS: The SCLC patients extracted from the Surveillance, Epidemiology, and End Results database between 2000 and 2014 were reviewed. Significant prognostic factors were identified and integrated to develop the nomogram using multivariable Cox regression. The model was then validated internally by bootstrap resampling, and externally using an independent SCLC cohort diagnosed between 2000 and 2015 at our institution. The prognostic performance was measured by the concordance index (C-index) and calibration curve. RESULTS: A total of 1006 resected limited-stage SCLC patients were included in the training cohort. Overall, 444 cases from our institution constituted the validation cohort. Seven prognostic factors were identified and entered into the nomogram construction. The C-indexes of this model in the training cohort were 0.723, 0.722, and 0.746 for predicting 1-, 3-, and 5-year overall survival (OS), respectively, and 0.816, 0.710, and 0.693, respectively, in the validation cohort. The calibration curve showed optimal agreement between nomogram-predicted survival and actual observed survival. Additionally, significant distinctions in survival curves between different risk groups stratified by prognostic scores were also observed. The proposed nomogram was then deployed into a website server for convenient application. CONCLUSIONS: We developed and validated novel nomograms for individual prediction of survival for resected limited-stage SCLC patients. These models perform better than the previously widely used staging system and may offer clinicians instructions for strategy making and the design of clinical trials.

Imaging Features and Clinical Decision Analysis of 110 Cases of Intrapulmonary Lymph Nodes.

OBJECTIVE: Through the summary and analysis of large samples, the characteristic imaging manifestations of intrapulmonary lymph nodes (IPLNs) were quantified, and two corresponding rating tables were developed. These rating tables could be used to distinguish the IPLNs from primary lung cancer, so as to improve the diagnostic accuracy and help clinicians make correct judgments and decisions. METHODS: A total of 82 patients with 110 IPLNs and 35 patients with primary lung cancer lesions were collected from June 2017 to December 2018. All lesions were solid nodules of less than 12 mm in diameter, which were confirmed by pathology. Observation indicators included location, size, shape, density, border and internal vacuoles of nodules, linear high-density shadow around the nodules, distance from the pleura, pleural indentation, and so on. RESULTS: There were statistically significant differences in the location, size, shape, internal vacuole of the nodules, and distance from the pleura (p < 0.05). The diagnostic scoring table of the nature of solid nodules and the malignant risk table were drawn. The nodule corresponding to Level A was most likely the primary lung cancer, and surgical resection was recommended. The nodule corresponding to Level C was most likely IPLNs, and it was better to receive no treatment currently. The positive predictive value was 81% (23/28), the negative predictive value was 97% (89/92), the sensitivity was 63% (23/35), and the specificity was 81% (89/110). CONCLUSION: For the pulmonary solid nodules of less than 12 mm in diameter and unknown nature, the evaluation in accordance with the Score Table and the Risk Level Table of this study can be more accurate and faster than the original judgment, which will help clinicians in diagnosis and treatment decisions.

Debulking Surgery Plus Radiation: Treatment Choice for Unresectable Stage III Thymic Carcinoma.

BACKGROUND: Total resection may not be achieved in patients with thymic carcinoma, particularly those with Masaoka stage III disease. Debulking surgery plus postoperative radiotherapy and radiation alone are treatment options for such patients. We aimed to compare the overall survival (OS) between patients with thymic carcinoma who underwent debulking surgery plus postoperative radiotherapy and those who underwent radiation alone. METHODS: This was a single-center retrospective study of patients histologically diagnosed as having Masaoka stage III thymic carcinoma between January 1980 and January 2010. Patients were classified into the following groups according to treatments received: debulking surgery plus radiotherapy (group A) and radiotherapy alone (group B). Data on demographics, histology, invasion, radiotherapy, chemotherapy, and survival were collected. Survival time was calculated and compared between the groups using the Kaplan-Meier method. Toxicities were graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events version 3.0. RESULTS: Of the 47 enrolled patients, 26 and 21 patients were categorized into groups A and B, respectively. There are no significant differences in the Eastern Cooperative Oncology Group performance status score, histological type, great vessel invasion, and chemotherapy proportion between the groups. The median radiation dose was 60 Gy in both groups. The 5-year OS rates were 54.4 and 0% in groups A and B, respectively (p = 0.019). No operation-induced mortality was recorded. CONCLUSION: For patients with unresectable Masaoka stage III disease, debulking surgery with radiotherapy is preferred, as this was proven to be more efficient than the radiation-alone procedure.

