Functional And Mechanistic Study And Clinical Relevance Analysis Of Long Noncoding RNA And Immune Related Genes In Esophageal Squamous Cell Carcinoma

Esophageal cancer is the sixth leading cause of cancer related death and the eighth most frequently diagnosed cancer worldwide.Over 90%of esophageal cancer in China are esophageal squamous cell carcinoma(ESCC)and China is one of the prevalent area of ESCC.Delayed diagnosis of most patients at an advanced stage accompanied by lymphatic metastasis that lack of successful therapeutic strategies accounts for the unsatisfactory prognosis of ESCC patients.Moreover,the molecular mechanism for ESCC remains largely unstudied,especially on tumorigenesis,progression and drug sensitivity.Therefore,better understanding and the identification of potential biomarkers or therapeutic targets are greatly needed.Long noncoding RNAs(lncRNAs)are a subgroup of noncoding RNAs(ncRNAs)which are longer than 200 nucleotides in length and lack of protein-coding ability.LncRNAs in cancer are getting more and more attentions in recent years and emerging evidences suggest that dysregulated lncRNAs in cancer have important roles in the initiation and progression of tumor.However,the molecular mechanisms of aberrantly expressed IncRNAs in ESCC remains unclear and investigations of ESCC-associated IncRNA might provide biomarkers for diagnosis or prognosis and potential therapeutic targets.Here,we identified a brand new IncRNA by integrated analysis of high-throughput expression data in ESCC and termed as IncRNA NMR(NSUN2 Methylated long noncoding RNA)afterwards.Compared with adjacent normal tissues,IncRNA NMR was significantly upregulated in ESCC tissues in the microarray data consisting of 119 paired tumor and normal tissues,meanwhile,lncRNA NMR was adverse prognosis factor for ESCC patients.We validated these findings in TCGA HNSC data and another 83 ESCC patients by PCR detection and the results were largely consistent.Functionally,lncRNA NMR played an oncogenic role in ESCC and was related to tumor cell metastasis and drug sensitivity.Knockdown of NMR significantly inhibited the migration and invasion of ESCC cells,promoted cisplatin-induced cell death,whereas overexpression of lncRNA NMR significantly promoted the migration and invasion of ESCC cells,inhibited cisplatin-induced cell death,and attenuated drug sensitivity to cisplatin and paclitaxel.Mechanically,upregulation of lncRNANMR might be related to NF-κB pathway.As a transcription factor,NF-κB could be activated by IL-1β and TNF-a treatment and promote the transcription of IncRNA NMR by binding to the promoter of IncRNA NMR.Meanwhile,IncRNA NMR could bind to NSUN2 and be methylated by NSUN2,and might competitively inhibit methylation of potential mRNAs.Moreover,IncRNA NMR could bind to chromatin regulator BPTF and influence gene expression,resulting in upregulation of MMP3 and MMP10 through ERK pathway activation.In summary,we reported the function and mechanism of a new lncRNA termed as lncRNA NMR in ESCC.Based on the oncogenic roles of lncRNA NMR in ESCC cells and correlations with clinical parameters of ESCC patients,lncRNA NMR could be the biomarker of tumor metastasis and prognosis,and might be potential therapeutic target for ESCC treatment.Immunotherapy is currently the most rapidly advancing area of clinical oncology,and immune checkpoint inhibitors targeting PD1,PD-L1 or CTLA4 provide the unprecedented opportunity to effectively treat,and even cure,several previously untreatable malignancies,with limited effects in other tumor types.Immune disorder is generally considered as one of the key regulators in the inithation and progression of tumor.With growing attention paied to immunotherapy,we are getting novel insights into the interactions between tumor cells and immune system within tumor microenvironment,high-throughput technology offers possible reflection of immune status and thus providing effective biomarkers or potential therapeutic targets.Thus,systematically profiling of immune signature in tumor microenvironment of ESCC might provide alternative options for immunotherapy in ESCC.In this study,immune signatures containing 708 immune related genes were curated from mRNA microarray data with tumor and paired normal tissues from 119 ESCC patients.We identified a total of 186 significantly dysregulated genes in ESCC,among which 99 genes were significantly upregulated and 87 genes were significantly downregulated genes.The top2 ranked downregulated genes were SPINK5,IL1RN and top2 ranked upregulated genes were SPP1 and PLAU,which were further confirmed in Human Protein Atlas data.These dysregulated genes were significantly enriched in important immune functions or pathways including T cell activation and NF-κB pathway,suggesting important roles of immune systems in the initiation or progression of ESCC and possible affection on the prognosis of ESCC patients.In the survival analyses,nine immune related genes(ABL1,ATF2,ATG5,C6,CD38,HMGB1,ICOSLG,IL12RB2 and PLAU)were significantly associated with patients’overall survival,among which,prognostic model was built including three independent factors ABL1,CD38 and ICOSLG.Validation by immunohistochemistry staining showed that ABL1,CD38 and ICOSLG were also significantly associated with prognosis in an independent cohort of 110 ESCC patients.Moreover,combination with tumor infiltrated CD4+ and CD8+ T lymphocytes would yield higher performance in distinguishing cases as high or low risk of unfavorable prognosis.In summary,several immune-related parameters,mainly tumor infiltrating lymphocytes,have been reported for predicting ESCC patient prognosis.For the first time,we profiled the immune signature in ESCC and established predictive and prognostic factors for ESCC,which could reflect immune disorders within tumor microenvironments and independently distinguish patients with a high risk of reduced survival,providing novel predictive and therapeutic targets for ESCC patients in the future.