Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer
- Authors: Jin Q.1, Yu K.2, Zhang X.3, Huo D.4, Zhang D.3, Liu L.5, Xie H.2, Liang B.6, Chen X.1
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Affiliations:
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology,, Harbin Medical University
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University,
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University
- Department of Pharmacogenomics, College of Bioinformatics and Science Technology,, Harbin Medical University,
- Department of Biochemistry and Medical Genetics,, University of Manitoba
- Issue: Vol 19, No 2 (2024)
- Pages: 129-143
- Section: Life Sciences
- URL: https://jdigitaldiagnostics.com/1574-8936/article/view/643788
- DOI: https://doi.org/10.2174/1574893618666230913110025
- ID: 643788
Cite item
Full Text
Abstract
Background:The oligometastatic disease has been proposed as an intermediate state between primary tumor and systemically metastatic disease, which has great potential curable with locoregional therapies. However, since no biomarker for the identification of patients with true oligometastatic disease is clinically available, the diagnosis of oligometastatic disease remains controversial.
Objective:We aim to identify potential biomarkers of colorectal cancer patients with true oligometastatic states, who will benefit most from local therapy.
Methods:This study retrospectively analyzed the transcriptome profiles and clinical parameters of 307 metastatic colorectal cancer patients. A novel network propagation method and network-based strategy were combined to identify oligometastatic biomarkers to predict the prognoses of metastatic colorectal cancer patients.
Results:We defined two metastatic risk groups according to twelve oligometastatic biomarkers, which exhibit distinct prognoses, clinicopathological features, immunological characteristics, and biological mechanisms. The metastatic risk assessment model exhibited a more powerful capacity for survival prediction compared to traditional clinicopathological features. The low-MRS group was most consistent with an oligometastatic state, while the high-MRS might be a potential polymetastatic state, which leads to the divergence of their prognostic outcomes and response to treatments. We also identified 22 significant immune check genes between the high-MRS and low- MRS groups. The difference in molecular mechanism between the two metastatic risk groups was associated with focal adhesion, nucleocytoplasmic transport, Hippo, PI3K-Akt, TGF-β, and EMCreceptor interaction signaling pathways.
Conclusion:Our study provided a molecular definition of the oligometastatic state in colorectal cancer, which contributes to precise treatment decision-making for advanced patients.
About the authors
Qing Jin
Department of Pharmacogenomics, College of Bioinformatics and Science Technology,, Harbin Medical University
Email: info@benthamscience.net
Kexin Yu
Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University
Email: info@benthamscience.net
Xianze Zhang
Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University,
Email: info@benthamscience.net
Diwei Huo
Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University
Email: info@benthamscience.net
Denan Zhang
Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University,
Email: info@benthamscience.net
Lei Liu
Department of Pharmacogenomics, College of Bioinformatics and Science Technology,, Harbin Medical University,
Email: info@benthamscience.net
Hongbo Xie
Department of Pharmacogenomics, College of Bioinformatics and Science Technology, Harbin Medical University
Email: info@benthamscience.net
Binhua Liang
Department of Biochemistry and Medical Genetics,, University of Manitoba
Author for correspondence.
Email: info@benthamscience.net
Xiujie Chen
Department of Pharmacogenomics, College of Bioinformatics and Science Technology,, Harbin Medical University
Author for correspondence.