Prophylactic ligation of the thoracic duct branch prevents chylothorax after pulmonary resection for right lung cancer.

PURPOSE: Chylothorax is a rare and challenging complication of thoracic surgery. Whereas most current studies focus on postoperative treatment and preventative measures for esophageal cancer surgery, the current study investigates the impact of prophylactic ligation of the thoracic duct branch on postoperative chylothorax after pulmonary resection for right lung cancer. METHODS: The subjects of this retrospective study were 1165 patients who underwent right pulmonary resection and mediastinal lymph-node dissection in our department between January 2015 and August 2019. Those who underwent prophylactic ligation of the thoracic duct branch after 4R lymph-node dissection were assigned to group A (n = 475), and those who did not were assigned to group B (n = 690). The incidence of postoperative chylothorax, the success rate of conservative treatment, the postoperative hospital stay, and the chest drainage volume were recorded and compared statistically between the two groups. RESULTS: The incidence of postoperative chylothorax was significantly lower in group A than in group B (0.84% vs. 2.90%, p = 0.015). Patients who had a chylothorax in group A had a significantly shorter postoperative hospital stay, less mean drainage volume per day, and less total drainage than those in group B (7.25 ± 0.50 days vs. 11.00 ± 2.81 days, p = 0.003; 0.64 ± 0.04 L vs. 0.80 ± 0.09 L, p = 0.003; 4.64 ± 0.40 L vs. 8.82 ± 2.84 L; p = 0.002). The success rate of conservative treatment was higher in group A than in group B, but the difference was not significant (100% vs. 75.0%, p = 0.544). CONCLUSION: Performing prophylactic ligation of the thoracic duct branch during right pulmonary resection and mediastinal lymph-node dissection is an effective and safe method of preventing postoperative chylothorax.

MiR-33a suppresses proliferation of NSCLC cells via targeting METTL3 mRNA.

Methyltransferase like 3 (METTL3) was incipiently known as a methyltransferase which was responsible for N6-methyladenosine (m6A) methylation. METTL3 can promote the expression of several crucial oncoproteins and its high expression enhanced proliferation, survival, and invasion of human lung cancer cells. However, how METTL3 was regulated is seldom understood in non-small-cell lung carcinoma (NSCLC). In the present study, miR-33a was suspicious to target to the 3'-untranslated region (3'UTR) of METTL3 mRNA via in silico prediction. Besides, the expressions of METTL3 were higher in NSCLC tissues than those in adjacent tissues, and METTL3 expressions were positively related to the expressions of miR-33a in NSCLC tissues which confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). MiR-33a can directly target to the 3'UTR of METTL3 mRNA which examined by luciferase reporter gene assay. Moreover, we found that miR-33a can reduce the expression of METTL3 at both mRNA and protein levels using reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis. Functionally, miR-33a can reduce the proliferation of A549 and NCI-H460 cells. Conversely, inhibition of miR-33a by anti-miR-33a can rescue that using 4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) and 5-ethynyl-2-deoxyuridine (EdU) assay. Similarly, miR-33a can reduce cellular anchorage-independent growth of A549 cells. Additionally, the negative influences of miR-33a on the downstream genes of METTL3 were examined by Western blot analysis. Thus, we concluded that miR-33a can attenuate NSCLC cells proliferation via targeting to the 3'UTR of METTL3 mRNA. Our findings provide new insights into the mechanism of METTL3 regulation by micro RNA, and supports METTL3 as a therapeutic target in NSCLC.

Pros and cons of the gasless laparoscopic transhiatal esophagectomy for upper esophageal carcinoma.

