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Yu SK, Yang J, Zhang Q, Yu T, Lu KH. A novel signature based on twelve programmed cell death patterns to predict the prognosis of lung adenocarcinoma. Am J Transl Res 2024; 16:2082-2102. [PMID: 38883377 PMCID: PMC11170577 DOI: 10.62347/uamn8558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/06/2024] [Indexed: 06/18/2024]
Abstract
Programmed cell death (PCD) plays a pivotal role in tumor initiation and progression. However, the prognostic value and clinical characteristics of PCD-related genes (PRGs) remain unclear. We collected and analyzed genes associated with twelve PCD patterns, including apoptosis, necroptosis, pyroptosis, ferroptosis, cuproptosis, entotic cell death, netotic cell death, parthanatos, lysosome-dependent cell death, autophagy-dependent cell death, alkaliptosis, and oxeiptosis to construct a gene signature. Our analysis identified 215 differentially expressed PRGs out of 1254 in lung adenocarcinoma (LUAD) and normal lung tissues. Subsequently, we performed univariate Cox regression analysis and identified 58 prognostic PRGs. Based on LASSO Cox regression analysis, we constructed a risk score using the expression levels of seven genes: DAPK2, DDIT4, E2F2, GAPDH, MET, PIM2, and FOXF1. Patients with lower risk scores showed earlier stages of cancer, longer survival times, and better immune infiltrations and functions. Notably, we found that knockdown of DDIT4 significantly increased apoptosis and impaired the proliferation of human LUAD cell lines. Our study proposes a PRG-based prognostic signature that sheds light on the potential role of PCD-related genes in LUAD and provides valuable insights into future therapeutic strategies.
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Affiliation(s)
- Shao-Kun Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University No. 300 Guangzhou Road, Nanjing, Jiangsu, China
| | - Jiu Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University No. 300 Guangzhou Road, Nanjing, Jiangsu, China
| | - Qi Zhang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University Taizhou, Jiangsu, China
| | - Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University No. 300 Guangzhou Road, Nanjing, Jiangsu, China
| | - Kai-Hua Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University No. 300 Guangzhou Road, Nanjing, Jiangsu, China
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Zhang L, Zhang X, Guan M, Zeng J, Yu F, Lai F. Machine-learning developed an iron, copper, and sulfur-metabolism associated signature predicts lung adenocarcinoma prognosis and therapy response. Respir Res 2024; 25:206. [PMID: 38745285 PMCID: PMC11092068 DOI: 10.1186/s12931-024-02839-6] [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] [Received: 11/08/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Previous studies have largely neglected the role of sulfur metabolism in LUAD, and no study has combine iron, copper, and sulfur-metabolism associated genes together to create prognostic signatures. METHODS This study encompasses 1564 LUAD patients, 1249 NSCLC patients, and over 10,000 patients with various cancer types from diverse cohorts. We employed the R package ConsensusClusterPlus to separate patients into different ICSM (Iron, Copper, and Sulfur-Metabolism) subtypes. Various machine-learning methods were utilized to develop the ICSMI. Enrichment analyses were conducted using ClusterProfiler and GSVA, while IOBR quantified immune cell infiltration. GISTIC2.0 and maftools were utilized for CNV and SNV data analysis. The Oncopredict package predicted drug information based on GDSC1. TIDE algorithm and cohorts GSE91061 and IMvigor210 evaluated patient response to immunotherapy. Single-cell data was processed using the Seurat package, AUCell package calculated cells geneset activity scores, and the Scissor algorithm identified ICSMI-associated cells. In vitro experiments was conducted to explore the role of ICSMRGs in LUAD. RESULTS Unsupervised clustering identified two distinct ICSM subtypes of LUAD, each with unique clinical characteristics. The ICSMI, comprising 10 genes, was constructed using integrated machine-learning methods. Its prognostic power was validated in 10 independent datasets, revealing that LUAD patients with higher ICSMI levels had poorer prognoses. Furthermore, ICSMI demonstrated superior predictive abilities compared to 102 previously published signatures. A nomogram incorporating ICSMI and clinical features exhibited high predictive performance. ICSMI positively correlated with patients gene mutations, and integrated analysis of bulk and single-cell transcriptome data revealed its association with TME modulators. Cells representing the high-ICSMI phenotype exhibited more malignant features. LUAD patients with high ICSMI levels exhibited sensitivity to chemotherapy and targeted therapy but displayed resistance to immunotherapy. In a comprehensive analysis across various cancers, ICSMI retained significant prognostic value and emerged as a risk factor for the majority of cancer patients. CONCLUSIONS ICSMI provides critical prognostic insights for LUAD patients, offering valuable insights into the tumor microenvironment and predicting treatment responsiveness.
