Determination of biomarker candidates with proteomics approach in small cell lung cancer: NCI-H209 cell line

Year 2024, , 188 - 194, 30.12.2024

Nebiye Pelin Türker , Saffet Çelik

https://doi.org/10.51753/flsrt.1511261

Abstract

Proteins, the primary building blocks of the cell membrane, play crucial roles in communication between cells as well as interactions with the extracellular matrix. They make for an excellent resource for disease identification due to their potential as biomarkers. In order to perform the study, HEL-299 (CCL-137™) and NCI-H209 lung cells were incubated at 37°C in a chamber that contained 5% CO2. Trypsinization was used to transfer the cells into Eppendorf tubes. Proteomics analyses were carried out using LC-QTOF equipment, and the corresponding procedures of denaturation, alkynylation, trypsinization, and purification were carried out by adding the required chemicals. The Searchquie and PeptideShacker software interfaces were used to assess the analysis findings. Proteins that differ across groups are displayed by classifying them based on their roles as cellular components, molecular activities, and biological processes. Proteomics data showed that the lung cancer cell line NCI-H209 lacked 14 proteins that were present in the healthy lung cell HEL-299. These are the proteins ANK3, PIK3R2, INPP5F, HSF1, VIM, NFAM1, SHROOM3, ETV4, RNF31, LMNA, BRD8, PRTN3, TERT, SMAD9. There were discovered to be 5 distinct proteins in the lung cancer group compared to healthy lung HEL-299 cells. These proteins are AHSG, NCOA6, VCP, DNAJC19, NCL. Given the heterogeneity of lung cancer, a thorough and in-depth investigation of lung cancer proteome profiling is necessary for effective target treatment. The examination of proteins as prospective lung cancer biomarker candidates shows that it will make up a viable source for clinical investigations. These proteins differ in the direction in this study. Potential clinical applications of the biomarkers identified in this study, such as early diagnosis, monitoring treatment response, and determining disease prognosis, may contribute to the development of personalized medicine approaches.

Keywords

Biomarker, cancer, proteomics, small cell, lung cancer

Ethical Statement

The development, acquisition, authentication, cryopreservation, and transfer of cell lines between laboratories were followed according to the guidelines published in the British Journal of Cancer, 2014.

