Identification of lncRNAs associated with T cells as potential biomarkers and therapeutic targets in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is the most common and deadliest subtype of lung cancer. To select more targeted and effective treatments for individuals, further advances in classifying LUAD are urgently needed. The number, type, and function of T cells in the tumor microenvironment (TME) determine the progression and treatment response of LUAD. Long noncoding RNAs (lncRNAs), may regulate T cell differentiation, development, and activation. Thus, our aim was to identify T cell-related lncRNAs (T cell-Lncs) in LUAD and to investigate whether T cell-Lncs could serve as potential stratifiers and therapeutic targets. Seven T cell-Lncs were identified to further establish the T cell-related lncRNA risk score (TRS) in LUAD. Low TRS individuals were characterized by robust immune status, fewer genomic alterations, and remarkably longer survival than high TRS individuals. The excellent accuracy of TRS in predicting overall survival (OS) was validated in the TCGA-LUAD training cohort and the GEO-LUAD validation cohort. Our data demonstrated the favorable predictive power of the TRS-based nomogram, which had important clinical significance in estimating the survival probability for individuals. In addition, individuals with low TRS could respond better to chemotherapy and immunotherapy than those with high TRS. LINC00525 was identified as a valuable study target, and the ability of LUAD to proliferate or invade was significantly attenuated by downregulation of LINC00525. In conclusion, the TRS established by T cell-Lncs could unambiguously classify LUAD patients, predict their prognosis and guide their management. Moreover, our identified T cell-Lncs could provide potential therapeutic targets for LUAD.

[1]  J. Joyce,et al.  The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth. , 2023, Cancer cell.

[2]  E. Pescarmona,et al.  Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma. , 2022, Annals of oncology : official journal of the European Society for Medical Oncology.

[3]  W. Hudson,et al.  Technology meets TILs: Deciphering T cell function in the -omics era. , 2022, Cancer cell.

[4]  Xuyu Gu,et al.  Development and Validation of a DNA Methylation-related Classifier of Circulating Tumour Cells to Predict Prognosis and to provide a therapeutic strategy in Lung Adenocarcinoma , 2022, International journal of biological sciences.

[5]  Yingfei Li,et al.  Instability Mechanism of Osimertinib in Plasma and a Solving Strategy in the Pharmacokinetics Study , 2022, Frontiers in Pharmacology.

[6]  W. Klapper,et al.  LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells , 2022, Non-coding RNA.

[7]  Ting Yu,et al.  Integratively Genomic Analysis Reveals the Prognostic and Immunological Characteristics of Pyroptosis and Ferroptosis in Pancreatic Cancer for Precision Immunotherapy , 2022, Frontiers in Cell and Developmental Biology.

[8]  N. Proudfoot,et al.  Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics , 2022, Nature Reviews Molecular Cell Biology.

[9]  S. Riddell,et al.  Tumor-infiltrating lymphocytes make inroads in non–small-cell lung cancer , 2021, Nature Medicine.

[10]  C. Boshoff,et al.  Toward personalized treatment approaches for non-small-cell lung cancer , 2021, Nature Medicine.

[11]  Shixiang Wang,et al.  Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes , 2021, PLoS genetics.

[12]  M. Kris,et al.  Evolution of systemic therapy for stages I–III non-metastatic non-small-cell lung cancer , 2021, Nature Reviews Clinical Oncology.

[13]  C. Subramanian,et al.  LIMIT is an immunogenic lncRNA in cancer immunity and immunotherapy , 2021, Nature Cell Biology.

[14]  D. Mathis,et al.  Tissue regulatory T cells: regulatory chameleons , 2021, Nature Reviews Immunology.

[15]  A. Jemal,et al.  Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries , 2021, CA: a cancer journal for clinicians.

[16]  M. Datta,et al.  LncRNAs in cancer: Regulatory and therapeutic implications. , 2020, Cancer letters.

[17]  M. Filetti,et al.  KEAP1-driven co-mutations in lung adenocarcinoma unresponsive to immunotherapy despite high tumor mutational burden. , 2020, Annals of oncology : official journal of the European Society for Medical Oncology.

[18]  Shuhua Wei,et al.  Regulatory T cells in tumor microenvironment: new mechanisms, potential therapeutic strategies and future prospects , 2020, Molecular Cancer.

[19]  Nicolai J. Birkbak,et al.  The T cell differentiation landscape is shaped by tumour mutations in lung cancer , 2020, Nature Cancer.

[20]  J. Luke,et al.  Dendritic Cells, the T-cell-inflamed Tumor Microenvironment, and Immunotherapy Treatment Response , 2020, Clinical Cancer Research.

[21]  J. Zhang,et al.  The role of macrophages during breast cancer development and response to chemotherapy , 2020, Clinical and Translational Oncology.

