1
|
He M, Wang L, Yue Z, Feng C, Dai G, Jiang J, Huang H, Ji Q, Zhou M, Li D, Chai W. Development and validation of glycosyltransferase related-gene for the diagnosis and prognosis of head and neck squamous cell carcinoma. Aging (Albany NY) 2024; 16:1750-1766. [PMID: 38244579 PMCID: PMC10866440 DOI: 10.18632/aging.205455] [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: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous cancer characterized by difficulties in early diagnosis and outcome prediction. Aberrant glycosylated structures produced by the aberrant expression of glycosyltransferases are prevalent in HNSCC. In this study, we aim to construct glycosyltransferase-related gene signatures with diagnostic and prognostic value to better stratify patients with HNSCC and improve their diagnosis and prognosis. METHODS Bioinformatic tools were used to process data of patients with HNSCC from The Cancer Genome Atlas (TCGA) database. The prognostic model was formatted using univariate and multivariate Cox regression methods, while the diagnostic signature was constructed using support vector machine (SVM) and LASSO analysis. The results were verified using the Gene Expression Omnibus (GEO) cohort. The tumor microenvironment and benefits of immune checkpoint inhibitor (ICI) therapy in subgroups defined by glycosyltransferase-related genes were analyzed. Molecular biology experiments, including western blotting, cell counting kit (CCK)-8, colony formation, wound healing, and Transwell assays, were conducted to confirm the oncogenic function of beta-1,4-galactosyltransferase 3 (B4GALT3) in HNSCC. RESULTS We established a five-gene prognostic signature and a 15-gene diagnostic model. Based on the median risk score, patients with low risk had longer overall survival than those in the high-risk group, which was consistent with the results of the GEO cohort. The concrete results suggested that high-risk samples were related to a high tumor protein (TP)53 mutation rate, high infiltration of resting memory cluster of differentiation (CD)4 T cells, resting natural killer (NK) cells, and M0 macrophages, and benefited from ICI therapy. In contrast, the low-risk subgroup was associated with a low TP53 mutation rate; and high infiltration of naive B cells, plasma cells, CD8 T cells, and resting mast cells; and benefited less from ICI therapy. In addition, the diagnostic model had an area under curve (AUC) value of 0.997 and 0.978 in the training dataset and validation cohort, respectively, indicating the high diagnostic potential of the model. Ultimately, the depletion of B4GALT3 significantly hindered the proliferation, migration, and invasion of HNSCC cells. CONCLUSIONS We established two new biomarkers that could provide clinicians with diagnostic, prognostic, and treatment guidance for patients with HNSCC.
Collapse
Affiliation(s)
- Miao He
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Li Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Zihan Yue
- Second Clinical College, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, Hubei, China
| | - Chunbo Feng
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Guosheng Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Jinsong Jiang
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Hui Huang
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Qingjun Ji
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Minglang Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Dapeng Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| | - Wei Chai
- Department of Otorhinolaryngology, Head and Neck Surgery, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
- Scientific Research and Experiment Center, The People’s Hospital of Bozhou, Bozhou 236000, Anhui, China
| |
Collapse
|
2
|
