Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patients
2.2. DNA Extraction and Sequencing
2.3. WES Analysis
2.4. Identification of Enrichment of Mutated Genes in the PR Cohort
2.5. Signature Analysis
2.6. CNV Analysis
2.7. RNA Extraction and Sequencing
2.8. Gene Expression Profiling and Data Analysis
2.9. Analysis of Immune Cell Infiltration
2.10. Inference of Clonal Evolution
2.11. Survival Analysis
2.12. Prediction Model Construction
2.13. Statistical Analysis and Visualization
3. Results
3.1. Clinical Characteristics of Patients
3.2. The Genetic Characteristics of PR and NR
3.3. PR Harbored Aberrant Immune and Metabolic Microenvironment
3.4. PR_TATs Showed an Inhibitory Immune Microenvironment
3.5. Genetic and Transcriptional Distinction between PR and RR
3.6. Establishing A Prognostic Model for Recurrent Stage I NSCLC
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
NSCLC | non-smallcell lung cancer |
TME | tumor microenvironment |
WES | Whole-exome sequencing |
RNA-seq | RNA sequencing |
TATs | tumor-adjacent tissues |
OR | odds ratio |
GSEA | gene set enrichment analysis |
NES | normalized enrichment score |
ssGSEA | single sample gene set enrichment analysis |
DFS | disease-free survival |
ROC | receiver operating characteristic |
AUC | areas under the curve |
PR | primary tumors with relapse |
RR | recurrent tumors |
NR | primary tumors without relapse |
CNV | copy-number variation |
TMB | tumor mutation burden |
TNB | tumor neoantigen burden |
DEGs | differentially expressed genes |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
HR | hazard ratio |
CI | confidence interval |
References
- Siegel, R.L.; Miller, K.D.; Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 2020, 70, 7–30. [Google Scholar] [CrossRef] [PubMed]
- Sugimura, H.; Nichols, F.C.; Yang, P.; Allen, M.S.; Cassivi, S.D.; Deschamps, C.; Williams, B.A.; Pairolero, P.C. Survival after recurrent nonsmall-cell lung cancer after complete pulmonary resection. Ann. Thorac. Surg. 2007, 83, 409–417; discussion 417–418. [Google Scholar] [CrossRef] [PubMed]
- Uramoto, H.; Tanaka, F. Recurrence after surgery in patients with NSCLC. Transl. Lung Cancer Res. 2014, 3, 242–249. [Google Scholar] [CrossRef] [PubMed]
- Friedlaender, A.; Addeo, A.; Russo, A.; Gregorc, V.; Cortinovis, D.; Rolfo, C.D. Targeted Therapies in Early Stage NSCLC: Hype or Hope? Int. J. Mol. Sci. 2020, 21, 6329. [Google Scholar] [CrossRef] [PubMed]
- Lee, W.C.; Reuben, A.; Hu, X.; McGranahan, N.; Chen, R.; Jalali, A.; Negrao, M.V.; Hubert, S.M.; Tang, C.; Wu, C.C.; et al. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol. 2020, 21, 271. [Google Scholar] [CrossRef]
- Laubli, H.; Borsig, L. Altered Cell Adhesion and Glycosylation Promote Cancer Immune Suppression and Metastasis. Front. Immunol. 2019, 10, 2120. [Google Scholar] [CrossRef] [Green Version]
- Arimoto, A.; Yamashita, K.; Hasegawa, H.; Sugita, Y.; Fukuoka, E.; Tanaka, T.; Suzuki, S.; Kakeji, Y. Immunosuppression Induced by Perioperative Peritonitis Promotes Lung Metastasis. Anticancer Res. 2018, 38, 4333–4338. [Google Scholar] [CrossRef]