BACKGROUND: Controversies on how to treat upper esophageal carcinoma have existed for several decades. With the application of minimally invasive techniques, surgical treatment to upper esophageal carcinoma tends to show more advantages and attract more patients. Up to now, most hospitals adopted the combined thoracoscopic and laparoscopic esophagectomy (CTLE) as the way of minimally invasive surgery for upper esophageal carcinoma. But CTLE to treat upper esophageal carcinoma has its drawbacks, such as demanding certain pulmonary function and severe postoperative regurgitation. In 2011, we developed the gasless laparoscopic transhiatal esophagectomy (LTE) to treat upper esophageal carcinoma, which showed some advantages. The aim of this article was to compare LTE with CTLE in treating upper thoracic or cervical esophageal carcinoma and assess the value of LTE. METHODS: From 2009 to 2014, esophagectomy has been performed by the introduction of minimally invasive surgery in a total of 83 patients with upper thoracic or cervical esophageal carcinoma. Among these patients, LTE was performed in 27 cases (Group 1), while CTLE was performed in the other 56 (Group 2). Neoadjuvant chemotherapy was done in patients of Group 1. RESULTS: There were no operation-related deaths and conversion to open procedure. There was no significant difference in postoperative complications, ventilation time, ICU stay, hospital stay, and anastomotic leak rates between the two groups. But LTE was associated with shorter operative time and less intraoperative blood loss. In Group 2, 21 (37.5 %) patients had postoperative pulmonary complications, while in Group 1, there were 6 (22.2 %) patients having pulmonary complications at least one time. Results of 24-h pH monitoring and manometry showed that postoperative laryngo-pharyngeal reflux (PLPR) was more severe in Group 2 patients than in Group 1; for Group 1, PLPR mainly occurred on sleep stage, while for Group 2, PLPR might exist all the day with short intervals and last longer at night. The median overall survival was 27.2 months after CTLE and 30.8 months after LTE (P = 0.962). There was no significant difference in survival at 2, 3 and 4 years between the two groups. CONCLUSIONS: Compared with CTLE, LTE is a more minimally invasive approach to effectively treat patients with upper esophageal carcinoma. Laryngo-pharyngeal reflux after LTE was less severe than that after CTLE, which might lower incidence of pulmonary complications. For the elderly patients, LTE seems more suitable.

[Comparison of the lymph node dissection and complications between video-assisted thoracoscopic (VATS) esophagectomy and conventional esophagectomy via right thoracotomic].

OBJECTIVE: Video-assisted thoracoscopic (VATS) esophagectomy has been performed for more than 10 years in China. However, compared with the conventional esophagectomy via right thoracotomy, whether VATS esophagectomy has more advantages or not in the lymph node (LN) dissection and prevention of perioperative complications is still controversial and deserves to be further investigated. The aim of this study was to explore whether there are significant differences in this issue between the two surgical modalities or not. METHODS: The results of lymph node dissection and perioperative complications as well as other parameters in the patients treated by VATS esophagectomy and those by conventional esophagectomy via right thoracotomy at our department from May 1, 2009 to July 30, 2013 were compared using SPSS 16.0 in order to investigate whether there was any significant difference between these two treatment modalities in the learning curve stage of VATS esophagectomy. RESULTS: One hundred and twenty-nine cases underwent VATS esophagectomy between May 1, 2009 and July 30, 2013, and another part 129 cases with the same preoperative cTNM stage treated by conventional esopahgectomy via right thoracotomy were selected in order to compare the results of lymph node dissection and perioperative complications as well as other parameters between those two groups of patients. There were no significant differences in the sex, age, lesion locations and cTNM stage between these two groups. The total LN metastatic rate in the VATS esophagectomy group was 35.7% and that of the conventional esophagectomy group was 37.2% (P > 0.05). The total average number of dissected lymph nodes was 12.1 vs. 16.2 (P < 0.001). The average dissected LN stations was 3.2 vs. 3.6 (P = 0.038). The total average number of dissected LN along the left recurrent laryngeal nerve was 2.0 vs. 3.7 (P = 0.012). The total average number of dissected LN along the right recurrent laryngeal nerve was 2.9 vs. 3.4 (P = 0.231). However, there was no significant difference in the total average number of dissected LN in the other thoracic LN stations, and in the perioperative complications between the two groups. The total postoperative complication rate was 41.1% in the VATS group versus 42.6% in the conventional group (P = 0.801). The cardiopulmonary complication rate was 25.6% vs. 27.1% (P = 0.777). The death rate was the same in the two groups (0.8%). The VATS group had less blood infusion (23.2% vs. 41.8%, P = 0.001) and shorter hospital stay (15.9 days vs. 19.2 days, P = 0.049) but longer operating time (161.3 min vs. 127.8 min, P < 0.01). CONCLUSIONS: In the learning curve stage of VATS esophagectomy, compared with the conventional esophagectomy, less LN number and stations can be dissected in the VATS group due to un-skillful VATS manipulation, especially it is more difficult in the LN dissection along the left recurrent laryngeal nerve. Therefore, it is more suitable to select patients with early esophageal cancer without obvious enlarged lymph nodes for VATS esophagectomy in the learning curve stage.