References

• Ahamed, M. T., Forshed, J., Levitsky, A., Lehtiö, J., Bajalan, A., Pernemalm, M., ... & Andersson, B. (2024). Multiplex plasma protein assays as a diagnostic tool for lung cancer. Cancer Science, 115(10), 3439-3454.
• Atasever, S. (2024). Identification of potential hub genes as biomarkers for breast, ovarian, and endometrial cancers. Front Life Sci RT, 5(1), 7482.
• Bache, N., Møller, H. D., Bjerregaard, M. R., & Müller, S. (2018). The impact of protein abundance on the detection of proteins in mass spectrometry. Journal of Proteomics, 177, 1-9.
• Chen, L., He, H., Wang, T., Wu, L., Xu, D., & Zhang, H. (2022). Mass spectrometry-based proteomics in cancer research: Challenges and opportunities. Molecular Cancer, 21(1), 37.
• Chen, X. P., Lu, Y. H., Xu, B., Wei, Y. X., Cui, X. L., Zhang, W. W., ... & Feng, C. G. (2024). Retention time-independent strategy for screening pesticide residues in herbs based on a fingerprint database and all ion fragmentation acquisition with LC-QTOF MS. Analytical Methods, 16(45), 7831-7841.
• Cho, C. K., Shan, S. J., Winsor, E. J., & Diamandis, E. P. (2007). Proteomics analysis of human amniotic fluid. Molecular & Cellular Proteomics, 6(8), 1406-1415.
• Compomics. (2024). PeptideShaker, https://compomics.github.io/projects/ peptide-shaker Last accessed on December 25, 2024.
• Costantini, S., Capone, F., Polo, A., Bagnara, P., & Budillon, A. (2021). Valosin-containing protein (VCP)/p97: A prognostic biomarker and therapeutic target in cancer. International Journal of Molecular Sciences, 22(18), 10177.
• Davies, M. P., Sato, T., Ashoor, H., Hou, L., Liloglou, T., Yang, R., & Field, J. K. (2023). Plasma protein biomarkers for early prediction of lung cancer. EBioMedicine, 93.
• Duffy, M. J., McDermott, E., & Clynes, M. (2023). Biomarkers for detection and treatment of cancer: A comprehensive review. Clinical Cancer Research, 29(4), 655-663.
• Fan, M., Liu, Q., Ma, X., Jiang, Y., Wang, Y., Jia, S., ... & Zhang, X. (2024). ZNF131-BACH1 transcriptionally accelerates RAD51-dependent homologous recombination repair and therapy-resistance of non-small-lung cancer cells by preventing their degradation from CUL3. Theranostics, 14(18), 7241.
• Fang, S., Wang, H., Lu, L., Jia, Y., & Xia, Z. (2020). Decreased complement C3 levels are associated with poor prognosis in patients with COVID-19: A retrospective cohort study. International immunopharmacology, 89, 107070.
• Gao, S., Xu, B., Sun, J., & Zhang, Z. (2024). Nanotechnological advances in cancer: Therapy a comprehensive review of carbon nanotube applications. Frontiers in Bioengineering and Biotechnology, 12, 1351787.
• Gasparri, R., Sabalic, A., & Spaggiari, L. (2023). The Early Diagnosis of Lung Cancer: Critical Gaps in the Discovery of Biomarkers. Journal of Clinical Medicine, 12(23), 7244.
• Ghosh, S., Bhan, M. K., & Ghosh, S. (2023). Trends in lung cancer incidence and mortality in India: A comprehensive review. Asian Pacific Journal of Cancer Prevention, 24(2), 453-460.
• Gonzalez, M., Guarino, V., & Friedrich, C. (2021). Proteomic analysis of lung cancer cell lines reveals unique secretome profiles. Journal of Proteomics, 240, 104178.
• Guan, P. P., Yu, X., Zou, Y. H., & Wang, P. (2019). Cyclooxygenase-2 is critical for the propagation of β-amyloid protein and reducing the glycosylation of tau in Alzheimer’s disease. Cellular & molecular immunology, 16(11), 892-894.
• Kawasaki, T., Takeda, Y., & Kumanogoh, A. (2024). Proteomics of blood extracellular vesicles in inflammatory respiratory diseases for biomarker discovery and new insights into pathophysio-logy. Inflammation and Regeneration, 44(1), 38.
• Kim, H., Lee, C., & Park, J. (2020). Challenges in proteomic analysis: The importance of sample preparation. Proteomics, 20(10), 1900076.
• Kalluri, R., & LeBleu, V. S. (2022). The biology of the extracellular matrix: Role in cancer and therapy. Nature Reviews Cancer, 22(12), 753-767.
• Kulasingam, V., & Diamandis, E. P. (2007). Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Molecular & cellular proteomics, 6(11), 1997-2011.
• Lee, J., Kim, H., & Hwang, S. (2023). Emerging trends in cancer proteomics: Applications and innovations. Journal of Proteomics, 250, 104304.
• Li, S., Qu, Y., Liu, L., Zhang, X., He, Y., Wang, C., Guo, Y., Yuan, L., Ma, Z., Bai, H., & Wang, J. (2023). Comparative proteomic profiling of plasma exosomes in lung cancer cases of liver and brain metastasis. Cell & Bioscience, 13(1), 180. https://doi.org/10.1186/s13578-023-01112-5.
• Liu, Y., Zhang, Y., & Wang, H. (2022). Proteomics in cancer research: Opportunities and challenges. Nature Reviews Cancer, 22(6), 325-339.
• Liu, Q., Zhang, J., Guo, C., Wang, M., Wang, C., Yan, Y., & Zhang, P. (2024). Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies. Cell, 187(1), 184-203.
• Lung Cancer Cohort Consortium (LC3) (2023). The blood proteome of imminent lung cancer diagnosis. Nature Communications, 14(1), 3042. https://doi.org/10.1038/s41467-023-37979-8.