- Li, B.; Cui, Y.; Diehn, M.; Li, R. Development and Validation of an Individualized Immune Prognostic Signature in Early-Stage Nonsquamous Non-Small Cell Lung Cancer. JAMA Oncol. 2017, 3, 1529–1537. [Google Scholar] [CrossRef]
- Li, R.; Gu, J.; Heymach, J.V.; Shu, X.; Zhao, L.; Han, B.; Ye, Y.; Roth, J.; Wu, X. Hypoxia pathway genetic variants predict survival of non-small-cell lung cancer patients receiving platinum-based chemotherapy. Carcinogenesis 2017, 38, 419–424. [Google Scholar] [CrossRef] [Green Version]
- Sun, J.; Zhao, T.; Zhao, D.; Qi, X.; Bao, X.; Shi, R.; Su, C. Development and validation of a hypoxia-related gene signature to predict overall survival in early-stage lung adenocarcinoma patients. Ther. Adv. Med. Oncol. 2020, 12, 1758835920937904. [Google Scholar] [CrossRef]
- Kim-Wanner, S.Z.; Assenov, Y.; Nair, M.B.; Weichenhan, D.; Benner, A.; Becker, N.; Landwehr, K.; Kuner, R.; Sultmann, H.; Esteller, M.; et al. Genome-Wide DNA Methylation Profiling in Early Stage I Lung Adenocarcinoma Reveals Predictive Aberrant Methylation in the Promoter Region of the Long Noncoding RNA PLUT: An Exploratory Study. J. Thorac. Oncol. 2020, 15, 1338–1350. [Google Scholar] [CrossRef] [PubMed]
- Jones, G.D.; Brandt, W.S.; Shen, R.; Sanchez-Vega, F.; Tan, K.S.; Martin, A.; Zhou, J.; Berger, M.; Solit, D.B.; Schultz, N.; et al. A Genomic-Pathologic Annotated Risk Model to Predict Recurrence in Early-Stage Lung Adenocarcinoma. JAMA Surg. 2021, 156, e205601. [Google Scholar] [CrossRef] [PubMed]
- Kim, I.A.; Hur, J.Y.; Kim, H.J.; Park, J.H.; Hwang, J.J.; Lee, S.A.; Lee, S.E.; Kim, W.S.; Lee, K.Y. Targeted Next-Generation Sequencing Analysis for Recurrence in Early-Stage Lung Adenocarcinoma. Ann. Surg. Oncol. 2021, 28, 3983–3993. [Google Scholar] [CrossRef]
- Wallerek, S.; Sorensen, J.B. Biomarkers for efficacy of adjuvant chemotherapy following complete resection in NSCLC stages I-IIIA. Eur. Respir. Rev. 2015, 24, 340–355. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rosenthal, R.; McGranahan, N.; Herrero, J.; Taylor, B.S.; Swanton, C. DeconstructSigs: Delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 2016, 17, 31. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Davoli, T.; Uno, H.; Wooten, E.C.; Elledge, S.J. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science 2017, 355, eaaf8399. [Google Scholar] [CrossRef] [Green Version]
- Hanzelmann, S.; Castelo, R.; Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013, 14, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Newman, A.M.; Liu, C.L.; Green, M.R.; Gentles, A.J.; Feng, W.; Xu, Y.; Hoang, C.D.; Diehn, M.; Alizadeh, A.A. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 2015, 12, 453–457. [Google Scholar] [CrossRef] [Green Version]
- Roth, A.; Khattra, J.; Yap, D.; Wan, A.; Laks, E.; Biele, J.; Ha, G.; Aparicio, S.; Bouchard-Cote, A.; Shah, S.P. PyClone: Statistical inference of clonal population structure in cancer. Nat. Methods 2014, 11, 396–398. [Google Scholar] [CrossRef]
