Genetic Links Between Common Lung Diseases and Lung Cancer Progression: Bioinformatics and Machine Learning Insights
Downloads
Doi: 10.28991/ESJ-2025-09-02-021
Full Text: PDF
Downloads
Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., & Jemal, A. (2018). Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, 68(6), 394–424. doi:10.3322/caac.21492.
Lemjabbar-Alaoui, H., Hassan, O. U., Yang, Y.-W., & Buchanan, P. (2015). Lung cancer: Biology and treatment options. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, 1856(2), 189–210. doi:10.1016/j.bbcan.2015.08.002.
Gridelli, C., Rossi, A., Carbone, D. P., Guarize, J., Karachaliou, N., Mok, T., Petrella, F., Spaggiari, L., & Rosell, R. (2015). Non-small-cell lung cancer. Nature Reviews Disease Primers, 1(1). doi:10.1038/nrdp.2015.9.
Sher, T., Dy, G. K., & Adjei, A. A. (2008). Small Cell Lung Cancer. Mayo Clinic Proceedings, 83(3), 355–367. doi:10.4065/83.3.355.
Navarro-Torné, A., Vidal, M., Trzaska, D. K., Passante, L., Crisafulli, A., Laang, H., van de Loo, J.-W., Berkouk, K., & Draghia-Akli, R. (2015). Chronic respiratory diseases and lung cancer research: a perspective from the European Union. European Respiratory Journal, 46(5), 1270–1280. doi:10.1183/13993003.00395-2015.
Sekine, Y., Katsura, H., Koh, E., Hiroshima, K., & Fujisawa, T. (2012). Early detection of COPD is important for lung cancer surveillance. European Respiratory Journal, 39(5), 1230–1240. doi:10.1183/09031936.00126011.
Young, A.Y., Shannon, V.R. (2020). Acute Respiratory Distress Syndrome in Cancer Patients. Oncologic Critical Care. Springer, Cham, Switzerland. doi:10.1007/978-3-319-74588-6_48.
Zhan, P., Suo, L. J., Qian, Q., Shen, X. K., Qiu, L. X., Yu, L. K., & Song, Y. (2011). Chlamydia pneumoniae infection and lung cancer risk: A meta-analysis. European Journal of Cancer, 47(5), 742–747. doi:10.1016/j.ejca.2010.11.003.
Xu, X., Liu, Z., Xiong, W., Qiu, M., Kang, S., Xu, Q., Cai, L., & He, F. (2020). Combined and interaction effect of chlamydia pneumoniae infection and smoking on lung cancer: A case-control study in Southeast China. BMC Cancer, 20(1), 1–10. doi:10.1186/s12885-020-07418-8.
Zhang, K., Qi, S., Cai, J., Zhao, D., Yu, T., Yue, Y., Yao, Y., & Qian, W. (2022). Content-based image retrieval with a Convolutional Siamese Neural Network: Distinguishing lung cancer and tuberculosis in CT images. Computers in Biology and Medicine, 140, 105096. doi:10.1016/j.compbiomed.2021.105096.
Qu, Y. L., Liu, J., Zhang, L. X., Wu, C. M., Chu, A. J., Wen, B. L., Ma, C., Yan, X. yan, Zhang, X., Wang, D. M., Lv, X., & Hou, S. J. (2017). Asthma and the risk of lung cancer: A meta-analysis. Oncotarget, 8(7), 11614–11620. doi:10.18632/oncotarget.14595.
Wang, Y., Liu, Y., Zhang, Q., Gao, R., & Wang, K. (2017). IPF and lung cancer: Homologous but different endings, the progress in the correlation research. International Journal of Clinical and Experimental Medicine, 10(3), 4319–4329.
Antoniou, K. M., Tomassetti, S., Tsitoura, E., & Vancheri, C. (2015). Idiopathic pulmonary fibrosis and lung cancer. Current Opinion in Pulmonary Medicine, 21(6), 626–633. doi:10.1097/mcp.0000000000000217.