• Matsuda, K., Ueha, S., & Mizuguchi, H. (2020). Recent advances in proteomic technologies for cancer research. Cancer Science, 111(6), 1950-1962.
• Meyer, C., Baessler, A., & Schmid, J. (2020). Protein-based biomarkers in cancer: Recent advances and clinical applications. Clinical Cancer Research, 26(24), 6151-6160.
• Nadaf, S. J., Killedar, S. G., Kumbar, V. M., Bhagwat, D. A., & Gurav, S. S. (2022). Pazopanib-laden lipid based nanovesicular delivery with augmented oral bioavailability and therapeutic efficacy against non-small cell lung cancer. International Journal of Pharmaceutics, 628, 122287.
• Petrik, V., Saadoun, S., Loosemore, A., Hobbs, J., Opstad, K. S., Sheldon, J., & Papadopoulos, M. C. (2008). Serum α2-HS glycoprotein predicts survival in patients with glioblastoma. Clinical Chemistry, 54(4), 713-722.
• Pérez-Rodríguez, M. L., González, R. A., & Martínez, A. (2021). The role of protein alterations in cancer progression: Insights from tumor development phases. Nature Reviews Cancer, 21(9), 617-630.
• Ren, Q., Zhu, P., Zhang, H., Ye, T., Liu, D., Gong, Z., & Xia, X. (2020). Identification and validation of stromal-tumor microenvironment-based subtypes tightly associated with PD-1/PD-L1 immunotherapy and outcomes in patients with gastric cancer. Cancer cell international, 20, 1-13.
• Qiu, Y., Patwa, T. H., Xu, L., Shedden, K., Misek, D. E., Tuck, M., & Lubman, D. M. (2008). Plasma glycoprotein profiling for colorectal cancer biomarker identification by lectin glycoarray and lectin blot. Journal of Proteome Research, 7(4), 1693-1703.
• Rusch, V., Asamura, H., & Wang, H. (2020). The role of low-dose computed tomography in lung cancer screening: A review. Journal of Thoracic Oncology, 15(2), 198-205.
• Sardana, G., Jung, K., Stephan, C., & Diamandis, E. P. (2008). Proteomic analysis of conditioned media from the PC3, LNCaP, and 22Rv1 prostate cancer cell lines: Discovery and validation of candidate prostate cancer biomarkers. Journal of Proteome Research, 7(8), 3329-3338.
• Schumacher, T. N., Klebanoff, C. A., & Gajewski, T. F. (2021). Cancer immunoediting and the tumor microenvironment: An overview. Nature Reviews Immunology, 21(10), 569-581.
• Shaw, J. L., Smith, C. R., & Diamandis, E. P. (2007). Proteomic analysis of human cervico-vaginal fluid. Journal of Proteome Research, 6(7), 2859-2865. https://doi.org/10.1021/pr0701658.
• Shin, T. H., Nithiyanandam, S., Lee, D. Y., Kwon, D. H., Hwang, J. S., Kim, S. G., ... & Lee, G. (2021). Analysis of nanotoxicity with integrated omics and mechanobiology. Nanomaterials, 11(9), 2385.
• Vu, H. M., Mohammad, H. B., Nguyen, T. N., Lee, J. H., Do, Y., Sung, J. Y., & Kim, M. S. (2023). Quantitative proteomic analysis of bronchoalveolar lavage fluids from patients with small cell lung cancers. PROTEOMICS-Clinical Applications, 17(5), 2300011.
• Wang, H., Zeng, Y., & Liu, C. (2021). Advancements in liquid biopsy for lung cancer: Opportunities and challenges. Cancer Letters, 508, 45-53.
• Wang, L., Yang, Y., & Zhou, Y. (2023). Current trends in cancer proteomics: Implications for early diagnosis and therapy. Frontiers in Oncology, 13, 814253.
• Wu, L., Zhao, K. Q., Wang, W., Cui, L. N., Hu, L. L., Jiang, X. X., ... & Sun, Y. P. (2020). Nuclear receptor coactivator 6 promotes HTR‐8/SVneo cell invasion and migration by activating NF‐κB‐mediated MMP9 transcription. Cell Proliferation, 53(9), e12876.
• Xing, Y., Zhang, D., Fang, L., Wang, J., Liu, C., Wu, D., ... & Min, W. (2023). Complement in Human Brain Health: Potential of Dietary Food in Relation to Neurodegenerative Diseases. Foods, 12(19), 3580.
• Xiong, J., Chen, M., & Wang, Q. (2023). Advances in understanding the tumor microenvironment: Implications for lung cancer therapy. Nature Reviews Clinical Oncology, 20(1), 15-32.
• Yanar, S., Kasap, M., Kanli, A., Akpinar, G., & Sarihan, M. (2023). Proteomics analysis of meclofenamic acid‐treated small cell lung carcinoma cells revealed changes in cellular energy metabolism for cancer cell survival. Journal of Biochemical and Molecular Toxicology, 37(4), e23289.
• Ye, Q., Raese, R., Luo, D., Cao, S., Wan, Y. W., Qian, Y., & Guo, N. L. (2023). Microrna, mrna, and proteomics biomarkers and therapeutic targets for improving lung cancer treatment outcomes. Cancers, 15(8), 2294.
• Zhang, Y., Li, S., & Chen, L. (2021). Integration of proteomics and genomics in cancer research: A new perspective. Nature Reviews Cancer, 21(5), 307-322.
• Zhang, Y., Zhang, X., & Zhao, J. (2022). Emerging protein biomarkers for cancer diagnosis and prognosis. Nature Reviews Clinical Oncology, 19(3), 166-182.
• Zhao, J., Li, H., & Wang, C. (2023). Application of proteomic technologies in cancer diagnosis and therapy. Journal of Proteomics, 266, 104560.
• Zhou, J., Peng, Y., Gao, Y. C., Chen, T. Y., Li, P. C., Xu, K., Liu, T., & Ren, T. (2021). Targeting DNAJC19 overcomes tumor growth and lung metastasis in NSCLC by regulating PI3K/AKT signaling. Cancer Cell International, 21(1), 338.