Abstract
Colorectal cancer (CRC) is the most common cancer in both men and women and is associated with increased telomerase levels and activity. The potential downstream effects of TERT and/or TERC downregulation by berberine (a telomerase inhibitor) or RNA interference (RNAi) on various target RNAs, proteins, relative telomerase activity (RTA), relative telomere length (RTL), hydrogen peroxide concentration [H2O2], percentage of cell cycle distribution, cell size and granularity as well as cellular metabolites were explored in HCT 116 cell line. Knockdown of TERT decreased TERC. The downregulation of TERT and/or TERC caused increment of [H2O2], G0/G1 phase arrest in addition to decreased S and G2/M phases, as well as diminished cell size. RTL was later reduced as a result of TERT, TERT and/or TERC downregulation which decreased RTA. It was discovered that xanthine oxidase (XO) was significantly and positively correlated at FDR-adjusted p value < 0.05 with RTA, TERT, TERT, TERC, and RTL. HCT 116 with decreased RTA was closely clustered in the Principal Component Analysis (PCA) indicating similarity of the metabolic profile. A total of 55 metabolites were putatively annotated in this study, potentially associated with RTA levels. The Debiased Sparse Partial Correlation (DSPC) Network revealed that RTA was directly correlated to TERT. There were 4 metabolic pathways significantly affected by low level of RTA which include (1) purine metabolism, (2) glycine, serine, and threonine metabolism, (3) glyoxylate and dicarboxylate metabolism, and (4) aminoacyl-tRNA biosynthesis. The Gene-Metabolite Interaction Network implied that reduced RTA level was related to the mechanism of oxidative stress. This study reveals the linkages between RTA to various selected RNAs, proteins, metabolites, oxidative stress mechanism and subsequently phenotypic changes in HCT 116 which is valuable to understand the intricate biological interactions and mechanism of telomerase in CRC.
Similar content being viewed by others
References
Ferlay, J., Colombet, M., Soerjomataram, I., Parkin, D. M., Piñeros, M., Znaor, A., & Bray, F. (2021). Cancer statistics for the year 2020: an overview. International Journal of Cancer, 149, 778–789.
Ferlay, J., Ervik, M., Lam, F., Colombet, M., Mery, L., Piñeros, M., Znaor, A., Soerjomataram, I., & Bray, F. (2020). Global Cancer Observatory: Cancer Today. Lyon, France: International Agency for Research on Cancer. Lyon, France: International Agency for Research on Cancer.
Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A., & Bray, F. (2021). Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA: A Cancer Journal for Clinicians, 71, 209–249.
Nikolouzakis, T. K., Vakonaki, E., Stivaktakis, P. D., Alegakis, A., Berdiaki, A., Razos, N., Souglakos, J., Tsatsakis, A., & Tsiaoussis, J. (2021). Novel prognostic biomarkers in metastatic and locally advanced colorectal cancer: Micronuclei frequency and telomerase activity in peripheral blood lymphocytes. Frontiers in Oncology, 11, 683605.
Peacock, S. D., Massey, T. E., Vanner, S. J., & King, W. D. (2018). Telomere length in the colon is related to colorectal adenoma prevalence. PloS One, 13, e0205697.
Jia, H., & Wang, Z. (2016). Telomere length as a prognostic factor for overall survival in colorectal cancer patients. Cellular Physiology and Biochemistry: International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, 38, 122–128.
Vishwakarma, K., Dey, R., Bhatt, H., 2023. Telomerase: A prominent oncological target for development of chemotherapeutic agents. European Journal of Medicinal Chemistry, 115121
Chen, Y.-X., Gao, Q.-Y., Zou, T.-H., Wang, B.-M., Liu, S.-D., Sheng, J.-Q., Ren, J.-L., Zou, X.-P., Liu, Z.-J., & Song, Y.-Y. (2020). Berberine versus placebo for the prevention of recurrence of colorectal adenoma: a multicentre, double-blinded, randomised controlled study. The Lancet Gastroenterology & Hepatology, 5, 267–275.