Yuan LY, Chen X, Pan KW, He Y, Li HY, Yu DS. Bioinformatic analysis and verification of a lipid metabolism-related long noncoding RNA prognostic signature for head and neck squamous cell carcinoma. Cell Signal 2023; 112:110903. [PMID: 37813294 DOI: 10.1016/j.cellsig.2023.110903] [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: 06/30/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Both lipid metabolism reprogramming and lncRNAs exert effects on tumor development. We aimed to predict the prognosis of head and neck squamous cell carcinoma (HNSCC) based on lipid metabolism-related (LR)-lncRNAs. METHODS LR-lncRNAs were determined from the RNA-ref profiles of HNSCC samples in The Cancer Genome Atlas (TCGA). The prognostic model was established by univariate Cox and Lasso regression analysis. Clinical relevance and predictive accuracy were investigated, and external validation was also performed in the Gene Expression Omnibus (GEO) cohort. Tumor immune infiltration and relevant functional analysis, including the association of autophagy with prognostic signatures, were conducted through single-sample gene set enrichment analysis (ssGSEA). The regulatory network of candidate LR-lncRNAs was investigated via coexpression, ceRNA and cis/trans acting interactions. Potential genes were selected through qRT-PCR analysis, and their effects on tumor biological activities and autophagic activity were explored after gene knockdown. RESULTS A total of 222 LR-lncRNAs were identified. Among the 41 genes with prognostic significance, 17 lncRNAs were eligible for the risk model. Patients in the high-risk group had a poorer prognosis than those in the low-risk group, and the risk score was found to be positively associated with tumor microenvironment infiltration via multiple algorithms. Furthermore, improved prognosis was found in patients with high autophagic scores and low risk scores, and autophagy-related genes such as PINK1 and CCL2 showed significantly lower expression in the low-risk group. The expression of immune checkpoint genes such as CD28, CTLA4 and PDCD1 decreased dramatically in the high-risk group. The target genes of candidate lncRNAs were confirmed, such as ENO2 and PPAR-gamma. Furthermore, MIR4435-2HG was the most significantly overexpressed lncRNA in HNSCC cell lines and tumor samples, which could promote proliferation and migration and inhibit apoptosis. Additionally, MIR4435-2HG silencing activated autophagy by increasing LC3B expression. CONCLUSION This study constructed an LR-lncRNA prognostic signature for HNSCC and indicated its relationships with tumor immunity and autophagy, which provides a promising future for LR-lncRNA-oriented prognostic tools and therapeutic targets.
Collapse
Affiliation(s)
- Ling-Yu Yuan
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xun Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Kuang-Wu Pan
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yi He
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hong-Yu Li
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Dong-Sheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
3
|
Wu D, Tian S, Zhu W. Modulating multidrug resistance to drug-based antitumor therapies through NF-κB signaling pathway: mechanisms and perspectives. Expert Opin Ther Targets 2023; 27:503-515. [PMID: 37314372 DOI: 10.1080/14728222.2023.2225767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Despite the advances made in cancer treatment in the past decades, therapeutic efficacy is still quite challenging, partially due to the emergence of multidrug resistance (MDR). It is crucial to decipher the underlying mechanisms of resistance in order to develop new therapeutic strategies for cancer patients. Previous studies have shown that activation of nuclear factor-κB (NF-κB) plays key roles in various cellular processes including proliferation, anti-apoptosis, metastasis, invasion, and chemoresistance. AREAS COVERED In this review, we conduct an integrated analysis of the evidence suggesting the vital roles of the NF-κB signaling pathway in MDR during chemotherapy, immunotherapy, endocrine, and targeted therapy. A literature search was performed on NF-κB and drug resistance in PubMed up to February 2023. EXPERT OPINION This review summarizes that the NF-κB signaling pathway exhibits a crucial role in enhancing drug resistance in chemotherapy, immunotherapy, endocrine, and targeted therapy. The application of combination therapy with existing antineoplastic drugs and a safe NF-κB inhibitor could become a promising strategy in cancer treatment. A better understanding of the pathway and mechanisms of drug resistance may help exploit safer and more effective NF-κB-targeting agents for clinical use in the future.