Qubo, A. A., Numan, J., Snijder, J., Padilla, M., Austin, J. H. M., Capaccione, K. M., Pernia, M., Bustamante, J., O'connor, T., & Salvatore, M. M. (2022). Idiopathic pulmonary fibrosis and lung cancer: future directions and challenges. Breathe, 18(4). doi:10.1183/20734735.0147-2022.
Ang, L., Ghosh, P., & Seow, W. J. (2021). Association between previous lung diseases and lung cancer risk: a systematic review and meta-analysis. Carcinogenesis, 42(12), 1461–1474. doi:10.1093/carcin/bgab082.
Li, J., Zhang, J. T., Jiang, X., Shi, X., Shen, J., Feng, F., Chen, J., Liu, G., He, P., Jiang, J., Tsang, L. L., Wang, Y., Rosell, R., Jiang, L., He, J., & Chan, H. C. (2015). The cystic fibrosis transmembrane conductance regulator as a biomarker in non-small cell lung cancer. International Journal of Oncology, 46(5), 2107–2115. doi:10.3892/ijo.2015.2921.
Miron, O., Afrasanie, V. A., Paduraru, M. I., Trandafir, L. M., & Miron, L. (2020). The relationship between chronic lung diseases and lung cancer-a narrative review. J BUON, 25, 1687-92.
Otálora-Otálora, B. A., Florez, M., López-Kleine, L., Canas Arboleda, A., Grajales Urrego, D. M., & Rojas, A. (2019). Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Frontiers in Genetics, 10, 1260. doi:10.3389/fgene.2019.01260.
Yao, Y., Li, Z., & Gao, W. (2022). Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and NSCLC Progression:Evidence From Bioinformatics Analysis. Frontiers in Genetics, 13, 855789. doi:10.3389/fgene.2022.855789.
Dasgupta, S. (2024). Identification of Hub Genes in Interstitial Lung Disease and their Association With Lung Cancer: An In-Silico Analysis. ICCECE 2024 - International Conference on Computer, Electrical and Communication Engineering, 1–8. doi:10.1109/ICCECE58645.2024.10497218.
Hossain, M. A., Rahman, M. Z., Bhuiyan, T., & Moni, M. A. (2024). Identification of Biomarkers and Molecular Pathways Implicated in Smoking and COVID-19 Associated Lung Cancer Using Bioinformatics and Machine Learning Approaches. International Journal of Environmental Research and Public Health, 21(11), 1392. doi:10.3390/ijerph21111392.
Ding, X., Liu, H., Xu, Q., Ji, T., Chen, R., Liu, Z., & Dai, J. (2024). Shared biomarkers and mechanisms in idiopathic pulmonary fibrosis and non-small cell lung cancer. International Immunopharmacology, 134, 112162. doi:10.1016/j.intimp.2024.112162.
Dasgupta, S. (2024). Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning. OMICS A Journal of Integrative Biology, 28(7), 347–356. doi:10.1089/omi.2024.0116.
Langfelder, P., & Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics, 9, 1–13. doi:10.1186/1471-2105-9-559.
Ali Hossain, M., Asa, T. A., Rabiul Auwul, M., Aktaruzzaman, M., Mahfizur Rahman, M., Rahman, M. Z., & Moni, M. A. (2023). The pathogenetic influence of smoking on SARS-CoV-2 infection: Integrative transcriptome and regulomics analysis of lung epithelial cells. Computers in Biology and Medicine, 159, 106885. doi:10.1016/j.compbiomed.2023.106885.
Hossain, Md. A., Saiful Islam, S. M., Quinn, J. M. W., Huq, F., & Moni, M. A. (2019). Machine learning and bioinformatics models to identify gene expression patterns of ovarian cancer associated with disease progression and mortality. Journal of Biomedical Informatics, 100, 103313. doi:10.1016/j.jbi.2019.103313.
Hossain, M. A., Asa, T. A., Rahman, M. M., Uddin, S., Moustafa, A. A., Quinn, J. M. W., & Moni, M. A. (2020). Network-based genetic profiling reveals cellular pathway differences between follicular thyroid carcinoma and follicular thyroid adenoma. International Journal of Environmental Research and Public Health, 17(4), 1373. doi:10.3390/ijerph17041373.