Email: info@benthamscience.net
References
- Wu C. Systemic therapy for colon cancer. Surg Oncol Clin N Am 2018; 27(2): 235-42. doi: 10.1016/j.soc.2017.11.001 PMID: 29496087
- Turajlic S, Swanton C. Metastasis as an evolutionary process. Science 2016; 352(6282): 169-75. doi: 10.1126/science.aaf2784 PMID: 27124450
- Pitroda SP, Weichselbaum RR. Integrated molecular and clinical staging defines the spectrum of metastatic cancer. Nat Rev Clin Oncol 2019; 16(9): 581-8. doi: 10.1038/s41571-019-0220-6 PMID: 31092903
- Hellman S, Weichselbaum RR. Oligometastases. J Clin Oncol 1995; 13(1): 8-10. doi: 10.1200/JCO.1995.13.1.8 PMID: 7799047
- Gomez DR, Tang C, Zhang J, et al. Local consolidative therapy Vs. Maintenance therapy or observation for patients with oligometastatic nonsmall-cell lung cancer: Long-term results of a multi-institutional, phase ii, randomized study. J Clin Oncol 2019; 37(18): 1558-65. doi: 10.1200/JCO.19.00201 PMID: 31067138
- Iyengar P, Wardak Z, Gerber DE, et al. Consolidative radiotherapy for limited metastatic nonsmall-cell lung cancer. JAMA Oncol 2018; 4(1): e173501. doi: 10.1001/jamaoncol.2017.3501 PMID: 28973074
- Ruers T, Van Coevorden F, Punt CJA, et al. Local treatment of unresectable colorectal liver metastases: Results of a randomized phase ii trial. J Natl Cancer Inst 2017; 109(9): djx015. doi: 10.1093/jnci/djx015 PMID: 28376151
- Kobayashi N, Abe T, Noda SE, et al. Stereotactic body radiotherapy for pulmonary oligometastasis from colorectal cancer. In Vivo 2020; 34(5): 2991-6. doi: 10.21873/invivo.12130 PMID: 32871842
- Rees M, Tekkis PP, Welsh FKS, ORourke T, John TG. Evaluation of long-term survival after hepatic resection for metastatic colorectal cancer: A multifactorial model of 929 patients. Ann Surg 2008; 247(1): 125-35. doi: 10.1097/SLA.0b013e31815aa2c2 PMID: 18156932
- Ashworth AB, Senan S, Palma DA, et al. An individual patient data metaanalysis of outcomes and prognostic factors after treatment of oligometastatic non-small-cell lung cancer. Clin Lung Cancer 2014; 15(5): 346-55. doi: 10.1016/j.cllc.2014.04.003 PMID: 24894943
- Navrátil J, Poprach A, Lakomý R, et al. Oligometastatic prostate cancer. Clin Oncol: J Czech Slovak Oncol Soc 2019; 32(2): 97-100. doi: 10.14735/amko201997
- Routman DM, Chera BS, Gupta GP. Circulating tumor DNA biomarkers for early detection of oligometastasis. Cancer J 2020; 26(2): 116-23. doi: 10.1097/PPO.0000000000000437 PMID: 32205535
- Kwapisz D. Oligometastatic breast cancer. Breast Cancer 2019; 26(2): 138-46. doi: 10.1007/s12282-018-0921-1 PMID: 30324552
- Uppal A, Ferguson MK, Posner MC, Hellman S, Khodarev NN, Weichselbaum RR. Towards a molecular basis of oligometastatic disease: Potential role of micro-RNAs. Clin Exp Metastasis 2014; 31(6): 735-48. doi: 10.1007/s10585-014-9664-3 PMID: 24968866
- Pitroda SP, Khodarev NN, Huang L, et al. Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis. Nat Commun 2018; 9(1): 1793. doi: 10.1038/s41467-018-04278-6 PMID: 29728604
- Cheng F, Kovács IA, Barabási AL. Network-based prediction of drug combinations. Nat Commun 2019; 10(1): 1197. doi: 10.1038/s41467-019-09186-x PMID: 30867426
- Tate JG, Bamford S, Jubb HC, et al. COSMIC: The catalogue of somatic mutations in cancer. Nucleic Acids Res 2019; 47(D1): D941-7. doi: 10.1093/nar/gky1015 PMID: 30371878
- Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R. Associating genes and protein complexes with disease via network propagation. PLOS Comput Biol 2010; 6(1): e1000641. doi: 10.1371/journal.pcbi.1000641 PMID: 20090828
- Valdeolivas A, Tichit L, Navarro C, et al. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics 2019; 35(3): 497-505. doi: 10.1093/bioinformatics/bty637 PMID: 30020411
- Jäger M. MCL: Markov cluster algorithm. 2015. Available from: https://cran.r-project.org/web/packages/MCL/MCL.pdf
- Studer MJBZGDDSUL. Clustering of weighted data. 2014. Available from: https://cran.r-project.org/web/packages/WeightedCluster/WeightedCluster.pdf
- Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst 2015; 1(6): 417-25. doi: 10.1016/j.cels.2015.12.004 PMID: 26771021
- Chin CH, Chen SH, Wu HH, et al. CytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Syst Biol 2014; 4(S4): S11.