[Exploration of lymph node metastasis and appropriate lymph node dissection modes in patients with clinical stage I non-small cell lung cancer].

OBJECTIVE: To explore the pattern of lymph node metastasis and evaluate the modes and extent of mediastinal lymph node dissection in patients with ≤ 3 cm, clinical stage I primary non-small cell lung cancer (NSCLC). METHODS: Data of 270 eligible patients who underwent pulmonary resection with systematic lymph node dissection in our hospital between March 2012 and August 2013 were retrospectively analyzed in order to investigate the relationship between the clinicopathological features and lymph node metastatic patterns. Patients with multiple primary carcinomas or non-primary pulmonary malignancies and those who received any chemotherapy or radiotherapy or did not undergo systematic nodal dissection were excluded. The criteria of systematic nodal dissection included the removal of at least six lymph nodes from at least three mediastinal stations, one of which must be subcarinal. The data were analyzed and compared using Chi-square test. RESULTS: The postoperative morbidity rate was 14.8% and no death occurred in this series. The imaging findings showed 34 cases of pure ground glass opacity lesions, 47 partial solid nodules, and 189 solid nodules. Apart from 34 p-GGO lesions, among the other 236 cases, ≤ 1 cm lesions were in 22 cases, 1 cm- ≤ 2 cm lesions in 138 cases, and >2 cm- ≤ 3 cm lesions in 76 cases based on radiologic findings. The pathological types included adenocarcinoma (n = 245), squamous cell carcinoma (n = 18) and other rare types (n = 7). The overall lymph node metastasis rate was 18.9% (51/270), and the incidence of lymph node involvement was 0(0/34) in cancers with p-GGO, 2.1% (1/47) in mixed solid nodules, 26.5% (50/189) in solid nodules, 18.2% (4/22) in nodules ≤ 1 cm, 14.5% (20/138) in 1 cm < nodules ≤ 2 cm, and 35.5% (27/76) in 2 cm < nodules ≤ 3 cm. The metastasis rates of non-specific tumor-draining region lymph nodes detected in the patients with positive and negative lobe-specific lymph node involvement were 20.0%-50.0% vs. 0-2.9% (P < 0.001). CONCLUSIONS: Usually NSCLC with p-GGO nodules has no lymph node metastasis, therefore, systematic nodal dissection may be not necessary. The larger the tumor size is, the higher the lymph node metastatic rate is for mixed or solid nodules. Intraoperative frozen-section examination of the lobe-specific lymph nodes should be performed routinely in patients with ≤ 2 cm stage I NSCLC, and systematic nodal dissection should be done if positive, but it may be not necessary if negative. However, the effectiveness of the systematic selective lymph node dissection still needs to be further confirmed.

FAK-LINC01089 negative regulatory loop controls chemoresistance and progression of small cell lung cancer.