Collapse
Affiliation(s)
- Dapeng Wu
- Department of Oncology, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Sai Tian
- Department of Pediatric Clinic, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Wenjing Zhu
- Clinical Research Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
- Department of Respiratory and Critical Care Medicine, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| |
Collapse
|
4
|
Li M, Mao S, Li L, Wei M. Hypoxia-related LncRNAs signature predicts prognosis and is associated with immune infiltration and progress of head and neck squamous cell carcinoma. Biochem Biophys Rep 2022; 31:101304. [PMID: 35818500 PMCID: PMC9270212 DOI: 10.1016/j.bbrep.2022.101304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 12/21/2022] Open
Abstract
Background Disclosing prognostic information is necessary to enable good treatment selection and improve patient outcomes. Previous studies suggest that hypoxia is associated with an adverse prognosis in patients with HNSCC and that long non-coding RNAs (lncRNAs) show functions in hypoxia-associated cancer biology. Nevertheless, the understanding of lncRNAs in hypoxia related HNSCC progression remains confusing. Methods Data were downloaded from TCGA and GEO database. Bioinformatic tools including R packages GEOquery, limma, pheatmap, ggplot2, clusterProfiler, survivalROC and survcomp and LASSO cox analysis were utilized. Si-RNA transfection, CCK8 and real-time quantified PCR were used in functional study. Results GEO data (GSE182734) revealed that lncRNA regulation may be important in hypoxia related response of HNSCC cell lines. Further analysis in TCGA data identified 314 HRLs via coexpression analysis between differentially expressed lncRNAs and hypoxia-related mRNAs. 23 HRLs were selected to build the prognosis predicting model using lasso Cox regression analyses. Our model showed excellent performance in predicting survival outcomes among patients with HNSCC in both the training and validation sets. We also found that the risk scores were related to tumor stage and to tumor immune infiltration. Moreover, LINC01116 were selected as a functional study target. The knockdown of LINC01116 significantly inhibited the proliferation of HNSCC cells and effected the hypoxia induced immune and the NF-κB/AKT signaling. Conclusions Data analysis of large cohorts and functional experimental validation in our study suggest that hypoxia related lncRNAs play an important role in the progression of HNSCC, and its expression model can be used for prognostic prediction. NcRNAs regulations showed significance in hypoxia related response in HNSCC. 314 lncRNAs coexpressed with hypoxia marker genes were identified as HRLs. An effective HRLs prognosis prediction model had been constructed and validated. Immune cells and pathways paly roles in hypoxia related progress of HNSCC. LINC01116 regulates HNSCC through hypoxia related immune and NF-κB/AKT signaling.
Collapse
Affiliation(s)
- Minhan Li
- School of Stomatology, Shandong University, Jinan, Shandong, China
| | - Shaowei Mao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
| | - Lixing Li
- Department of General Surgery, Shanghai Xuhui District Central Hospital, Shanghai, China
| | - Muyun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, China
| |
Collapse
|
5
|
Zhang Q, Liu X, Chen Z, Zhang S. Novel GIRlncRNA Signature for Predicting the Clinical Outcome and Therapeutic Response in NSCLC. Front Pharmacol 2022; 13:937531. [PMID: 35991889 PMCID: PMC9382191 DOI: 10.3389/fphar.2022.937531] [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: 05/06/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Non–small cell lung cancer (NSCLC) is highly malignant with driver somatic mutations and genomic instability. Long non-coding RNAs (lncRNAs) play a vital role in regulating these two aspects. However, the identification of somatic mutation-derived, genomic instability-related lncRNAs (GIRlncRNAs) and their clinical significance in NSCLC remains largely unexplored. Methods: Clinical information, gene mutation, and lncRNA expression data were extracted from TCGA database. GIRlncRNAs were screened by a mutator hypothesis-derived computational frame. Co-expression, GO, and KEGG enrichment analyses were performed to investigate the biological functions. Cox and LASSO regression analyses were performed to create a prognostic risk model based on the GIRlncRNA signature (GIRlncSig). The prediction efficiency of the model was evaluated by using correlation analyses with mutation, driver gene, immune microenvironment contexture, and therapeutic response. The prognostic performance of the model was evaluated by external datasets. A nomogram was established and validated in the testing set and TCGA dataset. Results: A total of 1446 GIRlncRNAs were selected from the screen, and the established GIRlncSig was used to classify patients into high- and low-risk groups. Enrichment analyses showed that GIRlncRNAs were mainly associated with nucleic acid metabolism and DNA damage repair pathways. Cox analyses further identified 19 GIRlncRNAs to construct a GIRlncSig-based risk score model. According to Cox regression and stratification analyses, 14 risk lncRNAs (AC023824.3, AC013287.1, AP000829.1, LINC01611, AC097451.1, AC025419.1, AC079949.2, LINC01600, AC004862.1, AC021594.1, MYRF-AS1, LINC02434, LINC02412, and LINC00337) and five protective lncRNAs (LINC01067, AC012645.1, AL512604.3, AC008278.2, and AC089998.1) were considered powerful predictors. Analyses of the model showed that these GIRlncRNAs were correlated with somatic mutation pattern, immune microenvironment infiltration, immunotherapeutic response, drug sensitivity, and survival of NSCLC patients. The GIRlncSig risk score model demonstrated good predictive performance (AUCs of ROC for 10-year survival was 0.69) and prognostic value in different NSCLC datasets. The nomogram comprising GIRlncSig and tumor stage exhibited improved robustness and feasibility for predicting NSCLC prognosis. Conclusion: The newly identified GIRlncRNAs are powerful biomarkers for clinical outcome and prognosis of NSCLC. Our study highlights that the GIRlncSig-based score model may be a useful tool for risk stratification and management of NSCLC patients, which deserves further evaluation in future prospective studies.