Xu, H., Moni, M. A., & Liò, P. (2015). Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer. Computational Biology and Chemistry, 59, 15–31. doi:10.1016/j.compbiolchem.2015.08.010.
Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, L. J., & Von Mering, C. (2019). STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), D607–D613. doi:10.1093/nar/gky1131.
Chen, S. H., Chin, C. H., Wu, H. H., Ho, C. W., Ko, M. T., & Lin, C. Y. (2009). cyto-Hubba: A Cytoscape plug-in for hub object analysis in network biology. 20th international conference on genome informatics. 14-16, December, 2009, Yokohama, Japan.
Ma, Z., Xu, J., Ru, L., & Zhu, W. (2021). Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis. Bioscience Reports, 41(4). doi:10.1042/BSR20203676.
Wei, J., Wang, Y., Shi, K., & Wang, Y. (2020). Identification of Core Prognosis"Related Candidate Genes in Cervical Cancer via Integrated Bioinformatical Analysis. BioMed Research International, 8959210. doi:10.1155/2020/8959210.
Gu, F. F., Zhang, Y., Liu, Y. Y., Hong, X. H., Liang, J. Y., Tong, F., Yang, J. S., & Liu, L. (2016). Lung adenocarcinoma harboring concomitant SPTBN1-ALK fusion, c-Met overexpression, and HER-2 amplification with inherent resistance to crizotinib, chemotherapy, and radiotherapy. Journal of Hematology & Oncology, 9(1), 1–3. doi:10.1186/s13045-016-0296-8.
Guo, S., Wu, X. Y., Lei, T., Zhong, R., Wang, Y. R., Zhang, L., Zhao, Q. Y., Huang, Y., Shi, Y., & Wu, L. (2022). The Role and Therapeutic Value of Syndecan-1 in Cancer Metastasis and Drug Resistance. Frontiers in Cell and Developmental Biology, 9, 3663. doi:10.3389/fcell.2021.784983.
Zheng, Y., Chen, L., Li, J., Yu, B., Su, L., Chen, X., Yu, Y., Yan, M., Liu, B., & Zhu, Z. (2011). Hypermethylated DNA as potential biomarkers for gastric cancer diagnosis. Clinical Biochemistry, 44(17–18), 1405–1411. doi:10.1016/j.clinbiochem.2011.09.006.
Angi, B., Muccioli, S., Szabò, I., & Leanza, L. (2023). A Meta-Analysis Study to Infer Voltage-Gated K+ Channels Prognostic Value in Different Cancer Types. Antioxidants, 12(3), 573. doi:10.3390/antiox12030573.
Liu, Y., Li, X., Chang, R., Chen, Y., & Gao, Y. (2020). PLEK2 and SCN7A: novel biomarkers of non-small cell lung cancer. Preprint: Research Square, 1-19. doi:10.21203/rs.3.rs-16005/v1.
Lv, H., Song, H., Qin, Z., Xing, R., & Chen, Y. (2023). Underexpression of SCN7A is associated with poor prognosis in lung adenocarcinoma. Gene & Protein in Disease, 2(1), 363. doi:10.36922/gpd.363.
Xu, C., Song, L., Yang, Y., Liu, Y., Pei, D., Liu, J., Guo, J., Liu, N., Li, X., Liu, Y., Li, X., Yao, L., & Kang, Z. (2022). Clinical M2 Macrophage-Related Genes Can Serve as a Reliable Predictor of Lung Adenocarcinoma. Frontiers in Oncology, 12, 919899. doi:10.3389/fonc.2022.919899.
Al-Dherasi, A., Huang, Q. T., Liao, Y., Al-Mosaib, S., Hua, R., Wang, Y., Yu, Y., Zhang, Y., Zhang, X., Huang, C., Mousa, H., Ge, D., Sufiyan, S., Bai, W., Liu, R., Shao, Y., Li, Y., Zhang, J., Shi, L., ... Liu, Q. (2021). A seven-gene prognostic signature predicts overall survival of patients with lung adenocarcinoma (LUAD). Cancer Cell International, 21(1), 1–16. doi:10.1186/s12935-021-01975-z.
