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Yu P, Ding G, Huang X, Wang C, Fang J, Huang L, Ye Z, Xu Q, Wu X, Yan J, Ou Q, Du Y, Cheng X. Genomic and immune microenvironment features influencing chemoimmunotherapy response in gastric cancer with peritoneal metastasis: a retrospective cohort study. Int J Surg 2024; 110:01279778-990000000-01231. [PMID: 38502852 DOI: 10.1097/js9.0000000000001281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Patients with peritoneal metastasis (PM) from gastric cancer (GC) exhibit poor prognosis. Chemoimmunotherapy offers promising clinical benefits; however, its efficacy and predictive biomarkers in a conversion therapy setting remain unclear. The authors aimed to retrospectively evaluate chemoimmunotherapy efficacy in a conversion therapy setting for GC patients with PM and establish a prediction model for assessing clinical benefits. MATERIALS AND METHODS A retrospective evaluation of clinical outcomes encompassed 55 GC patients with PM who underwent chemoimmunotherapy in a conversion therapy setting. Baseline PM specimens were collected for genomic and transcriptomic profiling. Clinicopathological factors, gene signatures, and tumor immune microenvironment were evaluated to identify predictive markers and develop a prediction model. RESULTS Chemoimmunotherapy achieved a 41.8% objective response rate and 72.4% R0 resection rate in GC patients with PM. Patients with conversion surgery showed better overall survival (OS) than those without the surgery (median OS: not reached vs 7.82 m, P<0.0001). Responders to chemoimmunotherapy showed higher ERBB2 and ERBB3 mutation frequencies, CTLA4 and HLA-DQB1 expression, and CD8+ T cell infiltration, but lower CDH1 mutation and naïve CD4+ T cell infiltration, compared to nonresponders. A prediction model was established integrating CDH1 and ERBB3 mutations, HLA-DQB1 expression, and naïve CD4+ T cell infiltration (AUC=0.918), which were further tested using an independent external cohort (AUC=0.785). CONCLUSION This exploratory study comprehensively evaluated clinicopathological, genomic, and immune features and developed a novel prediction model, providing a rational basis for the selection of GC patients with PM for chemoimmunotherapy-involved conversion therapy.
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Affiliation(s)
| | | | | | - Chenxuan Wang
- Medical department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, People's Republic of China
| | | | | | | | - Qi Xu
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang
| | - Xiaoying Wu
- Medical department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, People's Republic of China
| | - Junrong Yan
- Medical department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, People's Republic of China
| | - Qiuxiang Ou
- Medical department, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu 210032, People's Republic of China
| | - Yian Du
- Department of Gastric Surgery
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Attia A, Lagha A, Mezlini A, Ghazouani E, Yacoubi-Loueslati B, Namouchi I. HLA class II polymorphisms as prognostic biomarkers for right and left-sided colon cancer. Int J Biol Markers 2024; 39:40-51. [PMID: 38179594 DOI: 10.1177/03936155231224469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
BACKGROUND Colon cancer (CC) is one of the most common malignancies worldwide. Characterization of new prognostic biomarkers for right-sided CC (RCC) and left-sided CC (LCC) may contribute to improving early detection. An association of human leukocyte antigens class II (HLA-II) with the predisposition to CC was suggested. AIM OF THE STUDY We evaluated the association of DRB1 and DQB1 with the risk of LCC and RCC. PATIENTS AND METHODS Our study comprised 93 CC patients and 100 healthy controls. Genotyping of HLA class II alleles were performed by the Polymerase Chain Reaction Sequence-Specific Primers (PCR-SSP). RESULTS DRB1*03 was positively associated with CC. In contrast, DRB1*11, DRB1*13, DQB1*03, and DQB1*05 were negatively linked to CC. Haplotype analysis revealed that DRB1*04-DQB1*04 and DRB1*09-DQB1*02 were positive, while DRB1*01-DQB1*05, DRB1*04-DQB1*03, DRB1*07-DQB1*02, DRB1*11-DQB1*03, DRB1*11-DQB1*05, and DRB1*13-DQB1*06 were negatively associated with CC. For sigmoid CC, DRB1*13, DRB1*11, and DQB1*05 were negative, while DRB1*04-DQB1*02, and DRB1*07-DQB1*03 were positively associated. DRB1*03 and DRB1*04-DQB1*04 were positive, while DRB1*11 and DQB1*03 were negatively linked to RCC. According to the LCC, DRB1*07, DRB1*11, DQB1*03, DQB1*05, and DRB1*07-DQB1*02 were negative. In contrast, DRB1*09-DQB1*02 was positively associated with LCC. Stratified analysis revealed that DRB1*11 is associated with higher risk of metastasis in CC and sigmoid CC, and tolerance to treatment in RCC. DQB1*03 was associated with lymph-node invasion in CC. CONCLUSION DRB1 and DQB1 polymorphisms could be used as future biomarkers for the early detection of subjects at a higher risk of developing RCC and LCC, metastasis in sigmoid CC, and tolerance to treatment in RCC.