- Fitzgerald M, Saville BR, Lewis RJ. Decision curve analysis. JAMA 2015; 313(4): 409-10. doi: 10.1001/jama.2015.37 PMID: 25626037
- 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): 1747-56. doi: 10.1101/gr.239244.118 PMID: 30341162
- Guinney J, Dienstmann R, Wang X, et al. The consensus molecular subtypes of colorectal cancer. Nat Med 2015; 21(11): 1350-6. doi: 10.1038/nm.3967 PMID: 26457759
- Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun 2013; 4(1): 2612. doi: 10.1038/ncomms3612 PMID: 24113773
- Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 2015; 12(5): 453-7. doi: 10.1038/nmeth.3337 PMID: 25822800
- Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15(12): 550. doi: 10.1186/s13059-014-0550-8 PMID: 25516281
- Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation 2021; 2(3): 100141. doi: 10.1016/j.xinn.2021.100141 PMID: 34557778
- Yin H, Gao T, Xie J, et al. FUBP1 promotes colorectal cancer stemness and metastasis via DVL1‐mediated activation of Wnt/β‐catenin signaling. Mol Oncol 2021; 15(12): 3490-512. doi: 10.1002/1878-0261.13064 PMID: 34288405
- Cai Z, Mei Y, Jiang X, Shi X. WDR74 promotes proliferation and metastasis in colorectal cancer cells through regulating the Wnt/β-catenin signaling pathway. Open Life Sci 2021; 16(1): 920-9. doi: 10.1515/biol-2021-0096 PMID: 34553072
- Li Q, Lai Q, He C, et al. RUNX1 promotes tumour metastasis by activating the Wnt/β-catenin signalling pathway and EMT in colorectal cancer. J Exp Clin Cancer Res 2019; 38(1): 334. doi: 10.1186/s13046-019-1330-9 PMID: 31370857
- Zhao H, Wei J, Sun J. Roles of TGF-β signaling pathway in tumor microenvirionment and cancer therapy. Int Immunopharmacol 2020; 89(Pt B): 107101.
- Aoki M, Fujishita T. Oncogenic roles of the PI3K/AKT/mTOR axis. Curr Top Microbiol Immunol 2017; 407: 153-89. doi: 10.1007/82_2017_6 PMID: 28550454
- Ni J, Zheng H, Ou Y, et al. miR-5155p suppresses HCC migration and invasion via targeting IL6/JAK/STAT3 pathway. Surg Oncol 2020; 34: 113-20. doi: 10.1016/j.suronc.2020.03.003 PMID: 32891315
- Mele V, Basso C, Governa V, et al. Identification of TPM2 and CNN1 as novel prognostic markers in functionally characterized human colon cancer-associated stromal cells. Cancers 2022; 14(8): 2024. doi: 10.3390/cancers14082024 PMID: 35454931
- Hu FF, Liu CJ, Liu LL, Zhang Q, Guo AY. Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response. Brief Bioinform 2021; 22(3): bbaa176. doi: 10.1093/bib/bbaa176 PMID: 32814346
- Weichselbaum RR, Hellman S. Oligometastases revisited. Nat Rev Clin Oncol 2011; 8(6): 378-82. doi: 10.1038/nrclinonc.2011.44 PMID: 21423255
- Gutiontov SI, Pitroda SP, Tran PT, Weichselbaum RR. (Oligo)metastasis as a spectrum of disease. Cancer Res 2021; 81(10): 2577-83. doi: 10.1158/0008-5472.CAN-20-3337 PMID: 33452011
- Guckenberger M, Lievens Y, Bouma AB, et al. Characterisation and classification of oligometastatic disease: A european society for radiotherapy and oncology and european organisation for research and treatment of cancer consensus recommendation. Lancet Oncol 2020; 21(1): e18-28. doi: 10.1016/S1470-2045(19)30718-1 PMID: 31908301