Collapse
Affiliation(s)
- Qiangzhe Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Xicheng Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhinan Chen
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi’an, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin, China
- *Correspondence: Sihe Zhang, , https://orcid.org/0000-0002-8923-1993
| |
Collapse
|
6
|
Han Y, Ding Z, Chen B, Liu Y, Liu Y. A Novel Inflammatory Response–Related Gene Signature Improves High-Risk Survival Prediction in Patients With Head and Neck Squamous Cell Carcinoma. Front Genet 2022; 13:767166. [PMID: 35480305 PMCID: PMC9035793 DOI: 10.3389/fgene.2022.767166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/07/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a highly prevalent and malignant tumor that is difficult to effectively prognosticate outcomes. Recent reports have suggested that inflammation is strongly related to tumor progression, and several biomarkers linked to inflammation have been demonstrated to be useful for making a prognosis. The goal of this research was to explore the relevance between the inflammatory-related genes and HNSCC prognosis. Methods: The clinical information and gene expression data of patients with HNSCC were acquired from publicly available data sources. A multigene prognostic signature model was constructed in The Cancer Genome Atlas and verified in the Gene Expression Omnibus database. According to the risk score calculated for each patient, they were divided into low- and high-risk groups based on the median. The Kaplan–Meier survival curve and receiver operating characteristic curve were applied to determine the prognostic value of the risk model. Further analysis identified the independent prognostic factors, and a prognostic nomogram was built. The relationship between tumor immune infiltration status and risk scores was investigated using Spearman correlation analysis. Finally, to confirm the expression of genes in HNSCC, quantitative real-time polymerase chain reaction (qRT-PCR) was performed. Results: A prognostic model consisting of 14 inflammatory-related genes was constructed. The samples with a high risk had an apparently shorter overall survival than those with a low risk. Independent prognostic analysis found that risk scores were a separate prognostic factor in HNSCC patients. Immune infiltration analysis suggested that the abundance of B cells, CD8 T cells, M2 macrophages, myeloid dendritic cells, and monocytes in the low-risk group was higher, while that of M0, M1 macrophages, and resting NK cells was obviously higher in the high-risk group. The risk scores were related to chemotherapeutic sensitivity and the expression of several immune checkpoint genes. Moreover, CCL22 and IL10 were significantly higher in HNSCC tissues, as determined by qRT-PCR. Conclusion: Taken together, we constructed a novel inflammatory response–related gene signature, which may be used to estimate outcomes for patients with HNSCC and may be developed into a powerful tool for forecasting the efficacy of immunotherapeutic and chemotherapeutic drugs for HNSCC.
Collapse
Affiliation(s)
- Yanxun Han
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Zhao Ding
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Bangjie Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuchen Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yehai Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Yehai Liu,
| |
Collapse
|
7
|
Chen Y, Zhao Y, Lu R, Zhao H, Guo Y. Identification and Validation of a Novel Genomic Instability-Associated Long Non-Coding RNA Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2022; 9:787766. [PMID: 35127708 PMCID: PMC8812830 DOI: 10.3389/fcell.2021.787766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive malignant cancers worldwide, and accurate prognostic models are urgently needed. Emerging evidence revealed that long non-coding RNAs (lncRNAs) are related to genomic instability. We sought to identify and validate a genomic instability-associated lncRNA prognostic signature to assess HNSCC patient survival outcomes. Methods: RNA-sequencing data, somatic mutation files, and patient clinical data were downloaded from The Cancer Genome Atlas database. A total of 491 patients with completely clinical files were randomly divided into training and testing sets. In the training set, genomic instability-associated lncRNAs were screened through univariate Cox regression analyses and least absolute shrinkage and selection operator regression analyses to build a genomic instability-associated lncRNA signature (GILncSig). In addition, time-dependent receiver operating characteristic (ROC) curve, Kaplan-Meier survival curve, and clinical stratification analyses were used to evaluate the signature’s reliability. Finally, in situ hybridization experiments were performed to validate GILncSig expression levels between adjacent non-tumor tissues and tumor tissues from HNSCC patients. Results: Four genomic instability-associated lncRNAs (AC023310.4, AC091729.1, LINC01564, and MIR3142HG) were selected for the prognostic signature. The model was successfully validated using the testing cohort. ROC analysis demonstrated its strong predictive ability for HNSCC prognosis. Univariate and multivariate Cox analyses revealed that the GILncSig was an independent predictor of prognosis. HNSCC patients with a low-risk score showed a substantially better prognosis than the high-risk groups. The in situ hybridization experiments using human HNSCC tissue revealed high GILncSig expression in HNSCC tissues compared with adjacent non-tumor tissues. Conclusion: We developed a novel GILncSig for prognosis prediction in HNSCC patients, and the components of that signature might be therapeutic targets for HNSCC.