- Sun, Y.; Li, L.; Yao, W.; Liu, X.; Yang, Y.; Ma, B.; Xue, D. USH2A Mutation is Associated With Tumor Mutation Burden and Antitumor Immunity in Patients With Colon Adenocarcinoma. Front. Genet. 2021, 12, 762160. [Google Scholar] [CrossRef]
- Kar, S.P.; Tyrer, J.P.; Li, Q.; Lawrenson, K.; Aben, K.K.; Anton-Culver, H.; Antonenkova, N.; Chenevix-Trench, G.; Australian Cancer Study; Australian Ovarian Cancer Study Group; et al. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. Cancer Epidemiol. Biomark. Prev. 2015, 24, 1574–1584. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Goode, E.L.; Chenevix-Trench, G.; Song, H.; Ramus, S.J.; Notaridou, M.; Lawrenson, K.; Widschwendter, M.; Vierkant, R.A.; Larson, M.C.; Kjaer, S.K.; et al. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat. Genet. 2010, 42, 874–879. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ronn, T.; Poulsen, P.; Hansson, O.; Holmkvist, J.; Almgren, P.; Nilsson, P.; Tuomi, T.; Isomaa, B.; Groop, L.; Vaag, A.; et al. Age influences DNA methylation and gene expression of COX7A1 in human skeletal muscle. Diabetologia 2008, 51, 1159–1168. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chen, X.W.; Yu, T.J.; Zhang, J.; Li, Y.; Chen, H.L.; Yang, G.F.; Yu, W.; Liu, Y.Z.; Liu, X.X.; Duan, C.F.; et al. CYP4A in tumor-associated macrophages promotes pre-metastatic niche formation and metastasis. Oncogene 2017, 36, 5045–5057. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, H.Y.; Liao, P.C.; Chuang, K.T.; Kao, M.C. Mitochondrial targeting of human NADH dehydrogenase (ubiquinone) flavoprotein 2 (NDUFV2) and its association with early-onset hypertrophic cardiomyopathy and encephalopathy. J. Biomed. Sci. 2011, 18, 29. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Boland, B.S.; He, Z.; Tsai, M.S.; Olvera, J.G.; Omilusik, K.D.; Duong, H.G.; Kim, E.S.; Limary, A.E.; Jin, W.; Milner, J.J.; et al. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. Sci. Immunol. 2020, 5, eabb4432. [Google Scholar] [CrossRef]
- Guo, X.; Zhang, Y.; Zheng, L.; Zheng, C.; Song, J.; Zhang, Q.; Kang, B.; Liu, Z.; Jin, L.; Xing, R.; et al. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat. Med. 2018, 24, 978–985. [Google Scholar] [CrossRef]
- Michel, T.; Poli, A.; Cuapio, A.; Briquemont, B.; Iserentant, G.; Ollert, M.; Zimmer, J. Human CD56bright NK Cells: An Update. J. Immunol. 2016, 196, 2923–2931. [Google Scholar] [CrossRef] [Green Version]
- Bhat, A.A.; Syed, N.; Therachiyil, L.; Nisar, S.; Hashem, S.; Macha, M.A.; Yadav, S.K.; Krishnankutty, R.; Muralitharan, S.; Al-Naemi, H.; et al. Claudin-1, A Double-Edged Sword in Cancer. Int. J. Mol. Sci. 2020, 21, 569. [Google Scholar] [CrossRef] [Green Version]
- Patra, K.C.; Hay, N. The pentose phosphate pathway and cancer. Trends Biochem. Sci. 2014, 39, 347–354. [Google Scholar] [CrossRef] [Green Version]