- Gutiontov SI, Pitroda SP, Weichselbaum RR. Oligometastasis: Past, present, future. Int J Radiat Oncol Biol Phys 2020; 108(3): 530-8. doi: 10.1016/j.ijrobp.2020.02.019 PMID: 32976785
- Guo S, Deng CX. Effect of stromal cells in tumor microenvironment on metastasis initiation. Int J Biol Sci 2018; 14(14): 2083-93. doi: 10.7150/ijbs.25720 PMID: 30585271
- Denton AE, Roberts EW, Fearon DT. Stromal cells in the tumor microenvironment. Adv Exp Med Biol 2018; 1060: 99-114. doi: 10.1007/978-3-319-78127-3_6 PMID: 30155624
- Lorusso G, Rüegg C. The tumor microenvironment and its contribution to tumor evolution toward metastasis. Histochem Cell Biol 2008; 130(6): 1091-103. doi: 10.1007/s00418-008-0530-8 PMID: 18987874
- Zhu L, Fu X, Chen X, Han X, Dong P. M2 macrophages induce EMT through the TGF-β/Smad2 signaling pathway. Cell Biol Int 2017; 41(9): 960-8. doi: 10.1002/cbin.10788 PMID: 28493530
- Lu J, Kang X, Wang Z, Zhao G, Jiang B. The activity level of follicular helper T cells in the peripheral blood of osteosarcoma patients is associated with poor prognosis. Bioengineered 2022; 13(2): 3751-9. doi: 10.1080/21655979.2022.2031387 PMID: 35081874
- Yuen GJ, Demissie E, Pillai S. B lymphocytes and cancer: A love-hate relationship. Trends Cancer 2016; 2(12): 747-57. doi: 10.1016/j.trecan.2016.10.010 PMID: 28626801
- Dewan MZ, Terunuma H, Takada M, et al. Role of natural killer cells in hormone-independent rapid tumor formation and spontaneous metastasis of breast cancer cells In Vivo. Breast Cancer Res Treat 2007; 104(3): 267-75. doi: 10.1007/s10549-006-9416-4 PMID: 17066321
- Neophytou CM, Panagi M, Stylianopoulos T, Papageorgis P. The role of tumor microenvironment in cancer metastasis: Molecular mechanisms and therapeutic opportunities. Cancers 2021; 13(9): 2053. doi: 10.3390/cancers13092053 PMID: 33922795
- Geuijen C, Tacken P, Wang LC, et al. A human CD137×PD-L1 bispecific antibody promotes anti-tumor immunity via context-dependent T cell costimulation and checkpoint blockade. Nat Commun 2021; 12(1): 4445. doi: 10.1038/s41467-021-24767-5 PMID: 34290245
- Glorieux C, Huang P. Regulation of CD137 expression through K-Ras signaling in pancreatic cancer cells. Cancer Commun 2019; 39(1): 41. doi: 10.1186/s40880-019-0386-4 PMID: 31288851
- Wang J, Zhao W, Cheng L, et al. CD137-mediated pathogenesis from chronic hepatitis to hepatocellular carcinoma in hepatitis B virus-transgenic mice. J Immunol 2010; 185(12): 7654-62. doi: 10.4049/jimmunol.1000927 PMID: 21059892
- Wu J, Wang Y. Role of TNFSF9 bidirectional signal transduction in antitumor immunotherapy. Eur J Pharmacol 2022; 928: 175097. doi: 10.1016/j.ejphar.2022.175097 PMID: 35714694
- Broll K, Richter G, Pauly S, Hofstaedter F, Schwarz H. CD137 expression in tumor vessel walls. High correlation with malignant tumors. Am J Clin Pathol 2001; 115(4): 543-9. doi: 10.1309/E343-KMYX-W3Y2-10KY PMID: 11293902
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