Collapse
Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ruohuang Lu
- Department of Stomatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose and Throat Hospital of Fudan University, Shanghai, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- *Correspondence: Han Zhao, ; Yue Guo,
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Han Zhao, ; Yue Guo,
| |
Collapse
|
8
|
He S, Li JF, Tian H, Sang Y, Yang XJ, Guo GX, Yang JE. A long non-coding RNA-based signature predicts early recurrence in hepatocellular carcinoma. Cancer Biomark 2021; 34:309-318. [PMID: 34957996 DOI: 10.3233/cbm-210193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Early recurrence is the main obstacle for long-term survival of hepatocellular carcinoma (HCC) patients after curative resection. OBJECTIVE We aimed to develop a long non-coding RNA (lncRNA) based signature to predict early recurrence. METHODS Using bioinformatics analysis and quantitative reverse transcription PCR (RT-qPCR), we screened for lncRNA candidates that were abnormally expressed in HCC. The expression levels of candidate lncRNAs were analyzed in HCC tissues from 160 patients who underwent curative resection, and a risk model for the prediction of recurrence within 1 year (early recurrence) of HCCs was constructed with linear support vector machine (SVM). RESULTS A lncRNA-based classifier (Clnc), which contained nine differentially expressed lncRNAs including AF339810, AK026286, BC020899, HEIH, HULC, MALAT1, PVT1, uc003fpg, and ZFAS1 was constructed. In the test set, this classifier reliably predicted early recurrence (AUC, 0.675; sensitivity, 72.0%; specificity, 63.1%) with an odds ratio of 4.390 (95% CI, 2.120-9.090). Clnc showed higher accuracy than traditional clinical features, including tumor size, portal vein tumor thrombus (PVTT) in predicting early recurrence (AUC, 0.675 vs 0.523 vs 0.541), and had much higher sensitivity than Barcelona Clinical Liver Cancer (BCLC; 72.0% vs 50.0%), albeit their AUCs were comparable (0.675 vs 0.678). Moreover, combining Clnc with BCLC significantly increased the AUC, compared with Clnc or BCLC alone in predicting early recurrence (all P< 0.05). Finally, logistic and Cox regression analysis suggested that Clnc was an independent prognostic factor and associated with the early recurrence and recurrence-free survival of HCC patients after resection, respectively (all P= 0.001). CONCLUSIONS Our lncRNA-based classifier Clnc can predict early recurrence of patients undergoing surgical resection of HCC.
