196
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Fusing WGCNA and Machine Learning for Immune-Related Gene Prognostic Index in Lung Adenocarcinoma: Precision Prognosis, Tumor Microenvironment Profiling, and Biomarker Discovery

, , &
Pages 5309-5326 | Received 19 Sep 2023, Accepted 03 Nov 2023, Published online: 15 Nov 2023

References

  • André T, Shiu KK, Kim TW, et al. Pembrolizumab in Microsatellite-Instability-High Advanced Colorectal Cancer. N Engl J Med. 2020;383(23):2207–2218. doi:10.1056/NEJMoa2017699
  • Bellmunt J, de Wit R, Vaughn DJ, et al. Pembrolizumab as Second-Line Therapy for Advanced Urothelial Carcinoma. N Engl J Med. 2017;376(11):1015–1026. doi:10.1056/NEJMoa1613683
  • Larkin J, Chiarion-Sileni V, Gonzalez R, et al. Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma. N Engl J Med. 2015;373(1):23–34. doi:10.1056/NEJMoa1504030
  • Hodi FS, O’Day SJ, McDermott DF, et al. Improved survival with ipilimumab in patients with metastatic melanoma. N Engl J Med. 2010;363(8):711–723. doi:10.1056/NEJMoa1003466
  • Socinski MA, Jotte RM, Cappuzzo F, et al. Atezolizumab for First-Line Treatment of Metastatic Nonsquamous NSCLC. N Engl J Med. 2018;378(24):2288–2301. doi:10.1056/NEJMoa1716948
  • Brahmer J, Reckamp KL, Baas P, et al. Nivolumab versus Docetaxel in Advanced Squamous-Cell Non-Small-Cell Lung Cancer. N Engl J Med. 2015;373(2):123–135. doi:10.1056/NEJMoa1504627
  • Garon EB, Hellmann MD, Rizvi NA, et al. Five-Year Overall Survival for Patients With Advanced Non‒Small-Cell Lung Cancer Treated With Pembrolizumab: results From the Phase I KEYNOTE-001 Study. J Clin Oncol. 2019;37(28):2518–2527. doi:10.1200/JCO.19.00934
  • Borghaei H, Brahmer J. Nivolumab in Nonsquamous Non-Small-Cell Lung Cancer. N Engl J Med. 2016;374(5):493–494. doi:10.1056/NEJMc1514790
  • Borghaei H, Paz-Ares L, Horn L, et al. Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer. N Engl J Med. 2015;373(17):1627–1639. doi:10.1056/NEJMoa1507643
  • Herbst RS, Baas P, Kim DW, et al. Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial. Lancet. 2016;387(10027):1540–1550. doi:10.1016/S0140-6736(15)01281-7
  • Mazieres J, Drilon A, Lusque A, et al. Immune checkpoint inhibitors for patients with advanced lung cancer and oncogenic driver alterations: results from the IMMUNOTARGET registry. Ann Oncol. 2019;30(8):1321–1328. doi:10.1093/annonc/mdz167
  • Nishino M, Ramaiya NH, Hatabu H, Hodi FS. Monitoring immune-checkpoint blockade: response evaluation and biomarker development. Nat Rev Clin Oncol. 2017;14(11):655–668. doi:10.1038/nrclinonc.2017.88
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559. doi:10.1186/1471-2105-9-559
  • Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28(11):1747–1756. doi:10.1101/gr.239244.118
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457. doi:10.1038/nmeth.3337
  • Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 2020;48(W1):W509–W514. doi:10.1093/nar/gkaa407
  • Jiang P, Gu S, Pan D, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018;24(10):1550–1558. doi:10.1038/s41591-018-0136-1
  • Ayers M, Lunceford J, Nebozhyn M, et al. IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade. J Clin Invest. 2017;127(8):2930–2940. doi:10.1172/JCI91190
  • Tian Y, Yang J, Lan M, Zou T. Construction and analysis of a joint diagnosis model of random forest and artificial neural network for heart failure. Aging. 2020;12(24):26221–26235. doi:10.18632/aging.202405
  • Song Y, Yan S, Fan W, et al. Identification and Validation of the Immune Subtypes of Lung Adenocarcinoma: implications for Immunotherapy. Front Cell Dev Biol. 2020;8:550. doi:10.3389/fcell.2020.00550
  • Thorsson V, Gibbs DL, Brown SD, et al. The Immune Landscape of Cancer. Immunity. 2018;48(4):812–830.e14. doi:10.1016/j.immuni.2018.03.023
  • Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511(7511):543–550. doi:10.1038/nature13385
