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Ahmady F, Sharma A, Achuthan AA, Kannourakis G, Luwor RB. The Role of TIM-3 in Glioblastoma Progression. Cells 2025; 14:346. [PMID: 40072074 PMCID: PMC11899008 DOI: 10.3390/cells14050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 02/20/2025] [Accepted: 02/25/2025] [Indexed: 03/15/2025] Open
Abstract
Several immunoregulatory or immune checkpoint receptors including T cell immunoglobulin and mucin domain 3 (TIM-3) have been implicated in glioblastoma progression. Rigorous investigation over the last decade has elucidated TIM-3 as a key player in inhibiting immune cell activation and several key associated molecules have been identified both upstream and downstream that mediate immune cell dysfunction mechanistically. However, despite several reviews being published on other immune checkpoint molecules such as PD-1 and CTLA-4 in the glioblastoma setting, no such extensive review exists that specifically focuses on the role of TIM-3 in glioblastoma progression and immunosuppression. Here, we critically summarize the current literature regarding TIM-3 expression as a prognostic marker for glioblastoma, its expression profile on immune cells in glioblastoma patients and the exploration of anti-TIM-3 agents in glioblastoma pre-clinical models for potential clinical application.
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Affiliation(s)
- Farah Ahmady
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia; (F.A.); (G.K.)
- Federation University, Ballarat, VIC 3350, Australia
| | - Amit Sharma
- Department of Integrated Oncology, Center for Integrated Oncology (CIO) Bonn, University Hospital Bonn, 53127 Bonn, Germany;
- Department of Neurosurgery, University Hospital Bonn, 53127 Bonn, Germany
| | - Adrian A. Achuthan
- Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3350, Australia;
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia; (F.A.); (G.K.)
- Federation University, Ballarat, VIC 3350, Australia
| | - Rodney B. Luwor
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia; (F.A.); (G.K.)
- Federation University, Ballarat, VIC 3350, Australia
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3350, Australia
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211806, China
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Ju Y, Zhu F, Fang B. Biomarker Potential of LINC00313 in Head and Neck Squamous Cell Carcinoma: Correlation with Epithelial-Mesenchymal Transition and Immune Cell Infiltration. Int J Med Sci 2024; 21:921-936. [PMID: 38617010 PMCID: PMC11008489 DOI: 10.7150/ijms.93044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
Although LINC00313 is dysregulated in several tumors, its role in head and neck squamous cell carcinoma (HNSC) is not fully understood. The aim of this study was to analyze the role of LINC00313 in HNSC. The clinical information and LINC00313 expression data of HNSC were mined from the TCGA/GEO/cbioportal database. The correlation between LINC00313 expression and immune cell infiltration in HNSC tumors was analyzed by bioinformatics and gene enrichment analysis was performed. LINC00313 was silenced in HNSC cell lines, and changes at the genetic and molecular levels were verified through qRT-PCR and Western blotting. The researchers also validated its functional phenotype through a series of cell function experiments. The results showed that overexpression and copy number variation of LINC00313 in HNSC were associated with poorer prognosis. In addition, LINC00313 expression was significantly negatively correlated with immune cell infiltration. Silencing of LINC00313 in HNSC cells significantly reduced the rate of cell migration. LINC00313 may affect the progression of HNSC by regulating epithelial-mesenchymal transition. In conclusion, LINC00313 is a potential biomarker of HNSC prognosis and a potential target for immunotherapy.
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Affiliation(s)
- Yikun Ju
- Department of Plastic and Aesthetic (Burn) Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Zhu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bairong Fang
- Department of Plastic and Aesthetic (Burn) Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Yao S, Cao B, Li T, Kalos D, Yuan Y, Wang X. Prediction-oriented prognostic biomarker discovery with survival machine learning methods. NAR Genom Bioinform 2023; 5:lqad055. [PMID: 37332657 PMCID: PMC10273194 DOI: 10.1093/nargab/lqad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/21/2023] [Accepted: 05/26/2023] [Indexed: 06/20/2023] Open
Abstract
Identifying novel and reliable prognostic biomarkers for predicting patient survival outcomes is essential for deciding personalized treatment strategies for diseases such as cancer. Numerous feature selection techniques have been proposed to address the high-dimensional problem in constructing prediction models. Not only does feature selection lower the data dimension, but it also improves the prediction accuracy of the resulted models by mitigating overfitting. The performances of these feature selection methods when applied to survival models, on the other hand, deserve further investigation. In this paper, we construct and compare a series of prediction-oriented biomarker selection frameworks by leveraging recent machine learning algorithms, including random survival forests, extreme gradient boosting, light gradient boosting and deep learning-based survival models. Additionally, we adapt the recently proposed prediction-oriented marker selection (PROMISE) to a survival model (PROMISE-Cox) as a benchmark approach. Our simulation studies indicate that boosting-based approaches tend to provide superior accuracy with better true positive rate and false positive rate in more complicated scenarios. For demonstration purpose, we applied the proposed biomarker selection strategies to identify prognostic biomarkers in different modalities of head and neck cancer data.