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Affiliation(s)
- Amani Attia
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
| | - Awatef Lagha
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
- Laboratory of Immunology, Military Hospital of Tunis, Tunis, Tunisia
| | - Amel Mezlini
- Medical Oncology Department, Salah Azaiez Oncology Institute, Tunis, Tunisia
| | | | - Besma Yacoubi-Loueslati
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
| | - Imene Namouchi
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
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Luo H, Li Q, Wang RT, Zhang L, Zhang W, Deng MS, Luo YY, Ji X, Wen Y, Zhou XR, Xu B, Wang D, Hu B, Jin H, Xu CX. Downregulation of pro-surfactant protein B contributes to the recurrence of early-stage non-small cell lung cancer by activating PGK1-mediated Akt signaling. Exp Hematol Oncol 2023; 12:94. [PMID: 37946295 PMCID: PMC10633994 DOI: 10.1186/s40164-023-00455-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/19/2023] [Indexed: 11/12/2023] Open
Abstract
Recurrence is one of the main causes of treatment failure in early-stage non-small cell lung cancer (NSCLC). However, there are no predictors of the recurrence of early-stage NSCLC, and the molecular mechanism of its recurrence is not clear. In this study, we used clinical sample analysis to demonstrate that low levels of expression of precursor surfactant protein B (pro-SFTPB) in primary NSCLC tissue compared to their adjacent tissues are closely correlated with recurrence and poor prognosis in early-stage NSCLC patients. In vitro and in vivo experiments showed that downregulation of pro-SFTPB expression activates the Akt pathway by upregulating PGK1, which promotes metastasis and tumorigenicity in NSCLC cells. We then demonstrated that pro-SFTPB suppresses the formation of the ADRM1/hRpn2/UCH37 complex by binding to ADRM1, which inhibits PGK1 deubiquitination, thus accelerating ubiquitin-mediated PGK1 degradation. In summary, our findings indicate that low expression of pro-SFTPB in primary NSCLC compared to their adjacent tissue has potential as a predictor of recurrence and poor prognosis in early-stage NSCLC. Mechanistically, downregulation of pro-SFTPB attenuates inhibition of ADRM1-deubiquitinated PGK1, resulting in elevated levels of PGK1 protein; this activates the Akt pathway, ultimately leading to the progression of early-stage NSCLC.
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Affiliation(s)
- Hao Luo
- School of Medicine, Chongqing University, Chongqing, 400030, China
- Cancer Center, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Qing Li
- School of Medicine, Chongqing University, Chongqing, 400030, China
- Cancer Center, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ren-Tao Wang
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Liang Zhang
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Wei Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Meng-Sheng Deng
- State Key Laboratory of Trauma Burn and Combined Injury, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yuan-Yuan Luo
- School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Xintong Ji
- School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Yongheng Wen
- School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Xuan-Rui Zhou
- School of Medicine, Chongqing University, Chongqing, 400030, China
| | - Bo Xu
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and Chongqing University School of Medicine, Chongqing, 400030, China
| | - Dong Wang
- Cancer Center, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Bin Hu
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, 610041, China.
| | - Hua Jin
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Cheng-Xiong Xu
- School of Medicine, Chongqing University, Chongqing, 400030, China.