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Affiliation(s)
- Liangyu Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xun Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Maohao Guan
- Department of Thoracic Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Jianshen Zeng
- Department of Thoracic Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Fengqiang Yu
- Department of Thoracic Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
| | - Fancai Lai
- Department of Thoracic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
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Wang S, Huang C, Zheng Y, Wu X, Zhong Y. NPAS2, transcriptionally activated by ARRB1, promotes the malignant behaviours of lung adenocarcinoma cells and regulates the reprogramming of glucose metabolism. Clin Exp Pharmacol Physiol 2024; 51:e13860. [PMID: 38584327 DOI: 10.1111/1440-1681.13860] [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] [Received: 10/23/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
Lung adenocarcinoma (LUAD) is a serious threat to public health and is accompanied by increased morbidity and mortality worldwide. Neuronal PAS domain protein2 (NPAS2) has been confirmed as an oncogene in LUAD; however, little is known about its molecular mechanism. Here, the expression level of NPAS2 was detected in LUAD cell lines and 16HBE cells. Gain- and loss-of-function experiments were performed. Cell Counting Kit-8, colony formation, flow cytometry, wound-healing and Transwell assays were conducted to assess cell proliferation, apoptosis, migration and invasion, respectively. Reprogramming of glucose metabolism was evaluated via oxygen consumption rate (OCR), complexes activities, lactic production and glucose consumption. The expression of critical proteins was examined by western blot. We demonstrated aberrant upregulation of NPAS2 and β-arrestin-1 (ARRB1) in LUAD cell lines. ARRB1 was found to be a critical transcription factor of NPAS2 with binding sites within the promoter region of NPAS2, thereby causing its transcriptional activation. Functional experiments revealed that NPAS2 depletion significantly inhibited the malignant behaviours of A549 cells by suppressing cell proliferation, migration, invasion and epithelial-mesenchymal transition and promoting cell apoptosis. Meanwhile, NPAS2 depletion increased OCR and activities of complexes (I, II, III and V), and reduced lactic acid production and glucose uptake in A549 cells, indicating that NPAS2 depletion inhibited aerobic glycolysis, accompanied by reduced expression of glycolytic enzymes. However, the changes caused by NPAS2 knockdown were partly restored by ARRB1 overexpression. In conclusion, our study suggests that ARRB1 could transcriptionally activate NPAS2, facilitating malignant activities and glycolysis, and ultimately promoting the progression of LUAD, proving a novel therapeutic strategy for the treatment of LUAD.
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Affiliation(s)
- Shenglan Wang
- Department of Clinical Laboratory, LongYan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, China
| | - Chunhong Huang
- Department of Clinical Laboratory, LongYan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, China
| | - Yanbin Zheng
- Department of Clinical Laboratory, LongYan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, China
| | - Xinjie Wu
- Emergency Department, LongYan People Hospital of Fujian, Longyan, Fujian, China
| | - Yutong Zhong
- Department of Clinical Laboratory, LongYan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, China
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Lou H, Wu Z, Wei G. CDC6 may serve as an indicator of lung adenocarcinoma prognosis and progression based on TCGA and GEO data mining and experimental analyses. Oncol Rep 2024; 51:35. [PMID: 38186304 PMCID: PMC10807357 DOI: 10.3892/or.2024.8694] [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] [Received: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most lethal types of cancer worldwide, and accurately predicting patient prognosis is an important challenge. Gene prediction models, which are known for their simplicity and efficiency, have the potential to be used for prognostic predictions. However, the availability of models with true clinical value is limited. The present study integrated tissue sequencing and the clinical information of patients with LUAD from The Cancer Genome Atlas and Gene Expression Omnibus databases using bioinformatics. This comprehensive approach enabled the identification of 252 differentially expressed genes. Subsequently, univariate and multivariate Cox analyses were performed using these genes, and 14 and 3 genes [including cell division cycle 6 (CDC6), hyaluronan mediated motility receptor and STIL centriolar assembly protein] were selected for the construction of two prognostic models. Notably, the 3‑gene prognostic model exhibited a comparable predictive ability to that of the 14‑gene model. Functionally, pathway enrichment analysis revealed that CDC6 played a role in regulating the cell cycle and promoting tumor staging. To further investigate the relevance of CDC6, in vitro experiments involving the downregulation of CDC6 expression were conducted, which resulted in significant inhibition of tumor cell migration, invasion and proliferation. Moreover, in vivo experiments demonstrated that downregulating CDC6 expression significantly reduced the burden and metastasis of in situ lung tumors in mice. These findings suggested that CDC6 may be a critical gene involved in the development and prognosis of LUAD. In summary, the present study successfully constructed a simple yet accurate prognostic prediction model consisting of 3 genes. Additionally, the functional importance of CDC6 as a key gene in the model was identified. These findings lay a crucial foundation for further exploration of prognostic prediction models and a deeper understanding of the functional mechanisms of CDC6. Notably, these results have potential clinical implications for improving personalized treatment and prognosis evaluation for patients with LUAD.