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Affiliation(s)
- Sijie Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Tingyi Li
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Denise Kalos
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Yading Yuan
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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Zhang Z, Kim BS, Han W, Chen X, Yan Y, Lin L, Chai G. Identifying Oxidized Lipid Metabolism-Related LncRNAs as Prognostic Biomarkers of Head and Neck Squamous Cell Carcinoma. J Pers Med 2023; 13:jpm13030488. [PMID: 36983670 PMCID: PMC10054813 DOI: 10.3390/jpm13030488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
The relationship between oxidized lipid metabolism and the immunological function of cancer is well known. However, the functions and regulatory mechanisms of lncRNAs associated with oxidized lipid metabolism in head and neck squamous cell carcinoma (HNSCC) remain to be fully elucidated. In this study, we established an oxidized lipid metabolism-related lncRNA prognostic signature to assess the prognosis and immune infiltration of HNSCC patients. The HNSCC transcriptome was obtained from The Cancer Genome Atlas. The choice of the target genes with a relevance score greater than 10 was performed via a correlation analysis by GeneCards. Patients were categorized by risk score and generated with multivariate Cox regression, which was then validated and evaluated using the Kaplan–Meier analysis and time-dependent receiver operating characteristics (ROC). A nomogram was constructed by combining the risk score with the clinical data. We constructed a risk score with 24 oxidized lipid metabolism-related lncRNAs. The areas’ 1-, 2-, and 3-year OS under the ROC curve (AUC) were 0.765, 0.724, and 0.724, respectively. Furthermore, the nomogram clearly distinguished the survival probabilities of patients in high- and low-risk groups, between which substantial variations were revealed by immune infiltration analysis. The results supported the fact that oxidized lipid metabolism-related lncRNAs might predict prognoses and assist with differentiating amid differences in immune infiltration in HNSCC.
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Bueno-Urquiza LJ, Martínez-Barajas MG, Villegas-Mercado CE, García-Bernal JR, Pereira-Suárez AL, Aguilar-Medina M, Bermúdez M. The Two Faces of Immune-Related lncRNAs in Head and Neck Squamous Cell Carcinoma. Cells 2023; 12:cells12050727. [PMID: 36899863 PMCID: PMC10000590 DOI: 10.3390/cells12050727] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 03/02/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a group of cancers originating from the mucosal epithelium in the oral cavity, larynx, oropharynx, nasopharynx, and hypopharynx. Molecular factors can be key in the diagnosis, prognosis, and treatment of HNSCC patients. Long non-coding RNAs (lncRNAs) are molecular regulators composed of 200 to 100,000 nucleotides that act on the modulation of genes that activate signaling pathways associated with oncogenic processes such as proliferation, migration, invasion, and metastasis in tumor cells. However, up until now, few studies have discussed the participation of lncRNAs in modeling the tumor microenvironment (TME) to generate a protumor or antitumor environment. Nevertheless, some immune-related lncRNAs have clinical relevance, since AL139158.2, AL031985.3, AC104794.2, AC099343.3, AL357519.1, SBDSP1, AS1AC108010.1, and TM4SF19-AS1 have been associated with overall survival (OS). MANCR is also related to poor OS and disease-specific survival. MiR31HG, TM4SF19-AS1, and LINC01123 are associated with poor prognosis. Meanwhile, LINC02195 and TRG-AS1 overexpression is associated with favorable prognosis. Moreover, ANRIL lncRNA induces resistance to cisplatin by inhibiting apoptosis. A superior understanding of the molecular mechanisms of lncRNAs that modify the characteristics of TME could contribute to increasing the efficacy of immunotherapy.