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Hammouz RY, Orzechowska M, Anusewicz D, Bednarek AK. X or Y Cancer: An Extensive Analysis of Sex Differences in Lung Adenocarcinoma. Curr Oncol 2023; 30:1395-1415. [PMID: 36826068 PMCID: PMC9955992 DOI: 10.3390/curroncol30020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Background: Cellular metabolism is a tightly controlled process during which cell growth and survival are maintained. Lung cancer is a disease with clear sex differences, where female patients have better survival rates than males. Evidence of sex differences is demonstrated in cancer risk, prognosis and response to different therapies, yet a sex-specific approach to cancer studies is not widely considered. These different tumour characteristics attributed to sex that impact disease outcome, including constitutional genetic and somatic molecular differences, make it essential to assess viral and hormonal influences. Methods: In silico analysis of lung adenocarcinoma (LUAD) TCGA data, including K-means clustering algorithm, dimensional reduction with principal component analysis and differential expression analysis using EdgeR (p < 0.05), were used to explore some robust sex differences in LUAD that exist in core signalling pathways and metabolic processes between males and females. The correlation of differentially expressed genes (DEGs) expression with immune abundance in the LUAD cohort was analysed on TIMER2.0 and adjusted by tumour purity utilising Cox proportional hazard. Multiple factorial analysis heatmap visualisation was used to examine endogenous steroid hormonal effects on LUAD patients with different smoking status and age groups. Results: We found 161 DEGs showing key differences in regulation of immune system and cellular homeostasis, key elements of divergent cancer progression, between the two sexes. We also found male and female LUAD patients to favour different metabolic intermediates for energy production to support tumourigenesis. Additionally, high levels of Tregs accompanied by DEGs correlated with better LUAD prognosis, and circulating hormonal transcriptional targets affect proliferation and progression in males and females differently. Finally, we examined the role of oestrogen protection in men and pre-/postmenopausal women. Conclusions: Further studies should focus on sex-specific changes and investigate sex-specific gene regulatory networks of these DEGs. Several lifestyle factors, including tobacco smoking and diet, differ between males and females. These factors might affect metabolic pathways and can influence the activity of epigenetic regulators, resulting in significant global epigenetic changes.
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5
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Isik Z, Leblebici A, Demir Karaman E, Karaca C, Ellidokuz H, Koc A, Ellidokuz EB, Basbinar Y. In silico identification of novel biomarkers for key players in transition from normal colon tissue to adenomatous polyps. PLoS One 2022; 17:e0267973. [PMID: 35486660 PMCID: PMC9053805 DOI: 10.1371/journal.pone.0267973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Adenomatous polyps of the colon are the most common neoplastic polyps. Although most of adenomatous polyps do not show malign transformation, majority of colorectal carcinomas originate from neoplastic polyps. Therefore, understanding of this transformation process would help in both preventive therapies and evaluation of malignancy risks. This study uncovers alterations in gene expressions as potential biomarkers that are revealed by integration of several network-based approaches. In silico analysis performed on a unified microarray cohort, which is covering 150 normal colon and adenomatous polyp samples. Significant gene modules were obtained by a weighted gene co-expression network analysis. Gene modules with similar profiles were mapped to a colon tissue specific functional interaction network. Several clustering algorithms run on the colon-specific network and the most significant sub-modules between the clusters were identified. The biomarkers were selected by filtering differentially expressed genes which also involve in significant biological processes and pathways. Biomarkers were also validated on two independent datasets based on their differential gene expressions. To the best of our knowledge, such a cascaded network analysis pipeline was implemented for the first time on a large collection of normal colon and polyp samples. We identified significant increases in TLR4 and MSX1 expressions as well as decrease in chemokine profiles with mostly pro-tumoral activities. These biomarkers might appear as both preventive targets and biomarkers for risk evaluation. As a result, this research proposes novel molecular markers that might be alternative to endoscopic approaches for diagnosis of adenomatous polyps.