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Affiliation(s)
- Hao Lou
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
| | - Zelai Wu
- Department of Surgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P.R. China
| | - Guangyou Wei
- School of Medicine, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
- Department of Pediatrics, Bozhou Municipal People's Hospital, Bozhou, Anhui 236800, P.R. China
- Department of Pediatrics, Bozhou Clinical Medicine of Anhui University of Science and Technology School, Bozhou, Anhui 236800, P.R. China
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Bayanbold K, Singhania M, Fath MA, Searby CC, Stolwijk JM, Henrich JB, Pulliam CF, Schoenfeld JD, Mapuskar KA, Sho S, Caster JM, Allen BG, Buettner GR, Spies M, Goswami PC, Petronek MS, Spitz DR. Depletion of Labile Iron Induces Replication Stress and Enhances Responses to Chemoradiation in Non-Small-Cell Lung Cancer. Antioxidants (Basel) 2023; 12:2005. [PMID: 38001858 PMCID: PMC10669787 DOI: 10.3390/antiox12112005] [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: 10/12/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The intracellular redox-active labile iron pool (LIP) is weakly chelated and available for integration into the iron metalloproteins that are involved in diverse cellular processes, including cancer cell-specific metabolic oxidative stress. Abnormal iron metabolism and elevated LIP levels are linked to the poor survival of lung cancer patients, yet the underlying mechanisms remain unclear. Depletion of the LIP in non-small-cell lung cancer cell lines using the doxycycline-inducible overexpression of the ferritin heavy chain (Ft-H) (H1299 and H292), or treatment with deferoxamine (DFO) (H1299 and A549), inhibited cell growth and decreased clonogenic survival. The Ft-H overexpression-induced inhibition of H1299 and H292 cell growth was also accompanied by a significant delay in transit through the S-phase. In addition, both Ft-H overexpression and DFO in H1299 resulted in increased single- and double-strand DNA breaks, supporting the involvement of replication stress in the response to LIP depletion. The Ft-H and DFO treatment also sensitized H1299 to VE-821, an inhibitor of ataxia telangiectasis and Rad2-related (ATR) kinase, highlighting the potential of LIP depletion, combined with DNA damage response modifiers, to alter lung cancer cell responses. In contrast, only DFO treatment effectively reduced the LIP, clonogenic survival, cell growth, and sensitivity to VE-821 in A549 non-small-cell lung cancer cells. Importantly, the Ft-H and DFO sensitized both H1299 and A549 to chemoradiation in vitro, and Ft-H overexpression increased the efficacy of chemoradiation in vivo in H1299. These results support the hypothesis that the depletion of the LIP can induce genomic instability, cell death, and potentiate therapeutic responses to chemoradiation in NSCLC.
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Affiliation(s)
- Khaliunaa Bayanbold
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Mekhla Singhania
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Melissa A. Fath
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Charles C. Searby
- University of Iowa Hospitals and Clinics, Department Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey M. Stolwijk
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - John B. Henrich
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Casey F. Pulliam
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Joshua D. Schoenfeld
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Kranti A. Mapuskar
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Sei Sho
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Joseph M. Caster
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Bryan G. Allen
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Garry R. Buettner
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Maria Spies
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
- University of Iowa Hospitals and Clinics, Holden Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Iowa City, IA 52242, USA
| | - Prabhat C. Goswami
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Michael S. Petronek
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
| | - Douglas R. Spitz
- University of Iowa Hospitals and Clinics, Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, Iowa City, IA 52242, USA (M.A.F.); (G.R.B.)