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Affiliation(s)
- Lesly J. Bueno-Urquiza
- Department of Physiology, University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | - Marcela G. Martínez-Barajas
- Department of Physiology, University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | | | - Jonathan R. García-Bernal
- Department of Physiology, University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | - Ana L. Pereira-Suárez
- Department of Microbiology and Pathology, University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | - Maribel Aguilar-Medina
- Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Culiacán, Sinaloa 80030, Mexico
| | - Mercedes Bermúdez
- Faculty of Dentistry, Autonomous University of Chihuahua, Chihuahua 31000, Mexico
- Correspondence: ; Tel.: +52-(614)-439-1834
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Zhou Y, Dai X, Lyu J, Li Y, Bao X, Deng F, Liu K, Cui L, Cheng L. Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs. Medicine (Baltimore) 2022; 101:e31075. [PMID: 36281116 PMCID: PMC9592387 DOI: 10.1097/md.0000000000031075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND To construct and verify a novel prognostic model for thyroid cancer (THCA) based on N7-methylguanosine modification-related lncRNAs (m7G-lncRNAs) and their association with immune cell infiltration. METHODS In this study, we identified m7G-lncRNAs using co-expression analysis and performed differential expression analysis of m7G-lncRNAs between groups. We then constructed a THCA prognostic model, performed survival analysis and risk assessment for the THCA prognostic model, and performed independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, analysis of the regulatory relationship between prognostic differentially expressed m7G-related lncRNAs (PDEm7G-lncRNAs) and mRNAs and correlation analysis of immune cells and risk scores in THCA patients were carried out. RESULTS We identified 29 N7-methylguanosine modification-related mRNAs and 116 differentially expressed m7G-related lncRNAs, including 87 downregulated and 29 upregulated lncRNAs. Next, we obtained 8 PDEm7G-lncRNAs. A final optimized model was constructed consisting of 5 PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, TMEM105, SMG7-AS1 and HMGA2-AS1). Six PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, HMGA2-AS1, LINC01976, MID1IP1-AS1, and SMG7-AS1) had positive regulatory relationships with 10 PDEm7G-mRNAs, while 2 PDEm7G-lncRNAs (LINC02026 and TMEM105) had negative regulatory relationships with 2 PDEm7G-mRNAs. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with THCA. Forest maps and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Finally, we demonstrated a correlation between different immune cells and risk scores. CONCLUSION Our results will help identify high-risk or low-risk patients with THCA and facilitate early prediction and clinical intervention in patients with high risk and poor prognosis.
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Affiliation(s)
- Yang Zhou
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xuezhong Dai
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jianhong Lyu
- Department of Anesthesiology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yingyue Li
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xueyu Bao
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Fang Deng
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Kun Liu
- Department of Otorhinolaryngology, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Liming Cui
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Li Cheng
- Department of Endocrinology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- * Correspondence: Li Cheng, The Third People’s Hospital of Yunnan Province, 292 Beijing Road, Guandu District, Kunming City, Yunnan Province 650011, China (e-mail: )
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Shi D, Zhong W, Liu D, Sun X, Hao S, Yang Y, Ao L, Zhou J, Xia Y, Zhou Y, Yu H, Xia H. Computational identification of immune-related lncRNA signature for predicting the prognosis and immune landscape of human glioblastoma multiforme. Front Immunol 2022; 13:932938. [PMID: 36032137 PMCID: PMC9412749 DOI: 10.3389/fimmu.2022.932938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Emerging evidence shows immune-related long noncoding RNAs (ir-lncRNAs) perform critical roles in tumor progression and prognosis assessment. However, the identification of ir-lncRNAs and their clinical significance in human glioblastoma multiforme (GBM) remain largely unexplored. Here, a designed computational frame based on immune score was used to identify differentially expressed ir-lncRNAs (DEir-lncRNAs) from The Cancer Genome Atlas (TCGA) GBM program. The immune-related lncRNA signature (IRLncSig) composed of prognosis-related DEir-lncRNAs selected by Cox regression analysis and its clinical predictive values were verified, which was further validated by another dataset from the Gene Expression Omnibus database (GEO). Subsequently, the association between IRLncSig and immune cell infiltration, immune checkpoint inhibitor (ICI) biomarkers, O6-methylguanine-DNA methyltransferase (MGMT) gene expression, and biological function were also analyzed. After calculation, five prognosis-related ir-lncRNAs were included in the establishment of IRLncSig. The risk assessment based on IRLncSig indicated that the high-IRLncSig-score group was significantly associated with poor prognosis (p < 0.001), significant aggregation of macrophages (p < 0.05), higher ICI biomarker expression, and MGMT gene expression (p < 0.05). Signature-related lncRNAs may be involved in immune activities in the tumorigenesis and progression of GBM. In summary, the novel IRLncSig shows a promising clinical value in predicting the prognosis and immune landscape of GBM.
