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      Mitochondrial Homeostasis–Related lncRNAs are Potential Biomarkers for Predicting Prognosis and Immune Response in Lung Adenocarcinoma

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          Abstract

          The prognosis of the most common histological subtype of lung cancer, lung adenocarcinoma (LUAD), is relatively poor. Mitochondrial homeostasis depends to a great extent on the coordination between mitophagy and mitochondrial biogenesis, the deregulation of which causes various human diseases, including cancer. There is accumulating evidence that long noncoding RNAs (lncRNAs) are critical in predicting the prognosis and immune response in carcinoma. Therefore, it is critical to discern lncRNAs related to mitochondrial homeostasis in LUAD patients. In this study, we identified mitochondrial homeostasis–related lncRNAs (MHRlncRNAs) by coexpression analysis. In order to construct a prognostic signature composed of three MHRlncRNAs, univariate and multivariate Cox regression analyses were performed. Kaplan–Meier analysis, stratification analysis, principal component analysis (PCA), receiver operating characteristic (ROC) curve, gene set enrichment analysis (GSEA), and nomogram were applied to evaluate and optimize the risk model. Subsequently, we identified the mitochondrial homeostasis–related lncRNA signature (MHLncSig) as an independent predictive factor of prognosis. Based on the LUAD subtypes regrouped by this risk model, we further investigated the underlying tumor microenvironment, tumor mutation burden, and immune landscape behind different risk groups. Likewise, individualized immunotherapeutic strategies and candidate compounds were screened to aim at different risk subtypes of LUAD patients. Finally, we validated the expression trends of lncRNAs included in the risk model using quantitative real-time polymerase chain reaction (qRT-PCR) assays. The established MHLncSig may be a promising tool for predicting the prognosis and guiding individualized treatment in LUAD.

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          Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

          Cancer treatment by immune checkpoint blockade (ICB) can bring long-lasting clinical benefits, but only a fraction of patients respond to treatment. To predict ICB response, we developed TIDE, a computational method to model two primary mechanisms of tumor immune evasion: the induction of T cell dysfunction in tumors with high infiltration of cytotoxic T lymphocytes (CTL) and the prevention of T cell infiltration in tumors with low CTL level. We identified signatures of T cell dysfunction from large tumor cohorts by testing how the expression of each gene in tumors interacts with the CTL infiltration level to influence patient survival. We also modeled factors that exclude T cell infiltration into tumors using expression signatures from immunosuppressive cells. Using this framework and pre-treatment RNA-Seq or NanoString tumor expression profiles, TIDE predicted the outcome of melanoma patients treated with first-line anti-PD1 or anti-CTLA4 more accurately than other biomarkers such as PD-L1 level and mutation load. TIDE also revealed new candidate ICB resistance regulators, such as SERPINB9 , demonstrating utility for immunotherapy research.
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            Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.

            Immune checkpoint inhibitors, which unleash a patient's own T cells to kill tumors, are revolutionizing cancer treatment. To unravel the genomic determinants of response to this therapy, we used whole-exome sequencing of non-small cell lung cancers treated with pembrolizumab, an antibody targeting programmed cell death-1 (PD-1). In two independent cohorts, higher nonsynonymous mutation burden in tumors was associated with improved objective response, durable clinical benefit, and progression-free survival. Efficacy also correlated with the molecular smoking signature, higher neoantigen burden, and DNA repair pathway mutations; each factor was also associated with mutation burden. In one responder, neoantigen-specific CD8+ T cell responses paralleled tumor regression, suggesting that anti-PD-1 therapy enhances neoantigen-specific T cell reactivity. Our results suggest that the genomic landscape of lung cancers shapes response to anti-PD-1 therapy. Copyright © 2015, American Association for the Advancement of Science.
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              Innate and adaptive immune cells in the tumor microenvironment.

              Most tumor cells express antigens that can mediate recognition by host CD8(+) T cells. Cancers that are detected clinically must have evaded antitumor immune responses to grow progressively. Recent work has suggested two broad categories of tumor escape based on cellular and molecular characteristics of the tumor microenvironment. One major subset shows a T cell-inflamed phenotype consisting of infiltrating T cells, a broad chemokine profile and a type I interferon signature indicative of innate immune activation. These tumors appear to resist immune attack through the dominant inhibitory effects of immune system-suppressive pathways. The other major phenotype lacks this T cell-inflamed phenotype and appears to resist immune attack through immune system exclusion or ignorance. These two major phenotypes of tumor microenvironment may require distinct immunotherapeutic interventions for maximal therapeutic effect.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                13 June 2022
                2022
                : 13
                : 870302
                Affiliations
                [1] 1 Department of Thoracic Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin, China
                [2] 2 Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China and Key Laboratory of Cardiovascular Medicine Research, Ministry of Education) , College of Pharmacy , Harbin Medical University , Harbin, China
                [3] 3 Department of Gastrointestinal Medical Oncology , Harbin Medical University Cancer Hospital , Harbin, China
                [4] 4 The Fourth Department of Medical Oncology , Harbin Medical University Cancer Hospital , Harbin, China
                Author notes

                Edited by: Matthew B. Schabath, Moffitt Cancer Center, United States

                Reviewed by: Xingguo Liu, Guangzhou Institutes of Biomedicine and Health (CAS), China

                Yuvabharath Kondaveeti, University of North Carolina at Chapel Hill, United States

                *Correspondence: Xin Liu, freyaliuxin@ 123456163.com ; Linyou Zhang, lyzhang@ 123456hrbmu.edu.cn

                This article was submitted to Cancer Genetics and Oncogenomics, a section of the journal Frontiers in Genetics

                Article
                870302
                10.3389/fgene.2022.870302
                9234294
                35769997
                3f232c7a-e19f-428e-968a-38239796ac71
                Copyright © 2022 Peng, Lou, Chen, Wang, Li, Lu, Na, Xu, Xin, Yao, Xu, Wang, Liu and Zhang.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 11 February 2022
                : 11 May 2022
                Categories
                Genetics
                Original Research

                Genetics
                mitochondrial homeostasis,long noncoding rnas,lung adenocarcinoma,nomogram,prognosis,immunotherapy

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