Kumar-Singh, A., Parniewska, M. M., Giotopoulou, N., Javadi, J., Sun, W., Szatmári, T., Dobra, K., Hjerpe, A., & Fuxe, J. (2021). Nuclear syndecan-1 regulates epithelial-mesenchymal plasticity in tumor cells. Biology, 10(6), 521. doi:10.3390/biology10060521.
Shah, L., Walter, K. L., Borczuk, A. C., Kawut, S. M., Sonett, J. R., Gorenstein, L. A., Ginsburg, M. E., Steinglass, K. M., & Powell, C. A. (2004). Expression of syndecan-1 and expression of epidermal growth factor receptor are associated with survival in patients with nonsmall cell lung carcinoma. Cancer, 101(7), 1632–1638. doi:10.1002/cncr.20542.
Anttonen, A., Heikkilä, P., Kajanti, M., Jalkanen, M., & Joensuu, H. (2001). High syndecan-1 expression is associated with favourable outcome in squamous cell lung carcinoma treated with radical surgery. Lung Cancer, 32(3), 297–305. doi:10.1016/S0169-5002(00)00230-0.
Parimon, T., Brauer, R., Schlesinger, S. Y., Xie, T., Jiang, D., Ge, L., Huang, Y., Birkland, T. P., Parks, W. C., Habiel, D. M., Hogaboam, C. M., Gharib, S. A., Deng, N., Liu, Z., & Chen, P. (2018). Syndecan-1 Controls Lung Tumorigenesis by Regulating miRNAs Packaged in Exosomes. The American Journal of Pathology, 188(4), 1094–1103. doi:10.1016/j.ajpath.2017.12.009.
Zhai, Y., Chen, Y., Jiang, Y., & Li, Q. (2019). Weighted Gene Co-expression Network Analysis of Gene Modules for Lung Adenocarcinoma. 2018 5th International Conference on Systems and Informatics, ICSAI 2018, 473–477. doi:10.1109/ICSAI.2018.8599411.
Chen, M., Zeng, J., Chen, S., Li, J., Wu, H., Dong, X., Lei, Y., Zhi, X., & Yao, L. (2020). SPTBN1 suppresses the progression of epithelial ovarian cancer via SOCS3-mediated blockade of the JAK/STAT3 signaling pathway. Aging, 12(11), 10896–10911. doi:10.18632/aging.103303.
Ying, J., Lin, C., Wu, J., Guo, L., Qiu, T., Ling, Y., Shan, L., Zhou, H., Zhao, D., Wang, J., Liang, J., Zhao, J., Jiao, Y., Lu, N., & Zhao, H. (2015). Anaplastic lymphoma kinase rearrangement in digestive tract cancer: Implication for targeted therapy in Chinese population. PLoS ONE, 10(12), 144731. doi:10.1371/journal.pone.0144731.
Yang, P., Yang, Y., Sun, P., Tian, Y., Gao, F., Wang, C., Zong, T., Li, M., Zhang, Y., Yu, T., & Jiang, Z. (2020). βII spectrin (SPTBN1): Biological function and clinical potential in cancer and other diseases. International Journal of Biological Sciences, 17(1), 32–49. doi:10.7150/ijbs.52375.
Li, A., Zhang, W., Xia, H., Miao, Y., Zhou, H., Zhang, X., Dong, Q., Li, Q., Qiu, X., & Wang, E. (2016). Overexpression of CASS4 promotes invasion in non-small cell lung cancer by activating the AKT signaling pathway and inhibiting E-cadherin expression. Tumor Biology, 37(11), 15157–15164. doi:10.1007/s13277-016-5411-5.
Kang, J. Y., Yang, J., Lee, H., Park, S., Gil, M., & Kim, K. E. (2024). Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma. International Journal of Molecular Sciences, 25(1), 359. doi:10.3390/ijms25010359.