The focal adhesion kinase (FAK) tyrosine kinase is activated and upregulated in multiple cancer types including small cell lung cancer (SCLC). However, FAK inhibitors have shown limited efficacy in clinical trials for cancer treatment. With the aim of identifying potential therapeutic strategies to inhibit FAK for cancer treatment, we investigated long non-coding RNAs (lncRNAs) that potentially regulate FAK in SCLC. In this study, we identified a long non-coding RNA LINC01089 that binds and inhibits FAK phosphorylation (activation). Expression analysis revealed that LINC01089 was downregulated in SCLC tissues and negatively correlated with chemoresistance and survival in SCLC patients. Functionally, LINC01089 inhibited chemoresistance and progression of SCLC in vitro and in vivo. Mechanistically, LINC01089 inhibits FAK activation by blocking binding with Src and talin kinases, while FAK negatively regulates LINC01089 transcription by activating the ERK signaling pathway to recruit the REST transcription factor. Furthermore, LINC01089-FAK axis mediates the expression of drug resist-related genes by modulating YBX1 phosphorylation, leading to drug resistance in SCLC. Intriguingly, the FAK-LINC01089 interaction depends on the co-occurrence of the novel FAK variant and the non-conserved region of LINC01089 in primates. In Conclusion, our results indicated that LINC01089 may serve as a novel high-efficiency FAK inhibitor and the FAK-LINC01089 axis represents a valuable prognostic biomarker and potential therapeutic target in SCLC.

FSTL3 is associated with prognosis and immune cell infiltration in lung adenocarcinoma.

PURPOSE: FSTL3 expression is altered in various types of cancer. However, the role and mechanism of action of FSTL3 in lung adenocarcinoma development and tumor immunity are unknown. We investigated the association between FSTL3 expression and clinical characteristics and immune cell infiltration in lung adenocarcinoma samples from The Cancer Genome Atlas (TCGA) and a separate validation set from our hospital. METHODS: Data on immune system infiltration, gene expression, and relevant clinical information were obtained by analyzing lung adenocarcinoma sample data from TCGA database. Using online tools like GEPIA, the correlations between FSTL3 expression and prognosis, clinical stage, survival status, and tumor-infiltrating immune cells were examined. In a validation dataset, immunohistochemistry was performed to analyze FSTL3 expression and its related clinical characteristics. RESULTS: FSTL3 expression was markedly reduced in patients with lung adenocarcinoma. N stage, pathological stage, and overall survival were significantly correlated with FSTL3 expression. According to GSEA, FSTL3 is strongly linked to signaling pathways such as DNA replication and those involved in cell cycle regulation. Examination of TCGA database and TIMER online revealed a correlation between FSTL3 and B cell, T cell, NK cell, and neutrophil levels. The prognosis of patients with lung adenocarcinoma was significantly affected by six genes (KRT6A, VEGFC, KRT14, KRT17, SNORA12, and KRT81) related to FSTL3. CONCLUSION: FSTL3 is significantly associated with the prognosis and progression of lung adenocarcinoma and the infiltration of immune cells. Thus, targeting FSTL3 and its associated genes in immunotherapy could be potentially beneficial for the treatment of lung adenocarcinoma.

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.

Prognostic and immune correlation analysis of mitochondrial autophagy and aging-related genes in lung adenocarcinoma.

PURPOSE: Mitophagy and aging (MiAg) are very important pathophysiological mechanisms contributing to tumorigenesis. MiAg-related genes have prognostic value in lung adenocarcinoma (LUAD). However, prognostic, and immune correlation studies of MiAg-related genes in LUAD are lacking. METHODS: MiAg differentially expressed genes (DEGs) in LUAD were obtained from public sequencing datasets. A prognostic model including MiAg DEGs was constructed according to patients divided into low- and high-risk groups. Gene Ontology, gene set enrichment analysis, gene set variation analysis, CIBERSORT immune infiltration analysis, and clinical characteristic correlation analyses were performed for functional annotation and correlation of MiAgs with prognosis in patients with LUAD. RESULTS: Seven MiAg DEGs of LUAD were identified: CAV1, DSG2, DSP, MYH11, NME1, PAICS, PLOD2, and the expression levels of these genes were significantly correlated (P < 0.05). The RiskScore of the MiAg DEG prognostic model demonstrated high predictive ability of overall survival of patients diagnosed with LUAD. Patients with high and low MiAg phenotypic scores exhibited significant differences in the infiltration levels of eight types of immune cells (P < 0.05). The multi-factor DEG regression model showed higher efficacy in predicting 5-year survival than 3- and 1-year survival of patients with LUAD. CONCLUSIONS: Seven MiAg-related genes were identified to be significantly associated with the prognosis of patients diagnosed with LUAD. Moreover, the identified MiAg DEGs might affect the immunotherapy strategy of patients with LUAD.

Plasma metabolomics study in screening and differential diagnosis of multiple primary lung cancer.

