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Yang JJ, Yang YJ, Gu YL, Tong L, Liu YF, Zhang JG. High SNRPA1 expression leads to poor prognosis in patients with lung adenocarcinoma. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:719-732. [PMID: 37277111 PMCID: PMC10435942 DOI: 10.1111/crj.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
OBJECTIVE SNRPA1, a subunit of spliceosome complex, has been implicated in diverse cancers, while its biological effect in LUAD remains elusive. Therefore, we sought to decipher the relationship between SNRPA1 expression and the prognosis of patients with LUAD and reveal the underlying molecular mechanism. MATERIALS AND METHODS Based on the clinical data from TCGA databases, the multivariate Cox model was constructed to screen the prognostic value of SNRPA1. qRT-PCR and immunohistochemical staining were used to examine SNRPA1 mRNA and protein expression in LUAD. The effect of SNRPA1 on LUAD cell proliferation, migration, and epithelial mesenchymal transformation were examined using colony formation assays, wound healing, and western blot assays, respectively. Finally, the influence of SNRPA1 on LUAD immune microenvironment were validated from the Tumor Immune Estimation Resource database. RESULTS SNRPA1 was significantly upregulated in both LUAD tissues and cell lines, and highly expressed SNRPA1 contributed to poor prognosis of LUAD patients. In vitro, SNRPA1 knockdown inhibited the proliferation and migration, as well as delayed the EMT differentiation of LUAD cells. Lastly, SNRPA1 was found to be positively associated with immune infiltration and some immune-check-point markers. CONCLUSIONS Our findings indicate that SNRPA1 may be a new biomarker for prognostic prediction and a potential therapeutic target in the treatment of LUAD.
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Affiliation(s)
- Juan Juan Yang
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityNantongJiangsuChina
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yu Jia Yang
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yi Lu Gu
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Li Tong
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yi Fei Liu
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Jian Guo Zhang
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
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Grandt CL, Brackmann LK, Poplawski A, Schwarz H, Marini F, Hankeln T, Galetzka D, Zahnreich S, Mirsch J, Spix C, Blettner M, Schmidberger H, Marron M. Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls. Front Oncol 2023; 13:1158176. [PMID: 37182169 PMCID: PMC10174438 DOI: 10.3389/fonc.2023.1158176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Long non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular. Methods Primary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function. Results After irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation). Discussion For the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.
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Affiliation(s)
- Caine Lucas Grandt
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
- Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany
- *Correspondence: Caine Lucas Grandt,
| | - Lara Kim Brackmann
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heike Schwarz
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Zahnreich
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Claudia Spix
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maria Blettner
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
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Yang Y, Zhang S, Guo L. Characterization of Cell Cycle-Related Competing Endogenous RNAs Using Robust Rank Aggregation as Prognostic Biomarker in Lung Adenocarcinoma. Front Oncol 2022; 12:807367. [PMID: 35186743 PMCID: PMC8853726 DOI: 10.3389/fonc.2022.807367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD), one of the most common pathological subtypes in lung cancer, has been of concern because it is the leading cause of cancer-related deaths. Due to its poor prognosis, to identify a prognostic biomarker, this study performed an integrative analysis to screen curial RNAs and discuss their cross-talks. The messenger RNA (mRNA) profiles were primarily screened using robust rank aggregation (RRA) through several datasets, and these deregulated genes showed important roles in multiple biological pathways, especially for cell cycle and oocyte meiosis. Then, 31 candidate genes were obtained via integrating 12 algorithms, and 16 hub genes (containing homologous genes) were further screened according to the potential prognostic values. These hub genes were used to search their regulators and biological-related microRNAs (miRNAs). In this way, 10 miRNAs were identified as candidate small RNAs associated with LUAD, and then miRNA-related long non-coding RNAs (lncRNAs) were further obtained. In-depth analysis showed that 4 hub mRNAs, 2 miRNAs, and 2 lncRNAs were potential crucial RNAs in the occurrence and development of cancer, and a competing endogenous RNA (ceRNA) network was then constructed. Finally, we identified CCNA2/MKI67/KIF11:miR-30a-5p:VPS9D1-AS1 axis-related cell cycle as a prognostic biomarker, which provided RNA cross-talks among mRNAs and non-coding RNAs (ncRNAs), especially at the multiple isomiR levels that further complicated the coding–non-coding RNA regulatory network. Our findings provide insight into complex cross-talks among diverse RNAs particularly involved in isomiRs, which will enrich our understanding of mRNA–ncRNA interactions in coding–non-coding RNA regulatory networks and their roles in tumorigenesis.