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Affiliation(s)
- Dongjie Shi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenjie Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Liu
- Department of Pharmacy, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Yaying Yang
- Department of Pathology, Molecular Medicine and Tumor Center, Chongqing Medical University, Chongqing, China
| | - Lei Ao
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junjie Zhou
- Department of Pathology, Molecular Medicine and Tumor Center, Chongqing Medical University, Chongqing, China
| | - Yongzhi Xia
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yudong Zhou
- Department of Neurosurgery, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Yu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haijian Xia
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Haijian Xia,
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Gong X, Ren F. Identification of Gene-Tyrosine Kinase 2 (TYK2) in Head and Neck Squamous Cell Carcinoma Patients-An Integrated Bioinformatics Approach. DISEASE MARKERS 2022; 2022:5239033. [PMID: 35711568 PMCID: PMC9197628 DOI: 10.1155/2022/5239033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Background The human tyrosine kinase 2 (TYK2) has been found to be associated with at least 20 autoimmune diseases; however, its tumor-regulating role in head and neck squamous cell carcinoma (HNSC) has not been researched by using an integrative bioinformatics approach, yet. Objective To investigate the regulating mechanisms of the TYK2 gene in HNSC in terms of its expression pattern, prognostic values, involved biological functions, and implication of tumor immunity. Methods The TYK2 gene expression pattern and regulatory involvement in HNSC were investigated using publically accessible data from TCGA database. R software tools and public web servers were utilized to conduct statistical analysis on cancer and noncancerous samples. Results TYK2 was found to be significantly upregulated in HNSC samples compared with healthy control samples. The expression of TYK2 gene was shown to be associated with the prognosis of HNSC by showing its upregulation represented better survival outcome. The regulating role of TYK2 in HNSC was found mainly in several pathways including DNA replication, base excision repair, apoptosis, p53 signaling pathway, and NF-kappa B signaling pathway. The gene set enrichment analysis (GSEA) results showed that TYK2-significantly correlated genes were mainly enriched in several biological functional terms including cell cycle, DNA replication, PLK1 pathway, ATR pathway, and Rho GTPase pathway. In addition, TYK2 was found to be involved in tumor immunity, showing positive correlation with the majority of tumor infiltrating immune cells, immune checkpoint genes, and significant representative components of tumor microenvironment, according to the ESTIMATE-Stromal-Immune score. Conclusions Given the dysregulation, prognostic values, regulating tumor progression-related pathways, and the tumor immune-modulatory role of TYK2 in HNSC, the TYK2 gene should be regarded as a potential therapeutic target in treating head and neck cancer.
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Affiliation(s)
- Xiaoyan Gong
- Department of Stomatology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 046000 Shanxi Province, China
| | - Fukai Ren
- Department of Stomatology, Changzhi Medical College, Changzhi, 046000 Shanxi Province, China
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Jiang M, Liu F, Yang AG, Wang W, Zhang R. The role of long non-coding RNAs in the pathogenesis of head and neck squamous cell carcinoma. Mol Ther Oncolytics 2022; 24:127-138. [PMID: 35024439 PMCID: PMC8717422 DOI: 10.1016/j.omto.2021.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancers are a heterogeneous collection of malignancies of the upper aerodigestive tract, salivary glands, and thyroid. However, the molecular mechanisms underlying the carcinogenesis of head and neck squamous cell carcinomas (HNSCCs) remain poorly understood. Over the past decades, overwhelming evidence has demonstrated the regulatory roles of long non-coding RNAs (lncRNAs) in tumorigenesis, including HNSCC. Notably, these lncRNAs have vital roles in gene regulation and affect various aspects of cellular homeostasis, including proliferation, survival, and metastasis. They exert regulating functions by interacting with nucleic acids or proteins and affecting cancer cell signaling. LncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of lncRNAs in HNSCC. In this review, we summarize the deregulation and function of lncRNAs in human HNSCC. We also review the working mechanism of lncRNAs in HNSCC pathogenesis and discuss the potential application of lncRNAs as diagnostic/prognostic tools and therapeutic targets in human HNSCC.
