Comprehensive Analysis of Mitophagy-related Genes in NSCLC Diagnosis and Immune Scenery: Based on Bulk and Single-cell RNA Sequencing Data

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2023 Dec 29

PMID 38155968

Authors

Haibo Yu

Qingtao Liu

Mingming Jin

Gang Huang

Qianqian Cai

Affiliations

Soon will be listed here.

Abstract

Lung cancer is the main cause of cancer-related deaths, and non-small cell lung cancer (NSCLC) is the most common type. Understanding the potential mechanisms, prognosis, and treatment aspects of NSCLC is essential. This study systematically analyzed the correlation between mitophagy and NSCLC. Six mitophagy-related feature genes (, , , , , and ) were selected through machine learning and used to construct a diagnostic model for NSCLC. These feature genes are closely associated with the occurrence and development of NSCLC. Additionally, NSCLC was divided into two subtypes using unsupervised consensus clustering, and their differences in clinical characteristics, immune infiltration, and immunotherapy were systematically analyzed. Furthermore, the interaction between mitophagy-related genes (MRGs) and immune cells was analyzed using single-cell sequencing data. The findings of this study will contribute to the development of potential diagnostic biomarkers for NSCLC and the advancement of personalized treatment strategies.

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References

Chang G, Zhang W, Ma Y, Wen Q . PINK1 Expression Is Associated with Poor Prognosis in Lung Adenocarcinoma. Tohoku J Exp Med. 2018; 245(2):115-121. DOI: 10.1620/tjem.245.115. View

Liu L, Zuo Z, Lu S, Wang L, Liu A, Liu X . Silencing of PINK1 represses cell growth, migration and induces apoptosis of lung cancer cells. Biomed Pharmacother. 2018; 106:333-341. DOI: 10.1016/j.biopha.2018.06.128. View

Wilkerson M, Hayes D . ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010; 26(12):1572-3. PMC: 2881355. DOI: 10.1093/bioinformatics/btq170. View

Takanami I, Takeuchi K, Naruke M . Mast cell density is associated with angiogenesis and poor prognosis in pulmonary adenocarcinoma. Cancer. 2000; 88(12):2686-92. View

Zhang X, Lan Y, Xu J, Quan F, Zhao E, Deng C . CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res. 2018; 47(D1):D721-D728. PMC: 6323899. DOI: 10.1093/nar/gky900. View

Dery R, Lin T, Befus A, Milne C, Moqbel R, Menard G . Redundancy or cell-type-specific regulation? Tumour necrosis factor in alveolar macrophages and mast cells. Immunology. 2000; 99(3):427-34. PMC: 2327162. DOI: 10.1046/j.1365-2567.2000.00982.x. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Fu J, Li K, Zhang W, Wan C, Zhang J, Jiang P . Large-scale public data reuse to model immunotherapy response and resistance. Genome Med. 2020; 12(1):21. PMC: 7045518. DOI: 10.1186/s13073-020-0721-z. View

Song C, Pan S, Zhang J, Li N, Geng Q . Mitophagy: A novel perspective for insighting into cancer and cancer treatment. Cell Prolif. 2022; 55(12):e13327. PMC: 9715364. DOI: 10.1111/cpr.13327. View

10.

Xing S, Hu K, Wang Y . Tumor Immune Microenvironment and Immunotherapy in Non-Small Cell Lung Cancer: Update and New Challenges. Aging Dis. 2022; 13(6):1615-1632. PMC: 9662266. DOI: 10.14336/AD.2022.0407. View

11.

Sharma A, Ahmad S, Ahmad T, Ali S, Syed M . Mitochondrial dynamics and mitophagy in lung disorders. Life Sci. 2021; 284:119876. DOI: 10.1016/j.lfs.2021.119876. View

12.

Salcher S, Sturm G, Horvath L, Untergasser G, Kuempers C, Fotakis G . High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell. 2022; 40(12):1503-1520.e8. PMC: 9767679. DOI: 10.1016/j.ccell.2022.10.008. View

13.

Leek J, Johnson W, Parker H, Jaffe A, Storey J . The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012; 28(6):882-3. PMC: 3307112. DOI: 10.1093/bioinformatics/bts034. View

14.

Aran D, Looney A, Liu L, Wu E, Fong V, Hsu A . Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019; 20(2):163-172. PMC: 6340744. DOI: 10.1038/s41590-018-0276-y. View

15.

Wang Y, Liu H, Cao Y, Zhang L, Huang F, Yi C . The Role of Mitochondrial Dynamics and Mitophagy in Carcinogenesis, Metastasis and Therapy. Front Cell Dev Biol. 2020; 8:413. PMC: 7297908. DOI: 10.3389/fcell.2020.00413. View

16.

Sarraf S, Sideris D, Giagtzoglou N, Ni L, Kankel M, Sen A . PINK1/Parkin Influences Cell Cycle by Sequestering TBK1 at Damaged Mitochondria, Inhibiting Mitosis. Cell Rep. 2019; 29(1):225-235.e5. PMC: 6880866. DOI: 10.1016/j.celrep.2019.08.085. View

17.

Tang Y, Geng Y, Luo J, Shen W, Zhu W, Meng C . Downregulation of ubiquitin inhibits the proliferation and radioresistance of non-small cell lung cancer cells in vitro and in vivo. Sci Rep. 2015; 5:9476. PMC: 4377628. DOI: 10.1038/srep09476. View

18.

Mabbott N, Baillie J, Brown H, Freeman T, Hume D . An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics. 2013; 14:632. PMC: 3849585. DOI: 10.1186/1471-2164-14-632. View

19.

Vara-Perez M, Felipe-Abrio B, Agostinis P . Mitophagy in Cancer: A Tale of Adaptation. Cells. 2019; 8(5). PMC: 6562743. DOI: 10.3390/cells8050493. View

20.

Chen N, Karantza-Wadsworth V . Role and regulation of autophagy in cancer. Biochim Biophys Acta. 2009; 1793(9):1516-23. PMC: 3155287. DOI: 10.1016/j.bbamcr.2008.12.013. View