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Affiliation(s)
- Yifei Yang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Shiqi Zhang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, China
- *Correspondence: Li Guo,
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Weng C, Wang L, Liu G, Guan M, Lu L. Identification of a N6-Methyladenosine (m6A)-Related lncRNA Signature for Predicting the Prognosis and Immune Landscape of Lung Squamous Cell Carcinoma. Front Oncol 2021; 11:763027. [PMID: 34868980 PMCID: PMC8637334 DOI: 10.3389/fonc.2021.763027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background m6A-related lncRNAs emerged as potential targets for tumor diagnosis and treatment. This study aimed to identify m6A-regulated lncRNAs in lung squamous cell carcinoma (LUSC) patients. Materials and Methods RNA sequencing and the clinical data of LUSC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The m6A-related lncRNAs were identified by using Pearson correlation assay. Univariate and multivariate Cox regression analyses were utilized to construct a risk model. The performance of the risk model was validated using Kaplan–Meier survival analysis and receiver operating characteristics (ROC). Immune estimation of LUSC was downloaded from TIMER, and the correlations between the risk score and various immune cells infiltration were analyzed using various methods. Differences in immune functions and expression of immune checkpoint inhibitors and m6A regulators between high-risk and low-risk groups were further explored. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were utilized to explore the biological functions of AL122125.1. Results A total of 351 m6A-related lncRNAs were obtained from TCGA. Seven lncRNAs demonstrated prognostic values. A further multivariate Cox regression assay constructed a risk model consisting of two lncRNAs (AL122125.1 and HORMAD2-AS1). The Kaplan–Meier analysis and area under the curve indicated that this risk model could be used to predict the prognosis of LUSC patients. The m6A-related lncRNAs were immune-associated. There were significant correlations between risk score and immune cell infiltration, immune functions, and expression of immune checkpoint inhibitors. Meanwhile, there were significant differences in the expression of m6A regulators between the high- and low-risk groups. Moreover, GO and KEGG analyses revealed that the upregulated expression of AL122125.1 was tumor-related. Conclusion In this study, we constructed an m6A-related lncRNA risk model to predict the survival of LUSC patients. This study could provide a novel insight to the prognosis and treatment of LUSC patients.
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Affiliation(s)
- Chengyin Weng
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lina Wang
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guolong Liu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mingmei Guan
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Lu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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Tsai JC, Saad OA, Magesh S, Xu J, Lee AC, Li WT, Chakladar J, Fuster MM, Chang EY, Wang-Rodriguez J, Ongkeko WM. Tobacco Smoke and Electronic Cigarette Vapor Alter Enhancer RNA Expression That Can Regulate the Pathogenesis of Lung Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13164225. [PMID: 34439379 PMCID: PMC8391195 DOI: 10.3390/cancers13164225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary It is well established that tobacco smoke is the key player in lung squamous cell carcinoma (LUSC) pathogenesis, and there is growing evidence that electronic cigarette (e-cigarette) vapor may also cause LUSC. Recently, several studies have associated tobacco smoke with differential enhancer RNA (eRNA) expression. However, the effects of tobacco smoke and e-cigarette vapor on eRNA expression in correlation to LUSC outcomes have not been fully elucidated. This study demonstrates that tobacco smoke and e-cigarette vapor may decrease DNA methylation and increase chromosomal alterations at key sites, which ultimately upregulate the expression of oncogenic eRNAs and downregulate the expression of tumor-suppressing eRNAs. Subsequently, we demonstrate that these eRNAs may have altered interactions with immune cells to promote LUSC pathogenesis and reduced patient survival. We hope our results can be validated in future studies, and the key eRNAs we identified may be used as effective targets for more specialized treatments for smoking-mediated LUSC. Abstract Tobacco is the primary etiologic agent in worsened lung squamous cell carcinoma (LUSC) outcomes. Meanwhile, it has been shown that etiologic agents alter enhancer RNAs (eRNAs) expression. Therefore, we aimed to identify the effects of tobacco and electronic cigarette (e-cigarette) use on eRNA expression in relation to LUSC outcomes. We extracted eRNA counts from RNA-sequencing data of tumor/adjacent normal tissue and before/after e-cigarette tissue from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), respectively. Tobacco-mediated LUSC eRNAs were correlated to patient survival, clinical variables, and immune-associated elements. eRNA expression was also correlated to mutation rates through the Repeated Evaluation of Variables Conditional Entropy and Redundance (REVEALER) algorithm and methylated sites through methylationArrayAnalysis. Differential expression analysis was then completed for the e-cigarette data to compare with key tobacco-mediated eRNAs. We identified 684 downregulated eRNAs and 819 upregulated eRNAs associated with tobacco-mediated LUSC, specifically, with the cancer pathological stage. We also observed a decrease in immune cell abundance in tobacco-mediated LUSC. Yet, we found an increased association of eRNA expression with immune cell abundance in tobacco-mediated LUSC. We identified 16 key eRNAs with significant correlations to 8 clinical variables, implicating these eRNAs in LUSC malignancy. Furthermore, we observed that these 16 eRNAs were highly associated with chromosomal alterations and reduced CpG site methylation. Finally, we observed large eRNA expression upregulation with e-cigarette use, which corresponded to the upregulation of the 16 key eRNAs. Our findings provide a novel mechanism by which tobacco and e-cigarette smoke influences eRNA interactions to promote LUSC pathogenesis and provide insight regarding disease progression at a molecular level.
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Affiliation(s)
- Joseph C. Tsai
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Omar A. Saad
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Shruti Magesh
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jingyue Xu
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Abby C. Lee
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Mark M. Fuster
- VA San Diego Healthcare System, Medical and Research Sections, La Jolla, San Diego, CA 92161, USA;
- Department of Medicine, Division of Pulmonary and Critical Care, University of California, La Jolla, San Diego, CA 92037, USA
| | - Eric Y. Chang
- Department of Radiology, University of California, San Diego, CA 92093, USA;
- Radiology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jessica Wang-Rodriguez
- Department of Pathology, UC San Diego School of Medicine, San Diego, CA 92093, USA;
- Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Weg M. Ongkeko
- Department of Surgery, Division of Otolaryngology—Head and Neck Surgery, UC San Diego School of Medicine, San Diego, CA 92093, USA; (J.C.T.); (O.A.S.); (S.M.); (J.X.); (A.C.L.); (W.T.L.); (J.C.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
- Correspondence: ; Tel.: +1-(858)-552-8585-X-7165
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