- Zeng, D.; Li, M.; Zhou, R.; Zhang, J.; Sun, H.; Shi, M.; Bin, J.; Liao, Y.; Rao, J.; Liao, W. Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures. Cancer Immunol. Res. 2019, 7, 737–750. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yang, Y.; Ye, Y.C.; Chen, Y.; Zhao, J.L.; Gao, C.C.; Han, H.; Liu, W.C.; Qin, H.Y. Crosstalk between hepatic tumor cells and macrophages via Wnt/beta-catenin signaling promotes M2-like macrophage polarization and reinforces tumor malignant behaviors. Cell Death Dis. 2018, 9, 793. [Google Scholar] [CrossRef] [PubMed]
- Zhang, X.; Shi, M.; Chen, T.; Zhang, B. Characterization of the Immune Cell Infiltration Landscape in Head and Neck Squamous Cell Carcinoma to Aid Immunotherapy. Mol. Ther. Nucleic Acids 2020, 22, 298–309. [Google Scholar] [CrossRef]
- Zhang, G.; Zhou, S.; Zhong, W.; Hong, L.; Wang, Y.; Lu, S.; Pan, J.; Huang, Y.; Su, M.; Crawford, R.; et al. Whole-Exome Sequencing Reveals Frequent Mutations in Chromatin Remodeling Genes in Mammary and Extramammary Paget’s Diseases. J. Investig. Dermatol. 2019, 139, 789–795. [Google Scholar] [CrossRef] [Green Version]
- Zhao, G.; Chen, L.; Xiao, M.; Yang, S. Rare coexistence of three novel CDCA7-ALK, FSIP2-ALK, ALK-ERLEC1 fusions in a lung adenocarcinoma patient who responded to Crizotinib. Lung Cancer 2021, 152, 189–192. [Google Scholar] [CrossRef] [PubMed]
- Sun, Y.; Wu, L.; Zhong, Y.; Zhou, K.; Hou, Y.; Wang, Z.; Zhang, Z.; Xie, J.; Wang, C.; Chen, D.; et al. Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma. Cell 2021, 184, 404–421.e416. [Google Scholar] [CrossRef]
- Kim, N.; Kim, H.K.; Lee, K.; Hong, Y.; Cho, J.H.; Choi, J.W.; Lee, J.I.; Suh, Y.L.; Ku, B.M.; Eum, H.H.; et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat. Commun. 2020, 11, 2285. [Google Scholar] [CrossRef]
- Kamigaichi, A.; Tsutani, Y.; Fujiwara, M.; Mimae, T.; Miyata, Y.; Okada, M. Postoperative Recurrence and Survival After Segmentectomy for Clinical Stage 0 or IA Lung Cancer. Clin. Lung Cancer 2019, 20, 397–403.e1. [Google Scholar] [CrossRef]
- Aramini, B.; Casali, C.; Stefani, A.; Bettelli, S.; Wagner, S.; Sangale, Z.; Hughes, E.; Lanchbury, J.S.; Maiorana, A.; Morandi, U. Prediction of distant recurrence in resected stage I and II lung adenocarcinoma. Lung Cancer 2016, 101, 82–87. [Google Scholar] [CrossRef]
- Yin, J.; Guo, Y. HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2. Cancer Med. 2021, 10, 5524–5533. [Google Scholar] [CrossRef]
- Hu, Q.; Egranov, S.D.; Lin, C.; Yang, L. Long noncoding RNA loss in immune suppression in cancer. Pharmacol. Ther. 2020, 213, 107591. [Google Scholar] [CrossRef] [PubMed]
- Sakaguchi, S.; Miyara, M.; Costantino, C.M.; Hafler, D.A. FOXP3+ regulatory T cells in the human immune system. Nat. Rev. Immunol. 2010, 10, 490–500. [Google Scholar] [CrossRef] [PubMed]
- Aran, D.; Camarda, R.; Odegaard, J.; Paik, H.; Oskotsky, B.; Krings, G.; Goga, A.; Sirota, M.; Butte, A.J. Comprehensive analysis of normal adjacent to tumor transcriptomes. Nat. Commun. 2017, 8, 1077. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Huang, X.; Stern, D.F.; Zhao, H. Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival--Evidence from TCGA Pan-Cancer Data. Sci. Rep. 2016, 6, 20567. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Cen, B.; Wei, J.; Wang, D.; Xiong, Y.; Shay, J.W.; DuBois, R.N. Mutant APC promotes tumor immune evasion via PD-L1 in colorectal cancer. Oncogene 2021, 40, 5984–5992. [Google Scholar] [CrossRef]