Collapse
Affiliation(s)
- Shuai He
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jin-Feng Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hao Tian
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ye Sang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Jing Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Gui-Xin Guo
- National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jin-E Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
9
|
Wang E, Li Y, Ming R, Wei J, Du P, Zhou P, Zong S, Xiao H. The Prognostic Value and Immune Landscapes of a m 6A/m 5C/m 1A-Related LncRNAs Signature in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:718974. [PMID: 34917609 PMCID: PMC8670092 DOI: 10.3389/fcell.2021.718974] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Background: N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A) are the main RNA methylation modifications involved in the progression of cancer. However, it is still unclear whether m6A/m5C/m1A-related long non-coding RNAs (lncRNAs) affect the prognosis of head and neck squamous cell carcinoma (HNSCC). Methods: We summarized 52 m6A/m5C/m1A-related genes, downloaded 44 normal samples and 501 HNSCC tumor samples with RNA-seq data and clinical information from The Cancer Genome Atlas (TCGA) database, and then searched for m6A/m5C/m1A-related genes co-expressed lncRNAs. We adopt the least absolute shrinkage and selection operator (LASSO) Cox regression to obtain m6A/m5C/m1A-related lncRNAs to construct a prognostic signature of HNSCC. Results: This prognostic signature is based on six m6A/m5C/m1A-related lncRNAs (AL035587.1, AC009121.3, AF131215.5, FMR1-IT1, AC106820.5, PTOV1-AS2). It was found that the high-risk subgroup has worse overall survival (OS) than the low-risk subgroup. Moreover, the results showed that most immune checkpoint genes were significantly different between the two risk groups (p < 0.05). Immunity microenvironment analysis showed that the contents of NK cell resting, macrophages M2, and neutrophils in samples of low-risk group were significantly lower than those of high-risk group (p < 0.05), while the contents of B cells navie, plasma cells, and T cells regulatory (Tregs) were on the contrary (p < 0.05). In addition, patients with high tumor mutational burden (TMB) had the worse overall survival than those with low tumor mutational burden. Conclusion: Our study elucidated how m6A/m5C/m1A-related lncRNAs are related to the prognosis, immune microenvironment, and TMB of HNSCC. In the future, these m6A/m5C/m1A-related lncRNAs may become a new choice for immunotherapy of HNSCC.
Collapse
Affiliation(s)
- Enhao Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ruijie Ming
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Wei
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyu Du
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shimin Zong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongjun Xiao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
10
|
Cheng S, Guo J, Wang D, Fang Q, Liu Y, Xie W, Zhang Y, Li C. A Novel Three-LncRNA Signature Predicting Tumor Recurrence in Nonfunctioning Pituitary Adenomas. Front Genet 2021; 12:754503. [PMID: 34745223 PMCID: PMC8564111 DOI: 10.3389/fgene.2021.754503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
The nonfunctioning pituitary adenoma (NFPA) recurrence rate is relatively high after surgical resection. Here, we constructed effective long noncoding RNA (lncRNA) signatures to predict NFPA prognosis. LncRNAs expression microarray sequencing profiles were obtained from 66 NFPAs. Sixty-six patients were randomly separated into a training (n = 33) and test group (n = 33). Univariable Cox regression and a machine learning algorithm was used to filter lncRNAs. Time-dependent receiver operating characteristic (ROC) analysis was performed to improve the prediction signature. Three lncRNAs (LOC101927765, RP11-23N2.4 and RP4-533D7.4) were included in a prognostic signature with high prediction accuracy for tumor recurrence, which had the largest area under ROC curve (AUC) value in the training/test group (AUC = 0.87/0.73). The predictive ability of the signature was validated by Kaplan-Meier survival analysis. A signature-based risk score model divied patients into two risk group, and the recurrence-free survival rates of the groups were significantly different (log-rank p < 0.001). In addition, the ROC analysis showed that the lncRNA signature predictive ability was significantly better than that of age in the training/testing/entire group (AUC = 0.87/0.726/0.798 vs. AUC = 0.683/0.676/0.679). We constructed and verified a three-lncRNA signature predictive of recurrence, suggesting potential therapeutic targets for NFPA.