  • Snyder A, Nathanson T, Funt SA, et al. Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: an exploratory multi-omic analysis. PLoS Med. 2017;14(5):e1002309. doi:10.1371/journal.pmed.1002309
  • Sholl LM, Hirsch FR, Hwang D, et al. The Promises and Challenges of Tumor Mutation Burden as an Immunotherapy Biomarker: a Perspective from the International Association for the Study of Lung Cancer Pathology Committee. J Thorac Oncol. 2020;15(9):1409–1424. doi:10.1016/j.jtho.2020.05.019
  • Dubuisson A, Fahrner JE, Goubet AG, et al. Immunodynamics of explanted human tumors for immuno-oncology. EMBO Mol Med. 2021;13(1):e12850. doi:10.15252/emmm.202012850
  • Li S, Borowitz MJ. CD79a(+) T-cell lymphoblastic lymphoma with coexisting Langerhans cell histiocytosis. Arch Pathol Lab Med. 2001;125(7):958–960. doi:10.5858/2001-125-0958-CTCLLW
  • Mangogna A, Cox MC, Ruco L, et al. Rituximab Plus Chemotherapy Provides No Clinical Benefit in a Peripheral T-Cell Lymphoma Not Otherwise Specified with Aberrant Expression of CD20 and CD79a: a Case Report and Review of the Literature. Diagnostics. 2020;10(6):341. doi:10.3390/diagnostics10060341
  • Hof J, Visser L, Höppener DJ, et al. B Cells as Prognostic Biomarker After Surgery for Colorectal Liver Metastases. Front Oncol. 2020;10:249. doi:10.3389/fonc.2020.00249
  • Kishimoto T, Akira S, Narazaki M, Taga T. Interleukin-6 family of cytokines and gp130. Blood. 1995;86(4):1243–1254.
  • Garbers C, Hermanns HM, Schaper F, et al. Plasticity and cross-talk of interleukin 6-type cytokines. Cytokine Growth Factor Rev. 2012;23(3):85–97. doi:10.1016/j.cytogfr.2012.04.001
  • Schwertschlag US, Trepicchio WL, Dykstra KH, et al. Hematopoietic, immunomodulatory and epithelial effects of interleukin-11. Leukemia. 1999;13(9):1307–1315. doi:10.1038/sj.leu.2401514
  • Huang G, Yu L, Cooper LJ, et al. Genetically modified T cells targeting interleukin-11 receptor α-chain kill human osteosarcoma cells and induce the regression of established osteosarcoma lung metastases. Cancer Res. 2012;72(1):271–281. doi:10.1158/0008-5472.CAN-11-2778
  • Taniguchi K, Karin M. IL-6 and related cytokines as the critical lynchpins between inflammation and cancer. Semin Immunol. 2014;26(1):54–74. doi:10.1016/j.smim.2014.01.001
  • Pastor MD, Nogal A, Molina-Pinelo S, et al. IL-11 and CCL-1: novel Protein Diagnostic Biomarkers of Lung Adenocarcinoma in Bronchoalveolar Lavage Fluid (BALF). J Thorac Oncol. 2016;11(12):2183–2192. doi:10.1016/j.jtho.2016.07.026
  • Hellmann MD, Paz-Ares L, Bernabe Caro R, et al. Nivolumab plus Ipilimumab in Advanced Non-Small-Cell Lung Cancer. N Engl J Med. 2019;381(21):2020–2031. doi:10.1056/NEJMoa1910231
  • Collins AV, Brodie DW, Gilbert RJ, et al. The interaction properties of costimulatory molecules revisited. Immunity. 2002;17(2):201–210. doi:10.1016/s1074-7613(02)00362-x
  • Chambers CA, Kuhns MS, Egen JG, Allison JP. CTLA-4-mediated inhibition in regulation of T cell responses: mechanisms and manipulation in tumor immunotherapy. Annu Rev Immunol. 2001;19:565–594. doi:10.1146/annurev.immunol.19.1.565
  • Keir ME, Butte MJ, Freeman GJ, Sharpe AH. PD-1 and its ligands in tolerance and immunity. Annu Rev Immunol. 2008;26:677–704. doi:10.1146/annurev.immunol.26.021607.090331
  • Linsley PS, Bradshaw J, Greene J, et al. Intracellular trafficking of CTLA-4 and focal localization towards sites of TCR engagement. Immunity. 1996;4(6):535–543. doi:10.1016/s1074-7613(00)80480-x
  • Chae YK, Arya A, Iams W, et al. Current landscape and future of dual anti-CTLA4 and PD-1/PD-L1 blockade immunotherapy in cancer; lessons learned from clinical trials with melanoma and non-small cell lung cancer (NSCLC). J Immunother Cancer. 2018;6(1):39. doi:10.1186/s40425-018-0349-3