- Sanda, M.G.; Restifo, N.P.; Walsh, J.C.; Kawakami, Y.; Nelson, W.G.; Pardoll, D.M.; Simons, J.W. Molecular characterization of defective antigen processing in human prostate cancer. J. Natl. Cancer Inst. 1995, 87, 280–285. [Google Scholar] [CrossRef] [PubMed]
- Sahin, I.H.; Akce, M.; Alese, O.; Shaib, W.; Lesinski, G.B.; El-Rayes, B.; Wu, C. Immune checkpoint inhibitors for the treatment of MSI-H/MMR-D colorectal cancer and a perspective on resistance mechanisms. Br. J. Cancer 2019, 121, 809–818. [Google Scholar] [CrossRef]
- McGranahan, N.; Rosenthal, R.; Hiley, C.T.; Rowan, A.J.; Watkins, T.B.K.; Wilson, G.A.; Birkbak, N.J.; Veeriah, S.; Van Loo, P.; Herrero, J.; et al. Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution. Cell 2017, 171, 1259–1271.e11. [Google Scholar] [CrossRef] [Green Version]
- De Semir, D.; Bezrookove, V.; Nosrati, M.; Scanlon, K.R.; Singer, E.; Judkins, J.; Rieken, C.; Wu, C.; Shen, J.; Schmudermayer, C.; et al. PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex. Proc. Natl. Acad. Sci. USA 2020, 117, 9064–9073. [Google Scholar] [CrossRef]
- Goetze, K.; Walenta, S.; Ksiazkiewicz, M.; Kunz-Schughart, L.A.; Mueller-Klieser, W. Lactate enhances motility of tumor cells and inhibits monocyte migration and cytokine release. Int. J. Oncol. 2011, 39, 453–463. [Google Scholar] [CrossRef]
- Gadgeel, S.M. Role of Chemotherapy and Targeted Therapy in Early-Stage Non-Small Cell Lung Cancer. Am. Soc. Clin. Oncol. Educ. Book 2017, 37, 630–639. [Google Scholar] [CrossRef] [PubMed]
- Ettinger, D.S.; Wood, D.E.; Aisner, D.L.; Akerley, W.; Bauman, J.; Chirieac, L.R.; D’Amico, T.A.; DeCamp, M.M.; Dilling, T.J.; Dobelbower, M.; et al. Non-Small Cell Lung Cancer, Version 5.2017, NCCN Clinical Practice Guidelines in Oncology. J. Natl. Compr. Canc. Netw. 2017, 15, 504–535. [Google Scholar] [CrossRef] [PubMed]
- Gerstung, M.; Pellagatti, A.; Malcovati, L.; Giagounidis, A.; Porta, M.G.; Jadersten, M.; Dolatshad, H.; Verma, A.; Cross, N.C.; Vyas, P.; et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nat. Commun. 2015, 6, 5901. [Google Scholar] [CrossRef] [PubMed]
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Zhang, S.; Xiao, X.; Zhu, X.; Chen, X.; Zhang, X.; Xiang, J.; Xu, R.; Shao, Z.; Bai, J.; Xun, Y.; et al. Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer. Cancers 2022, 14, 3061. https://doi.org/10.3390/cancers14133061
Zhang S, Xiao X, Zhu X, Chen X, Zhang X, Xiang J, Xu R, Shao Z, Bai J, Xun Y, et al. Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer. Cancers. 2022; 14(13):3061. https://doi.org/10.3390/cancers14133061
Chicago/Turabian StyleZhang, Shirong, Xiao Xiao, Xiuli Zhu, Xueqin Chen, Xiaochen Zhang, Jingjing Xiang, Rujun Xu, Zhuo Shao, Jing Bai, Yanping Xun, and et al. 2022. "Dysregulated Immune and Metabolic Microenvironment Is Associated with the Post-Operative Relapse in Stage I Non-Small Cell Lung Cancer" Cancers 14, no. 13: 3061. https://doi.org/10.3390/cancers14133061