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Chen Q, Zhao H, Hu J. A robust six-gene prognostic signature based on two prognostic subtypes constructed by chromatin regulators is correlated with immunological features and therapeutic response in lung adenocarcinoma. Aging (Albany NY) 2023; 15:12330-12368. [PMID: 37938151 PMCID: PMC10683604 DOI: 10.18632/aging.205183] [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] [Received: 02/20/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023]
Abstract
Accumulating evidence has demonstrated that chromatin regulators (CRs) regulate immune cell infiltration and are correlated with prognoses of patients in some cancers. However, the immunological and prognostic roles of CRs in lung adenocarcinoma (LUAD) are still unclear. Here, we systematically revealed the correlations of CRs with immunological features and the survival in LUAD patients based on a cohort of gene expression datasets from the public TCGA and GEO databases and real RNA-seq data by an integrative analysis using a comprehensive bioinformatics method. Totals of 160 differentially expressed CRs (DECRs) were identified between LUAD and normal lung tissues, and two molecular prognostic subtypes (MPSs) were constructed and evaluated based on 27 prognostic DECRs using five independent datasets (p =0.016, <0.0001, =0.008, =0.00038 and =0.00055, respectively). Six differentially expressed genes (DEGs) (CENPK, ANGPTL4, CCL20, CPS1, GJB3, TPSB2) between two MPSs had the most important prognostic feature and a six-gene prognostic model was established. LUAD patients in the low-risk subgroup showed a higher overall survival (OS) rate than those in the high-risk subgroup in nine independent datasets (p <0.0001, =0.021, =0.016, =0.0099, <0.0001, =0.0045, <0.0001, =0.0038 and =0.00013, respectively). Six-gene prognostic signature had the highest concordance index of 0.673 compared with 19 reported prognostic signatures. The risk score was significantly correlated with immunological features and activities of oncogenic signaling pathways. LUAD patients in the low-risk subgroup benefited more from immunotherapy and were less sensitive to conventional chemotherapy agents. This study provides novel insights into the prognostic and immunological roles of CRs in LUAD.
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Affiliation(s)
- Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hongbo Zhao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, China
| | - Jing Hu
- Department of Medical Oncology, First People’s Hospital of Yunnan Province, Kunming, China
- Department of Medical Oncology, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
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Wang Y, Wang K, Zhang H, Jia X, Li X, Sun S, Sun D. Cell death-related biomarker SLC2A1 has a significant role in prognosis prediction and immunotherapy efficacy evaluation in pan-cancer. Front Genet 2023; 13:1068462. [PMID: 36712872 PMCID: PMC9873976 DOI: 10.3389/fgene.2022.1068462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction: SLC2A1, a member of the SLC transporter family, is involved in a variety of cell death modalities and has been found to be associated with the prognosis and immune microenvironment of a variety of tumors. However, there is a lack of systematic and comprehensive studies on the role of SLC2A1 in pan-cancer. Methods: The mRNA, promoter methylation, and protein expression levels of SLC2A1 in pan-cancer were comprehensively evaluated using GEPIA2.0, TIMER2.0, and UALCAN databases. UCSCXenaShiny based on the cancer genomic atlas pan-cancer data and GEPIA2.0 database were used to assess the prognostic significance of SLC2A1 in pan-cancer. Genetic alterations in SLC2A1 were also evaluated using cBioPortal. The relevance of SLC2A1 to immune infiltrating cells in pan-cancer was evaluated using the XCELL algorithm in combination with the TIMER2.0 database. The correlation of SLC2A1 with the efficacy of immune checkpoint blocker (ICB) therapy was evaluated using the tumor immune dysfunction and exclusion (TIDE) score. The correlation of SLC2A1 with numerous immune-related markers was also evaluated using the TISIDB database. The correlation of SLC2A1 with tumor biological function was evaluated at the single-cell level using the CancerSEA database. Finally, the biological function of SLC2A1 was comprehensively evaluated using gene set enrichment analysis (GSEA) and protein interaction networks. Results: SLC2A1 expression is aberrant in a variety of tumors and is strongly associated with the prognosis of several cancers. SLC2A1 is significantly associated with a variety of immune infiltrating cells including CD8+ T cells, myeloid-derived suppressor cells and macrophages in a variety of tumors. Meanwhile, the expression of SLC2A1 significantly correlated with multiple immune-related markers. In addition, SLC2A1 can also predict the effect of immune checkpoint blocker therapy in some tumors. In a functional analysis, SLC2A1 was significantly associated with hypoxia, epithelial-mesenchymal transition, mTORC1 signaling, and multiple metabolic pathways in pan-cancer. Conclusion: Our study systematically and comprehensively summarizes the prognostic significance and immune-related role of SLC2A1 in pan-cancer and reveals the potential mechanism of SLC2A1 in regulating the tumor microenvironment and tumor behavior, providing a new effective pan-applicable biomarker for prognostic prediction and the evaluation of immunotherapeutic strategies for tumors.