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Affiliation(s)
- Zerrin Isik
- Faculty of Engineering, Department of Computer Engineering, Dokuz Eylul University, Izmir, Turkey
- * E-mail:
| | - Asım Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Demir Karaman
- Department of Computer Engineering, Institute of Natural and Applied Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Caner Karaca
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
| | - Altug Koc
- Gentan Genetic Medical Genetics Diagnosis Center, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Faculty of Medicine, Department of Gastroenterology, Dokuz Eylul University, Izmir, Turkey
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
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6
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Cheng N, Cui X, Chen C, Li C, Huang J. Exploration of Lung Cancer-Related Genetic Factors via Mendelian Randomization Method Based on Genomic and Transcriptomic Summarized Data. Front Cell Dev Biol 2021; 9:800756. [PMID: 34938740 PMCID: PMC8686495 DOI: 10.3389/fcell.2021.800756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Lung carcinoma is one of the most deadly malignant tumors in mankind. With the rising incidence of lung cancer, searching for the high effective cures become more and more imperative. There has been sufficient research evidence that living habits and situations such as smoking and air pollution are associated with an increased risk of lung cancer. Simultaneously, the influence of individual genetic susceptibility on lung carcinoma morbidity has been confirmed, and a growing body of evidence has been accumulated on the relationship between various risk factors and the risk of different pathological types of lung cancer. Additionally, the analyses from many large-scale cancer registries have shown a degree of familial aggregation of lung cancer. To explore lung cancer-related genetic factors, Genome-Wide Association Studies (GWAS) have been used to identify several lung cancer susceptibility sites and have been widely validated. However, the biological mechanism behind the impact of these site mutations on lung cancer remains unclear. Therefore, this study applied the Summary data-based Mendelian Randomization (SMR) model through the integration of two GWAS datasets and four expression Quantitative Trait Loci (eQTL) datasets to identify susceptibility genes. Using this strategy, we found ten of Single Nucleotide Polymorphisms (SNPs) sites that affect the occurrence and development of lung tumors by regulating the expression of seven genes. Further analysis of the signaling pathway about these genes not only provides important clues to explain the pathogenesis of lung cancer but also has critical significance for the diagnosis and treatment of lung cancer.
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Affiliation(s)
- Nitao Cheng
- Department of Thoracic Surgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Xinran Cui
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Changsheng Li
- Department of Thoracic Surgery, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jingyu Huang
- Department of Thoracic Surgery, Zhongnan Hospital, Wuhan University, Wuhan, China
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7
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Halle MK, Sødal M, Forsse D, Engerud H, Woie K, Lura NG, Wagner-Larsen KS, Trovik J, Bertelsen BI, Haldorsen IS, Ojesina AI, Krakstad C. A 10-gene prognostic signature points to LIMCH1 and HLA-DQB1 as important players in aggressive cervical cancer disease. Br J Cancer 2021; 124:1690-1698. [PMID: 33723390 PMCID: PMC8110544 DOI: 10.1038/s41416-021-01305-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced cervical cancer carries a particularly poor prognosis, and few treatment options exist. Identification of effective molecular markers is vital to improve the individualisation of treatment. We investigated transcriptional data from cervical carcinomas related to patient survival and recurrence to identify potential molecular drivers for aggressive disease. METHODS Primary tumour RNA-sequencing profiles from 20 patients with recurrence and 53 patients with cured disease were compared. Protein levels and prognostic impact for selected markers were identified by immunohistochemistry in a population-based patient cohort. RESULTS Comparison of tumours relative to recurrence status revealed 121 differentially expressed genes. From this gene set, a 10-gene signature with high prognostic significance (p = 0.001) was identified and validated in an independent patient cohort (p = 0.004). Protein levels of two signature genes, HLA-DQB1 (n = 389) and LIMCH1 (LIM and calponin homology domain 1) (n = 410), were independent predictors of survival (hazard ratio 2.50, p = 0.007 for HLA-DQB1 and 3.19, p = 0.007 for LIMCH1) when adjusting for established prognostic markers. HLA-DQB1 protein expression associated with programmed death ligand 1 positivity (p < 0.001). In gene set enrichment analyses, HLA-DQB1high tumours associated with immune activation and response to interferon-γ (IFN-γ). CONCLUSIONS This study revealed a 10-gene signature with high prognostic power in cervical cancer. HLA-DQB1 and LIMCH1 are potential biomarkers guiding cervical cancer treatment.