  • Burris HA, Infante JR, Ansell SM, et al. Safety and Activity of Varlilumab, a Novel and First-in-Class Agonist Anti-CD27 Antibody, in Patients With Advanced Solid Tumors. J Clin Oncol. 2017;35(18):2028–2036. doi:10.1200/JCO.2016.70.1508
  • Chudnovsky Y, Kim D, Zheng S, et al. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep. 2014;6(2):313–324. doi:10.1016/j.celrep.2013.12.032
  • Xia W, Mao Q, Chen B, et al. The TWIST1-centered competing endogenous RNA network promotes proliferation, invasion, and migration of lung adenocarcinoma. Oncogenesis. 2019;8(11):62. doi:10.1038/s41389-019-0167-6
  • Pacholsky D, Vakeel P, Himmel M, et al. Xin repeats define a novel actin-binding motif. J Cell Sci. 2004;117(Pt 22):5257–5268. doi:10.1242/jcs.01406
  • Paul MR, Pan TC, Pant DK, et al. Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets. J Clin Invest. 2020;130(8):4252–4265. doi:10.1172/JCI129941
  • Li X, Wu WK, Xing R, et al. Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability. Cancer Res. 2016;76(7):1724–1732. doi:10.1158/0008-5472.CAN-15-2443
  • Chen H, Chong W, Wu Q, et al. Association of LRP1B Mutation With Tumor Mutation Burden and Outcomes in Melanoma and Non-small Cell Lung Cancer Patients Treated With Immune Check-Point Blockades. Front Immunol. 2019;10:1113. doi:10.3389/fimmu.2019.01113
  • Barlesi F, Mazieres J, Merlio JP, et al. Routine molecular profiling of patients with advanced non-small-cell lung cancer: results of a 1-year nationwide programme of the French Cooperative Thoracic Intergroup (IFCT). Lancet. 2016;387(10026):1415–1426. doi:10.1016/S0140-6736(16)00004-0
  • Jeanson A, Tomasini P, Souquet-Bressand M, et al. Efficacy of Immune Checkpoint Inhibitors in KRAS-Mutant Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol. 2019;14(6):1095–1101. doi:10.1016/j.jtho.2019.01.011
  • Marinelli D, Mazzotta M, Scalera S, et al. KEAP1-driven co-mutations in lung adenocarcinoma unresponsive to immunotherapy despite high tumor mutational burden. Ann Oncol. 2020;31(12):1746–1754. doi:10.1016/j.annonc.2020.08.2105
  • Frank R, Scheffler M, Merkelbach-Bruse S, et al. Clinical and Pathological Characteristics of KEAP1- and NFE2L2-Mutated Non-Small Cell Lung Carcinoma (NSCLC). Clin Cancer Res. 2018;24(13):3087–3096. doi:10.1158/1078-0432.CCR-17-3416
  • Hellmann MD, Nathanson T, Rizvi H, et al. Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer. Cancer Cell. 2018;33(5):843–852.e4. doi:10.1016/j.ccell.2018.03.018
  • Topalian SL, Taube JM, Anders RA, Pardoll DM. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer. 2016;16(5):275–287. doi:10.1038/nrc.2016.36
  • Dong ZY, Zhong WZ, Zhang XC, et al. Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma. Clin Cancer Res. 2017;23(12):3012–3024. doi:10.1158/1078-0432.CCR-16-2554
  • Ma W, Gilligan BM, Yuan J, Li T. Current status and perspectives in translational biomarker research for PD-1/PD-L1 immune checkpoint blockade therapy. J Hematol Oncol. 2016;9(1):47. doi:10.1186/s13045-016-0277-y
  • Binnewies M, Roberts EW, Kersten K, et al. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med. 2018;24(5):541–550. doi:10.1038/s41591-018-0014-x
  • Bindea G, Mlecnik B, Tosolini M, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39(4):782–795. doi:10.1016/j.immuni
  • Ruffell B, Coussens LM. Macrophages and therapeutic resistance in cancer. Cancer Cell. 2015;27(4):462–472. doi:10.1016/j.ccell.2015.02.015
  • Fridman WH, Zitvogel L, Sautès-Fridman C, Kroemer G. The immune contexture in cancer prognosis and treatment. Nat Rev Clin Oncol. 2017;14(12):717–734. doi:10.1038/nrclinonc.2017.101
  • Danaher P, Warren S, Lu R, et al. Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA). J Immunother Cancer. 2018;6(1):63. doi:10.1186/s40425-018-0367-1
  • Damotte D, Warren S, Arrondeau J, et al. The tumor inflammation signature (TIS) is associated with anti-PD-1 treatment benefits in the CERTIM pan-cancer cohort. J Transl Med. 2019;17(1):357. doi:10.1186/s12967-019-2100-3