Collapse
Affiliation(s)
- Sen Cheng
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Dawei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Qiuyue Fang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yulou Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yazhuo Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Chuzhong Li
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Institute for Brain Disorders Brain Tumor Center, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| |
Collapse
|
11
|
Ma B, Jiang H, Luo Y, Liao T, Xu W, Wang X, Dong C, Ji Q, Wang Y. Tumor-Infiltrating Immune-Related Long Non-Coding RNAs Indicate Prognoses and Response to PD-1 Blockade in Head and Neck Squamous Cell Carcinoma. Front Immunol 2021; 12:692079. [PMID: 34737735 PMCID: PMC8562720 DOI: 10.3389/fimmu.2021.692079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) in immune cells play critical roles in tumor cell–immune cell interactions. This study aimed to characterize the landscape of tumor-infiltrating immune-related lncRNAs (Ti-lncRNAs) and reveal their correlations with prognoses and immunotherapy response in head and neck squamous cell carcinoma (HNSCC). We developed a computational model to identify Ti-lncRNAs in HNSCC and analyzed their associations with clinicopathological features, molecular alterations, and immunotherapy response. A signature of nine Ti-lncRNAs demonstrated an independent prognostic factor for both overall survival and disease-free survival among the cohorts from Fudan University Shanghai Cancer Center, The Cancer Genome Atlas, GSE41613, and GSE42743. The Ti-lncRNA signature scores in immune cells showed significant associations with TP53 mutation, CDKN2A mutation, and hypoxia. Inferior signature scores were enriched in patients with high levels of PDCD1 and CTLA4 and high expanded immune gene signature (IGS) scores, who displayed good response to PD-1 blockade in HNSCC. Consistently, superior clinical response emerged in melanoma patients with low signature scores undergoing anti-PD-1 therapy. Moreover, the Ti-lncRNA signature was a prognostic factor independent of PDCD1, CTLA4, and the expanded IGS score. In conclusion, tumor-infiltrating immune profiling identified a prognostic Ti-lncRNA signature indicative of clinical response to PD-1 blockade in HNSCC.
Collapse
Affiliation(s)
- Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyi Jiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Luo
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weibo Xu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuanpeng Dong
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Biohealth Informatics, School of Informatics and Computing, Indiana University, Indianapolis, IN, United States
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
12
|
Chen L, Cai Z, Lyu K, Cai Z, Lei W. A novel immune-related long non-coding RNA signature improves the prognosis prediction in the context of head and neck squamous cell carcinoma. Bioengineered 2021; 12:2311-2325. [PMID: 34167440 PMCID: PMC8806432 DOI: 10.1080/21655979.2021.1943284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The tumor immune microenvironment plays an important role in head and neck squamous cell carcinoma (HNSCC). Reliable prognostic signatures able to accurately predict the immune landscape and survival rate of HNSCC patients are crucial to ensure an individualized/effective treatment. Here, we used HNSCC transcriptomic and clinical data retrieved from The Cancer Genome Atlas and identified differentially expressed immune-related long non-coding RNAs (DEirlncRNAs). DEirlncRNA pairs were recognized using univariate analysis. Cox and Lasso regression analyses were used to determine the association between DEirlncRNA pairs and the patients’ overall survival and build the prediction model. Receiver operating characteristic curves and Kaplan–Meier survival curves were used to validate the prediction model. We then reevaluated the model based on the clinical factors, tumor-infiltrating immune cells, chemotherapeutic efficacy, and immunosuppression biomarkers. We built a risk score model based on 18 DEirlncRNA pairs, closely related to the overall survival of patients (hazard ratio: 1.376; 95% confidence interval: 1.302–1.453; P < 0.0001). Compared with two recently published lncRNA signatures, our DEirlncRNA pair signature had a higher area under the curve, indicating better prognostic performance. Additionally, the signature score positively correlated with aggressive HNSCC outcomes (low immunity score, significantly reduced CD8 + T cell infiltration, and low expression of immunosuppression biomarkers). However, high-risk patients might have high chemosensitivity. Overall, the lncRNAs signature established here shows promising clinical prediction and the effective disclosure of the tumor immune microenvironment in HNSCC patients; therefore, such signature might help distinguish patients that could benefit from immunotherapy.
Collapse
Affiliation(s)
- Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Zhimou Cai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Kexing Lyu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Zhiwei Cai
- Guangzhou Brain Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Wenbin Lei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| |
Collapse
|
13
|
Jiang H, Ma B, Xu W, Luo Y, Lu Z, Liao T, Wang X, Wen S, Yang S, Wang Y. ASO Author Reflections: A Novel Three-lncRNA Signature Predictive of Prognoses of HNSCC Patients. Ann Surg Oncol 2020; 28:3407. [PMID: 33200328 DOI: 10.1245/s10434-020-09235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/18/2022]
Affiliation(s)
- Hongyi Jiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China. .,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Weibo Xu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yi Luo
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zhongwu Lu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xiao Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shishuai Wen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuwen Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| |
Collapse
|