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Affiliation(s)
- Mari K. Halle
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Marte Sødal
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - David Forsse
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Hilde Engerud
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Kathrine Woie
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
| | - Njål G. Lura
- grid.7914.b0000 0004 1936 7443Department of Clinical Medicine, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Radiology, Mohn Medical Imaging and Visualization Centre, Haukeland University Hospital, Bergen, Norway
| | - Kari S. Wagner-Larsen
- grid.7914.b0000 0004 1936 7443Department of Clinical Medicine, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Radiology, Mohn Medical Imaging and Visualization Centre, Haukeland University Hospital, Bergen, Norway
| | - Jone Trovik
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Bjørn I. Bertelsen
- grid.412008.f0000 0000 9753 1393Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Ingfrid S. Haldorsen
- grid.7914.b0000 0004 1936 7443Department of Clinical Medicine, University of Bergen, Bergen, Norway ,grid.412008.f0000 0000 9753 1393Department of Radiology, Mohn Medical Imaging and Visualization Centre, Haukeland University Hospital, Bergen, Norway
| | - Akinyemi I. Ojesina
- grid.265892.20000000106344187Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA ,grid.265892.20000000106344187O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA ,grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Camilla Krakstad
- grid.412008.f0000 0000 9753 1393Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
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Yin YZ, Yao SH, Li CG, Ma YS, Kang ZJ, Zhang JJ, Jia CY, Hou LK, Qin SS, Fan X, Zhang H, Yang MD, Zhang DD, Lu GX, Wang HM, Gu LP, Tian LL, Wang PY, Cao PS, Wu W, Cao ZY, Lv ZW, Shi BW, Wu CY, Jiang GX, Fu D, Yu F. Systematic analysis using a bioinformatics strategy identifies SFTA1P and LINC00519 as potential prognostic biomarkers for lung squamous cell carcinoma. Am J Transl Res 2021; 13:168-182. [PMID: 33527016 PMCID: PMC7847518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Lung cancer has high incidence and mortality rates, in which lung squamous cell carcinoma (LUSC) is a primary type of non-small cell lung carcinoma (NSCLC). The aim of our study was to discover long non-coding RNAs (lncRNAs) associated with diagnose and prognosis for LUSC. RNA sequencing data obtained from LUSC samples were extracted from The Cancer Genome Atlas database (TCGA). Two prognosis-associated lncRNAs (including SFTA1P and LINC00519) were selected from LUSC samples, and the expression levels were also verified to be associated abnormal in LUSC clinical samples. Our findings demonstrate that lncRNAs SFTA1P and LINC00519 exert important functions in human LUSC and may serve as new targets for LUSC diagnosis and therapy.
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Affiliation(s)
- Yu-Zhen Yin
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
- Shanghai Clinical College, Anhui Medical UniversityHefei 230032, China
| | - Shi-Hua Yao
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai HospitalShanghai 200433, China
| | - Chun-Guang Li
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai HospitalShanghai 200433, China
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
- Pancreatic Cancer Institute, Fudan UniversityShanghai 200032, China
- Department of Pancreatic and Hepatobiliary Surgery, Cancer Hospital, Fudan University Shanghai Cancer CenterShanghai 200032, China
| | - Zhou-Jun Kang
- Department of Emergency, Navy Military Medical University Affiliated Changhai HospitalShanghai 200433, China
| | - Jia-Jia Zhang
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of MedicineShanghai 200433, China
| | - Shan-Shan Qin
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Xin Fan
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Han Zhang
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Meng-Die Yang
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Gai-Xia Lu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Li-Peng Gu
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Lin-Lin Tian
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Ping-Sheng Cao
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of MedicineShanghai 200433, China
| | - Zi-Yang Cao
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of MedicineShanghai 200433, China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Bo-Wen Shi
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai HospitalShanghai 200433, China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of MedicineShanghai 200433, China
| | - Geng-Xi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai HospitalShanghai 200433, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai 200072, China
- Shanghai Clinical College, Anhui Medical UniversityHefei 230032, China
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Bassaganyas L, Pinyol R, Esteban-Fabró R, Torrens L, Torrecilla S, Willoughby CE, Franch-Expósito S, Vila-Casadesús M, Salaverria I, Montal R, Mazzaferro V, Camps J, Sia D, Llovet JM. Copy-Number Alteration Burden Differentially Impacts Immune Profiles and Molecular Features of Hepatocellular Carcinoma. Clin Cancer Res 2020; 26:6350-6361. [PMID: 32873569 DOI: 10.1158/1078-0432.ccr-20-1497] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/08/2020] [Accepted: 08/28/2020] [Indexed: 12/25/2022]