BACKGROUND: Multiple primary lung cancer (MPLC) is becoming increasingly common in clinical practice. Imaging examination is sometimes difficult to differentiate from intrapulmonary metastasis (IM) or single primary lung cancer (SPLC) before surgery. There is a lack of effective blood biomarkers as an auxiliary diagnostic method. PARTICIPANTS AND METHODS: A total of 179 patients who were hospitalized and operated in our department from January to June 2019 were collected, and they were divided into SPLC with 136 patients, MPLC with 24 patients, and IM with 19 patients. In total, 96 healthy people without lung cancer were enrolled. Medical history, imaging, and pathology data were assembled from all participants. Plasma metabolomics analysis was performed by quadrupole time-of-flight tandem mass spectrometry, and data were analyzed using SPSS19.0/Simca 14.1/MetaboAnalyst5.0 software. Significant metabolites were selected by variable importance in projection, P value, and fold change. The area under the receiver operating characteristic curve was used to evaluate their diagnostic ability. RESULTS: There were significant differences in plasma metabolite profiles between IM and MPLC. Seven metabolites were screened out. Two metabolites had higher levels in IM, and five metabolites had higher levels in MPLC. All had favorable discriminating capacity. Phosphatidyl ethanolamine (38:5) showed the highest sensitivity (0.95) and specificity (0.92). It was followed by l -histidine with sensitivity 0.92 and specificity 0.84. l -tyrosine can be used to identify SPLC and MPLC. The panel composed of related metabolites exhibited higher diagnostic ability. Eight principal metabolites caused remarkable differences between healthy people and MPLC, and five of them had area under the curves greater than 0.85, showing good discriminating power. CONCLUSION: Through the study of plasma metabolomics, it was found that there were obvious differences in the metabolite profiles of MPLC, IM, SPLC, and the healthy population. Some discovered metabolites possessed excellent diagnostic competence with high sensitivity and specificity. They had the potential to act as biomarkers for the screening and differential diagnosis of MPLCs.

A risk score model based on lipid metabolism-related genes could predict response to immunotherapy and prognosis of lung adenocarcinoma: a multi-dataset study and cytological validation.

BACKGROUND: Lipid metabolism is a key factor in tumorigenesis and drug resistance, and models related to lipid metabolism have shown potential to predict survival and curative effects of adjuvant therapy in various cancers. However, the relationship between lipid metabolism and prognosis and treatment response of lung adenocarcinoma (LUAD) are still unclear. METHODS: We enrolled seven bulk RNA-sequence datasets (GSE37745, GSE19188, GSE30219, GSE31547, GSE41271, GSE42127, and GSE72094) from the GEO database and one single-cell RNA-sequencing dataset (GSE117570) from the TISCH2 database. Non-negative matrix factorization (NMF) was utilized to construct the risk score model based on lipid score calculated by GSVA algorithm. Phs000452.v3, PMID: 26359337, PMID: 32472114, PRJEB23709 datasets were used to test the response to immunotherapy. Drug sensitivity analysis was assessed according to the GDSC database, and immunotherapy response was evaluated using the Wilcoxon test. Cellular function assays including clone formation, EDU assays and flow cytometry were implemented to explore the phenotype alteration caused by the knockdown of PTDSS1, which is one of key gene in risk score model. RESULTS: We analyzed both bulk and single-cell RNA sequencing data to establish and validate a risk score model based on 18 lipid metabolism-related genes with significant impact on prognosis. After divided the patients into two groups according to risk score, we identified differences in lipid-related metabolic processes and a detailed portrait of the immune landscapes of high- and low-risk groups. Moreover, we investigated the potentials of our risk score in predicting response to immunotherapy and drug sensitivity. In addition, we silenced PTDSS1 in LUAD cell lines, and found that the proliferation of the cells was weakened, and the apoptosis of the cells was increased. CONCLUSION: Our study highlights the crucial roles of lipid metabolism in LUAD and provides a reliable risk score model, which can aid in predicting prognosis and response to immunotherapy. Furthermore, we investigated the roles of PTDSS1 in LUAD carcinogenesis, which showed that PTDSS1 regulated proliferation and apoptosis of LUAD cells.