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Affiliation(s)
- Yuhang Wang
- Graduate School, Tianjin Medical University, Tianjin, China,Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Kai Wang
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Han Zhang
- Graduate School, Tianjin Medical University, Tianjin, China,Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Jia
- Graduate School, Tianjin Medical University, Tianjin, China,Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Xin Li
- Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China
| | - Shuai Sun
- Graduate School, Tianjin Medical University, Tianjin, China,Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Daqiang Sun
- Graduate School, Tianjin Medical University, Tianjin, China,Clinical School of Thoracic, Tianjin Medical University, Tianjin, China,Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China,*Correspondence: Daqiang Sun,
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Screening and Biological Function Analysis of miRNA and mRNA Related to Lung Adenocarcinoma Based on Bioinformatics Technology. JOURNAL OF ONCOLOGY 2022; 2022:4339391. [PMID: 36090902 PMCID: PMC9452934 DOI: 10.1155/2022/4339391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022]
Abstract
Objective. To screen the differentially expressed miRNAs (DEMs) and the differentially expressed gene mRNAs (DEGs) in lung adenocarcinoma (LUAD) from the TCGA database and to explore the relationship between miRNAs and the prognosis of lung adenocarcinoma and their biological functions. Methods. The RNA-seq and miRNA-seq data of lung adenocarcinoma samples were downloaded from the TCGA database for analysis, and the R program was used to screen for differentially expressed miRNAs and mRNAs. Then, the molecular functions, biological processes, cellular components, and signaling pathways involved in the occurrence and development of LUAD were analyzed using the functional accumulation analysis software of GSEA. The relationship between the integrated differentially expressed RNAs was analyzed by miRcode, TargetScan, and miRTarbase databases, and the miRNA-mRNA network was constructed. Result. A total of 516 differentially expressed miRNAs and 5464 differentially expressed mRNAs were identified in LUAD. The GSEA enrichment analysis showed that miRNAs and mRNAs were mainly enriched in extracellular structure organization, external encapsulating structure organization, extracellular matrix organization, and gated channel activity. They were mainly involved in neuroactive ligand-receptor interaction signaling pathway. Some miRNAs and mRNAs in clustering modules were found to be associated with the prognosis of LUAD. Four targeting networks consisting of 22 miRNAs and 531 mRNAs were constructed. Conclusion. The miRNA and mRNA related to the prognosis of LUAD were screened out, which provided a valuable preliminary basis for the follow-upin-depth clinical research and basic experimental research of LUAD.
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Gu Y, Tang S, Wang Z, Cai L, Lian H, Shen Y, Zhou Y. A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers. Bioengineered 2021; 12:6166-6185. [PMID: 34486492 PMCID: PMC8806805 DOI: 10.1080/21655979.2021.1973220] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Beta-actin (ACTB), a highly conserved cytoskeleton structural protein, has been regarded as a common housekeep gene and used as a reference gene for years. However, accumulating evidence indicates that ACTB is abnormally expressed in multiple cancers and hence changes the cytoskeleton to affect the invasiveness and metastasis of tumors. This study aimed to investigate the function and clinical significance of ACTB in pan-cancer. The role of ACTB for prognosis and immune regulation across 33 tumors was explored based on the datasets of gene expression omnibus and the cancer genome atlas. Differential expression of ACTB was found between cancer and adjacent normal tissues, and significant associations was found between ACTB expression and prognosis of tumor patients. In most cancers, ACTB expression was associated with immune cells infiltration, immune checkpoints and other immune modulators. Relevance between ACTB and metastasis and invasion was identified in various types of cancers by CancerSEA. Moreover, focal adhesion and actin regulation-associated pathways were included in the functional mechanisms of ACTB. The expression of ACTB was verified by quantitative real-time polymerase chain reaction. Knockdown of ACTB inhibited head and neck squamous carcinoma cell migration and invasion by NF-κB and Wnt/β-catenin pathways. Our first pan-cancer study of ACTB offers insight into the prognostic and immunological roles of ACTB across different tumors, indicating ACTB may be a potential biomarker for poor prognosis and immune infiltration in cancers, and the role of ACTB as a reference gene in cancers was challenged.
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Affiliation(s)
- Yuxi Gu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haosen Lian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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