Abstract
PURPOSE Chromosomal instability is a hallmark of cancer that results in broad and focal copy-number alterations (CNAs), two events associated with distinct molecular, immunologic, and clinical features. In hepatocellular carcinoma (HCC), the role of CNAs has not been thoroughly assessed. Thus, we dissected the impact of CNA burdens on HCC molecular and immune features. EXPERIMENTAL DESIGN We analyzed SNP array data from 452 paired tumor/adjacent resected HCCs and 25 dysplastic nodules. For each sample, broad and focal CNA burdens were quantified using CNApp, and the resulting broad scores (BS) and focal scores (FS) were correlated with transcriptomic, mutational, and methylation profiles, tumor immune composition, and clinicopathologic data. RESULTS HCCs with low broad CNA burdens (defined as BS ≤ 4; 17%) presented high inflammation, active infiltrate signaling, high cytolytic activity, and enrichment of the "HCC immune class" and gene signatures related to antigen presentation. Conversely, tumors with chromosomal instability (high broad CNA loads, BS ≥ 11; 40%), displayed immune-excluded traits and were linked to proliferation, TP53 dysfunction, and DNA repair. Candidate determinants of the low cytotoxicity and immune exclusion features of high-BS tumors included alterations in antigen-presenting machinery (i.e., HLA), widespread hypomethylation, and decreased rates of observed/expected neoantigenic mutations. High FSs were independent of tumor immune features, but were related to proliferation, TP53 dysfunction, and progenitor cell traits. CONCLUSIONS HCCs with high chromosomal instability exhibit features of immune exclusion, whereas tumors displaying low burdens of broad CNAs present an immune active profile. These CNA scores can be tested to predict response to immunotherapies.
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Affiliation(s)
- Laia Bassaganyas
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roser Pinyol
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roger Esteban-Fabró
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Laura Torrens
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sara Torrecilla
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Catherine E Willoughby
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | | | - Itziar Salaverria
- Lymphoid Neoplasms Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.,Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERonc), Madrid, Spain
| | - Robert Montal
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Vincenzo Mazzaferro
- Gastrointestinal Surgery and Liver Transplantation Unit, National Cancer Institute, Milan, Italy
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Daniela Sia
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Josep M Llovet
- Liver Cancer Translational Research Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain. .,Mount Sinai Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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10
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Yao J, Xue X, Qu D, Westphalen CB, Ge Y, Zhang L, Li M, Gao T, Chandrakesan P, Vega KJ, Peng J, An G, Weygant N. Reverse engineering a predictive signature characterized by proliferation, DNA damage, and immune escape from stage I lung adenocarcinoma recurrence. Acta Biochim Biophys Sin (Shanghai) 2020; 52:638-653. [PMID: 32395755 DOI: 10.1093/abbs/gmaa036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/14/2020] [Indexed: 12/24/2022] Open
Abstract
Identifying early-stage cancer patients at risk for progression is a major goal of biomarker research. This report describes a novel 19-gene signature (19-GCS) that predicts stage I lung adenocarcinoma (LAC) recurrence and response to therapy and performs comparably in pancreatic adenocarcinoma (PAC), which shares LAC molecular traits. Kaplan-Meier, Cox regression, and cross-validation analyses were used to build the signature from training, test, and validation sets comprising 831 stage I LAC transcriptomes from multiple independent data sets. A statistical analysis was performed using the R language. Pathway and gene set enrichment were used to identify underlying mechanisms. 19-GCS strongly predicts overall survival and recurrence-free survival in stage I LAC (P=0.002 and P<0.001, respectively) and in stage I-II PAC (P<0.0001 and P<0.0005, respectively). A multivariate cox regression analysis demonstrated the independence of 19-GCS from significant clinical factors. Pathway analyses revealed that 19-GCS high-risk LAC and PAC tumors are characterized by increased proliferation, enhanced stemness, DNA repair deficiency, and compromised MHC class I and II antigen presentation along with decreased immune infiltration. Importantly, high-risk LAC patients do not appear to benefit from adjuvant cisplatin while PAC patients derive additional benefit from FOLFIRINOX compared with gemcitabine-based regimens. When validated prospectively, this proof-of-concept biomarker may contribute to tailoring treatment, recurrence reduction, and survival improvements in early-stage lung and pancreatic cancers.