Xu, J., Zheng, H., Yuan, S., Zhou, B., Zhao, W., Pan, Y., & Qi, D. (2019). Overexpression of ANLN in lung adenocarcinoma is associated with metastasis. Thoracic Cancer, 10(8), 1702–1709. doi:10.1111/1759-7714.13135.
Ru, M., Liu, Y.-B., Tian, Z.-H., GODJE, I. S. G., & Li, J.-Q. (2021). ANLN and Lung Adenocarcinoma Prognosis and Immune Infiltration Research. Preprint: Research Square, 1-21. doi:10.21203/rs.3.rs-826813/v1.
Kasprowicz, A., Sophie, G. D., Lagadec, C., & Delannoy, P. (2022). Role of GD3 Synthase ST8Sia I in Cancers. Cancers, 14(5), 1299. doi:10.3390/cancers14051299.
Tang, W., Wang, J., Dai, T., Qiu, H., Liu, C., Chen, S., & Hu, Z. (2024). Association of leptin receptor polymorphisms with susceptibility of non-small cell lung cancer: Evidence from 2249 subjects. Cancer Medicine, 13(8), 7178. doi:10.1002/cam4.7178.
Ji, X., Bossé, Y., Landi, M. T., Gui, J., Xiao, X., Qian, D., Joubert, P., Lamontagne, M., Li, Y., Gorlov, I., de Biasi, M., Han, Y., Gorlova, O., Hung, R. J., Wu, X., McKay, J., Zong, X., Carreras-Torres, R., Christiani, D. C., ... Amos, C. I. (2018). Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk. Nature Communications, 9(1). doi:10.1038/s41467-018-05074-y.
Galluzzi, L., Vitale, I., Senovilla, L., Olaussen, K. A., Pinna, G., Eisenberg, T., Goubar, A., Martins, I., Michels, J., Kratassiouk, G., Carmona-Gutierrez, D., Scoazec, M., Vacchelli, E., Schlemmer, F., Kepp, O., Shen, S., Tailler, M., Niso-Santano, M., Morselli, E., ... Kroemer, G. (2012). Prognostic Impact of Vitamin B6 Metabolism in Lung Cancer. Cell Reports, 2(2), 257–269. doi:10.1016/j.celrep.2012.06.017.
Zuo, H., Ueland, P. M., Midttun, í˜., Tell, G. S., Fanidi, A., Zheng, W., Shu, X., Xiang, Y., Wu, J., Prentice, R., Pettinger, M., Thomson, C. A., Giles, G. G., Hodge, A., Cai, Q., Blot, W. J., Johansson, M., Hultdin, J., Grankvist, K., ... Ulvik, A. (2019). Vitamin B6 catabolism and lung cancer risk: results from the Lung Cancer Cohort Consortium (LC3). Annals of Oncology, 30(3), 478–485. doi:10.1093/annonc/mdz002.
Ahmed, M. B., Alghamdi, A. A. A., Islam, S. U., Lee, J.-S., & Lee, Y.-S. (2022). cAMP Signaling in Cancer: A PKA-CREB and EPAC-Centric Approach. Cells, 11(13), 2020. doi:10.3390/cells11132020.
Han, K., Wang, J., Qian, K., Zhao, T., & Zhang, Y. (2021). Establishment of non-small-cell lung cancer risk prediction model based on prognosis-associated ADME genes. Bioscience Reports, 41(10), BSR20211433. doi:10.1042/BSR20211433.
Zhuo, D., Li, X., & Guan, F. (2018). Biological Roles of Aberrantly Expressed Glycosphingolipids and Related Enzymes in Human Cancer Development and Progression. Frontiers in Physiology, 9. doi:10.3389/fphys.2018.00466.
Wei, Z., Liu, X., Cheng, C., Yu, W., & Yi, P. (2021). Metabolism of Amino Acids in Cancer. Frontiers in Cell and Developmental Biology, 8. doi:10.3389/fcell.2020.603837.
- This work (including HTML and PDF Files) is licensed under a Creative Commons Attribution 4.0 International License.