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Affiliation(s)
- Man Jiang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Fang Liu
- Department of Dermatology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - An-Gang Yang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wei Wang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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Wang J, Wang B, Zhou B, Chen J, Qi J, Shi L, Yu S, Chen G, Kang M, Jin X, Wang L, Xu J, Zhu L, Chen J. A novel immune-related lncRNA pair signature for prognostic prediction and immune response evaluation in gastric cancer: a bioinformatics and biological validation study. Cancer Cell Int 2022; 22:69. [PMID: 35144613 PMCID: PMC8832759 DOI: 10.1186/s12935-022-02493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background Gastric cancer (GC), the most commonly diagnosed cancer worldwide with poor 5-year survival rate in advanced stages. Although immune-related and survival-related biomarkers, which typically comprise aberrantly expressed long non-coding RNAs (lncRNAs) and genes, have been identified, there are no reports of immune-related lncRNA pair (IRLP) signatures for GC. Methods In this study, we acquired lncRNA expression profiles from The Cancer Genome Atlas (TCGA) and used the least absolute shrinkage and selection operator (LASSO) Cox proportional hazards model (iteration = 1000) to develop a IRLP prognostic signature. The area under curve (AUC) was used to assess the prognosis predictive power. The multivariate Cox regression analysis was performed to identify whether this signature was an independent prognostic factor. The immune cell infiltration analysis was performed between the two risk groups. Last, molecular experiments were performed to explore LINC01082 is involved in the development of GC. Results We acquired lncRNA expression profiles and used the LASSO Cox model to develop an 18-IRLP signature with a strong prognostic predictive power. The 5-year AUC values of the training, validation, and overall TCGA datasets were 0.77, 0.86, and 0.80, respectively. The different prognostic outcomes between the high- and low-risk groups were determined using our 18-IRLP signature. Moreover, our 18-IRLP signature was an independent prognostic factor as per the multivariate Cox regression analysis, and showed better prognostic evaluation than the traditional TNM staging system as well as other clinical features. We also found differences in cancer-associated fibroblast and macrophage M2 infiltration and the expression of PD-L1, CTLA4, LAG3, and HLA were also observed between the two risk groups (P < 0.05). Analysis of biological functions revealed that target genes of the lncRNAs in the IRLP signature were enriched in focal adhesion and regulation of actin cytoskeleton. Finally, as one of significant candidates of IRLP signature, overexpression of LINC01082 suppressed the invasion ability of GC cells as well as PD-L1 expression profiles. Conclusions Our novel 18-IRLP signature provides new insights regarding immunological biomarkers, imparts a better understanding of the tumor immune microenvironment, and can be used for predicting prognosis and evaluating immune response in GC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02493-2.
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Affiliation(s)
- Jun Wang
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Beidi Wang
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Biting Zhou
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Jing Chen
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Jia Qi
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Le Shi
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Shaojun Yu
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Guofeng Chen
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Muxing Kang
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Xiaoli Jin
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Lie Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Jinghong Xu
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Linghua Zhu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China.
| | - Jian Chen
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China.
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Wang J, Bian Q, Liu J, Moming A. Identification and in vitro validation of prognostic lncRNA signature in head and neck squamous cell carcinoma. Bioengineered 2021; 12:10049-10062. [PMID: 34872450 PMCID: PMC8809959 DOI: 10.1080/21655979.2021.1995577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are promising cancer prognostic markers. However, the clinical significance of lncRNA signatures in evaluating overall survival (OS) outcomes of head and neck squamous cell carcinoma (HNSCC) has not been explored. This study aimed to assess the significance of lncRNA in HNSCC and to develop a lncRNA signature related to OS in HNSCC. LncRNA expression matrices were retrieved from the Cancer Genome Atlas (TCGA) data. Least Absolute Shrinkage and Selection of the Operator (LASSO), univariate and multivariate Cox regression were used for establishing a prognostic model. In vitro experiments were carried out to demonstrate the biological role of lncRNA. A prognosis model based on 7 DElncRNAs was finally established.The patients were then divided into high-risk and low-risk groups. Relative to the low-risk group, overall survival times for patients in the high-risk group were significantly low (P=2.466e−07). Risk score remained an independent prognostic factor in univariate (HR=1.329, 95%CI=1.239−1.425, p < 0.001) and multivariate (HR=1.279, 95%CI=1.184−1.382, p < 0.001) Cox regression analyses. The area under the curve (AUC) of the signature was as high as 0.78. Expressions of FOXD2-AS1 in tumor tissues were elevated, and significantly correlated with OS (P=0.008). FOXD2-AS1 silencing then significantly reduced HNSCC cell proliferation, invasion, and migration. In conclusion, a lncRNA signature was established for HNSCC prognostic prediction and FOXD2-AS1 was identified as an HNSCC oncogene.
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Affiliation(s)
- Jian Wang
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital of The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China.,Xinjiang Uygur Autonomous Region Institute of Stomatology, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China
| | - Qinjiang Bian
- Department of Maxillofacial Surgery, Gansu Provincial Hospital, Lanzhou, Gansu province, 730000, P.R. China
| | - Jialin Liu
- Xinjiang Uygur Autonomous Region Institute of Stomatology, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China.,Department of Prosthodontics, The Affiliated Stomatology Hospital of The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China
| | - Adili Moming
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital of The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China.,Xinjiang Uygur Autonomous Region Institute of Stomatology, Xinjiang Uyghur Autonomous Region, Urumqi, 830054, P.R. China
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