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Affiliation(s)
- Jiannan Yao
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Xinying Xue
- Department of Respiratory and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Dongfeng Qu
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, 73103, OK, USA
- Stephenson Cancer Center, Oklahoma City, 73104, OK, USA
| | - C Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III, Ludwig Maximilian University of Munich, 81377, Munich, Germany
| | - Yang Ge
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Liyang Zhang
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Manyu Li
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Tianbo Gao
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Parthasarathy Chandrakesan
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, 73103, OK, USA
- Stephenson Cancer Center, Oklahoma City, 73104, OK, USA
| | - Kenneth J Vega
- Division of Gastroenterology and Hepatology, Augusta University, Augusta, 30912, GA, USA
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fuzhou 350122, China
| | - Guangyu An
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Nathaniel Weygant
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Fujian Key Laboratory of Integrative Medicine in Geriatrics, Fuzhou 350122, China
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11
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Yuan J, Yuan B, Zeng L, Liu B, Chen Y, Meng X, Sun R, Lv X, Wang W, Yang S. Identification and validation of tumor microenvironment-related genes of prognostic value in lung adenocarcinoma. Oncol Lett 2020; 20:1772-1780. [PMID: 32724420 PMCID: PMC7377199 DOI: 10.3892/ol.2020.11735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/17/2020] [Indexed: 12/30/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a major subtype of non-small cell lung cancer. Despite significant progress in its diagnosis and treatment, the mortality and morbidity rate of LUAD remains high worldwide. The aim of the present study was to perform a systematic investigation of the tumor microenvironment (TME) and identify TME-related genes of prognostic value in patients with LUAD. Firstly, the immune scores and stromal scores of patients with LUAD from The Cancer Genome Atlas were calculated using the Estimation of STromal and Immune cells in MAlignant Tumors using Expression data algorithm, and a total of 281 prognostic TME-related genes were identified. Subsequently, functional analysis and protein-protein interaction network analysis revealed that these genes were mainly related to immune response, inflammatory response and chemotaxis. Finally, two independent LUAD cohorts from the Gene Expression Omnibus database were used to validate these genes, and 4 genes (GTPase IMAP family member 1, T-cell surface glycoprotein CD1b, integrin alpha-L and leukocyte surface antigen CD53) were identified, and downregulation of these genes was indicated to be associated with poor overall survival rate in patients with LUAD. In conclusion, a comprehensive analysis of TME was performed and 4 prognostic TME-related genes in patients with LUAD were identified.