[22]  Thomas D. Wu,et al.  Peripheral T cell expansion predicts tumour infiltration and clinical response , 2020, Nature.

[23]  Xia Li,et al.  Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers , 2020, Nature Communications.

[24]  T. Schumacher,et al.  CD8+ T cell states in human cancer: insights from single-cell analysis , 2020, Nature Reviews Cancer.

[25]  Zhengrong Yin,et al.  The roles of exosomal miRNAs and lncRNAs in lung diseases , 2019, Signal Transduction and Targeted Therapy.

[26]  Sara R. Selitsky,et al.  Alternative tumour-specific antigens , 2019, Nature Reviews Cancer.

[27]  Xiaopeng Yang,et al.  Long Non-Coding RNA LINC00525 Promotes the Stemness and Chemoresistance of Colorectal Cancer by Targeting miR-507/ELK3 Axis , 2019, International journal of stem cells.

[28]  K. Kerr,et al.  Comparing and contrasting predictive biomarkers for immunotherapy and targeted therapy of NSCLC , 2019, Nature Reviews Clinical Oncology.

[29]  Gary D Bader,et al.  Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap , 2019, Nature Protocols.

[30]  Yassen Assenov,et al.  Maftools: efficient and comprehensive analysis of somatic variants in cancer , 2018, Genome research.

[31]  H. Yao,et al.  NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death , 2018, Nature Immunology.

[32]  J. Meléndez-Zajgla,et al.  The emerging role of lncRNAs in the regulation of cancer stem cells , 2018, Cellular Oncology.

[33]  Boxi Kang,et al.  Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing , 2018, Nature Medicine.

[34]  Jing Pan,et al.  LncRNA DGCR5 promotes lung adenocarcinoma (LUAD) progression via inhibiting hsa‐mir‐22‐3p , 2018, Journal of cellular physiology.

[35]  Min Zhang,et al.  lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. , 2018, Cancer cell.

[36]  R. Weinberg,et al.  Understanding the tumor immune microenvironment (TIME) for effective therapy , 2018, Nature Medicine.

[37]  Steven J. M. Jones,et al.  The Immune Landscape of Cancer , 2018, Immunity.

[38]  P. Khavari,et al.  The functions and unique features of long intergenic non-coding RNA , 2017, Nature Reviews Molecular Cell Biology.

[39]  Wei Jia,et al.  The long noncoding RNA lnc-EGFR stimulates T-regulatory cells differentiation thus promoting hepatocellular carcinoma immune evasion , 2017, Nature Communications.

[40]  Angela N. Brooks,et al.  A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles , 2017, Cell.

[41]  J. Wargo,et al.  Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy , 2017, Cell.

[42]  M. Philip,et al.  CD8+ T cell differentiation and dysfunction in cancer , 2016, Nature Reviews Immunology.

[43]  Pornpimol Charoentong,et al.  Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade , 2016, bioRxiv.

[44]  L. Zitvogel,et al.  Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents. , 2015, Cancer cell.

[45]  Maite Huarte The emerging role of lncRNAs in cancer , 2015, Nature Medicine.

[46]  I. Keklikoglou,et al.  Perivascular M2 Macrophages Stimulate Tumor Relapse after Chemotherapy. , 2015, Cancer research.

[47]  T. Shichinohe,et al.  Chemotherapy-Derived Inflammatory Responses Accelerate the Formation of Immunosuppressive Myeloid Cells in the Tissue Microenvironment of Human Pancreatic Cancer. Full Text with Supplemental Figure Legends , 2018 .

[48]  O. Griffith,et al.  COSMIC (Catalogue of Somatic Mutations in Cancer) , 2014 .

[49]  R. S. Huang,et al.  Abstract 5561: Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines , 2014 .

[50]  Daniel R. Caffrey,et al.  Long noncoding RNAs in innate and adaptive immunity. , 2014, Current opinion in immunology.

[51]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[52]  E. Brogi,et al.  Macrophages and cathepsin proteases blunt chemotherapeutic response in breast cancer. , 2011, Genes & development.

[53]  Matthew D. Wilkerson,et al.  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking , 2010, Bioinform..

[54]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[55]  T. Dønnem,et al.  Prognostic Effect of Epithelial and Stromal Lymphocyte Infiltration in Non–Small Cell Lung Cancer , 2008, Clinical Cancer Research.

[56]  R. Pirker Chemotherapy remains a cornerstone in the treatment of nonsmall cell lung cancer. , 2019, Current Opinion in Oncology.

[57]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[58]  H. Hansen,et al.  Lung cancer. , 1990, Cancer chemotherapy and biological response modifiers.

[59]  Markus S. Schröder,et al.  survcomp: an R/Bioconductor package for performance assessment and comparison of survival models , 2011, Bioinform..