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Affiliation(s)
- Jingyan Yuan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Bo Yuan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Lizhong Zeng
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Boxuan Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Xia Meng
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Ruiying Sun
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Xin Lv
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Wei Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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12
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Qiu LM, Sun YH, Chen TT, Chen JJ, Ma HT. STRIP2, a member of the striatin-interacting phosphatase and kinase complex, is implicated in lung adenocarcinoma cell growth and migration. FEBS Open Bio 2020; 10:351-361. [PMID: 31901223 PMCID: PMC7050248 DOI: 10.1002/2211-5463.12785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/14/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma (LUAD) accounts for ~40% of lung cancer cases, and the 5-year relative survival rate is no more than 1%. Dysregulation of components of striatin-interacting phosphatase and kinase (STRIPAK) complexes is associated with various diseases, including cancer. Striatin-interacting protein 2 (STRIP2), also called Fam40b, has been reported to regulate tumor cell growth and migration. Here, we investigated the role of STRIP2 in LUAD growth, migration and the underlying mechanisms. Analysis of data from The Cancer Genome Atlas database revealed that STRIP2 is highly expressed and predicted poor outcomes in patients with LUAD. Moreover, quantitative RT-PCR (qRT-PCR) analysis revealed that the mRNA expression of STRIP2 is greater in all tested LUAD cells than in a normal lung cell line. To investigate the function of STRIP2, we overexpressed STRIP2 in SPC-A1 cells and depleted STRIP2 in Calu-3 cells. Cell proliferation was evaluated by Cell Counting Kit-8 and colony-forming assays, and Transwell assay was employed to test cell invasion and migration. Our results indicate that STRIP2 depletion suppressed cell proliferation, invasion and migration in Calu-3 cells, and overexpression of STRIP2 had the opposite effects in SPC-A1 cells. Moreover, we discovered that STRIP2 depletion reduced the protein levels of p-Akt and phosphorylated-mammalian target of rapamycin (p-mTOR) in Calu-3 cells, whereas STRIP2 overexpression increased levels of these proteins in SPC-A1 cells. Furthermore, we found that silencing of STRIP2 clearly enhanced protein levels of E-cadherin and reduced levels of N-cadherin, Vimentin and matrix metalloproteinase-9 in Calu-3 cells, whereas overexpression of STRIP2 had the opposite effect in SPC-A1 cells. Our data indicate that STRIP2 promotes the proliferation and motility of LUAD cells, and this may be mediated through the regulation of the Akt/mTOR pathway and epithelial-mesenchymal transition. These results may facilitate the development of therapeutic strategies to treat LUAD.
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Affiliation(s)
- Li-Min Qiu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Thoracic Surgery, Yancheng City No. 1 People's Hospital, Yancheng City, China
| | - Yun-Hao Sun
- Department of Thoracic Surgery, Yancheng City No. 1 People's Hospital, Yancheng City, China
| | - Ting-Ting Chen
- Department of Emergency, Yancheng City No. 1 People's Hospital, Yancheng City, China
| | - Jin-Jin Chen
- Department of Oncology, Yancheng City No. 1 People's Hospital, Yancheng City, China
| | - Hai-Tao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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13
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Yin XH, Yu LP, Zhao XH, Li QM, Liu XP, He L. Development and validation of a 4-gene combination for the prognostication in lung adenocarcinoma patients. J Cancer 2020; 11:1940-1948. [PMID: 32194805 PMCID: PMC7052877 DOI: 10.7150/jca.37003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023] Open
Abstract
Objective: To identify a multi-gene prognostic factor in patients with lung adenocarcinoma (LUAD). Materials and methods Prognosis-related genes were screened in the TCGA-LUAD cohort. Then, patients in this cohort were randomly separated into training set and test set. Least absolute shrinkage and selection operator (LASSO) regression was performed to the penalized the Cox proportional hazards regression (CPH) model on the training set, and a prognostication combination based on the result of LASSO analysis was developed. By performing Kaplan-Meier curve analysis, univariate and multivariable CPH model on the overall survival (OS) as well as recurrence free survival (RFS), the prognostication performance of the multigene combination were evaluated. Moreover, we constructed a nomogram and performed decision curve analysis to evaluate the clinical application of the multigene combination. Results We obtained 99 prognosis-related genes and screened out a 4-gene combination (including CIDEC, ZFP3, DKK1, and USP4) according to the LASSO analysis. The results of survival analyses suggested that patients in the 4-gene combination low-risk group had better OS and RFS than those in the 4-gene combination high-risk group. The 4-gene mentioned was demonstrated to be independent prognostic factor of patients with LUAD in the training set(OS, HR=11.962, P<0.001; RFS, HR=9.281, P<0.001) and test set (OS, HR=5.377, P=0.003; RFS, HR=2.949, P=0.104). More importantly, its prognosis performance was well in the validation set (OS, HR=0.955, P=0.002; RFS, HR=1.042, P<0.001). Conclusions We introduced a 4-gene combination which could predict the survival of LUAD patients and might be an independent prognostic factor in LUAD.
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Affiliation(s)
- Xiao-Hong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China.,Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Li-Ping Yu
- Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Xiao-Hong Zhao
- Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Qin-Mei Li
- Department of Epidemiology, Department of Epidemiology, School of Health Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China
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