Samad, M. A., Saiman, M. Z., Abdul Majid, N., Karsani, S. A., & Yaacob, J. S. (2021). Berberine inhibits telomerase activity and induces cell cycle arrest and telomere erosion in colorectal cancer cell line, HCT 116. Molecules (Basel, Switzerland), 26, 376.
Tillhon, M., Ortiz, L. M. G., Lombardi, P., & Scovassi, A. I. (2012). Berberine: new perspectives for old remedies. Biochemical Pharmacology, 84, 1260–1267.
Zou, K., Li, Z., Zhang, Y., Zhang, H.-Y., Li, B., Zhu, W.-L., Shi, J.-Y., Jia, Q., & Li, Y.-M. (2017). Advances in the study of berberine and its derivatives: a focus on anti-inflammatory and anti-tumor effects in the digestive system. Acta Pharmacologica Sinica, 38, 157–167.
Luck, K., Jailkhani, N., Cusick, M., Rolland, T., Calderwood, M., Charloteaux, B., Vidal, M., 2016. Interactomes-Scaffolds of Cellular Systems
Ge, L., Shao, W., Zhang, Y., Qiu, Y., Cui, D., Huang, D., & Deng, Z. (2011). RNAi targeting of hTERT gene expression induces apoptosis and inhibits the proliferation of lung cancer cells. Oncology Letters, 2, 1121–1129.
Klein, E. A., & Assoian, R. K. (2008). Transcriptional regulation of the cyclin D1 gene at a glance. Journal of Cell Science, 121, 3853–3857.
Bardelčíková, A., Šoltys, J., & Mojžiš, J. (2023). Oxidative stress, inflammation and colorectal cancer: an overview. Antioxidants, 12, 901.
Vasilishina, A., Kropotov, A., Spivak, I., & Bernadotte, A. 2019. Relative Human Telomere Length Quantification by Real-Time PCR, in: Demaria, M. (Ed.), Cellular Senescence: Methods and Protocols. Springer New York, New York, pp. 39-44
Junglee, S., Urban, L., Sallanon, H., & Lopez-Lauri, F. (2014). Optimized assay for hydrogen peroxide determination in plant tissue using potassium iodide. American Journal of Analytical Chemistry, 5, 730. https://doi.org/10.4236/ajac.2014.511081.
Bi, H., Krausz, K. W., Manna, S. K., Li, F., Johnson, C. H., & Gonzalez, F. J. (2013). Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells. Analytical and Bioanalytical Chemistry, 405, 5279–5289.
Hoffmann, M. A., Nothias, L.-F., Ludwig, M., Fleischauer, M., Gentry, E. C., Witting, M., Dorrestein, P. C., Dührkop, K., & Böcker, S. (2022). High-confidence structural annotation of metabolites absent from spectral libraries. Nature Biotechnology, 40, 411–421. https://doi.org/10.1038/s41587-021-01045-9.
Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W., Fiehn, O., Goodacre, R., Griffin, J. L., Hankemeier, T., Hardy, N., Harnly, J., Higashi, R., Kopka, J., Lane, A. N., Lindon, J. C., Marriott, P., Nicholls, A. W., Reily, M. D., Thaden, J. J., & Viant, M. R. (2007). Proposed minimum reporting standards for chemical analysis. Metabolomics, 3, 211–221. https://doi.org/10.1007/s11306-007-0082-2.
Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., & Egertson, J. (2012). A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 30, 918–920.
Pluskal, T., Castillo, S., Villar-Briones, A., & Orešič, M. (2010). MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics, 11, 1–11.
R Core Team, 2022. R: A language and environment for statistical computing. R Foundation for Statistical Computing.
Hoffmann, M. A., Nothias, L.-F., Ludwig, M., Fleischauer, M., Gentry, E. C., Witting, M., Dorrestein, P. C., Dührkop, K., Böcker, S., 2021. Assigning confidence to structural annotations from mass spectra with COSMIC. BioRxiv, 2021.2003. 2018.435634.
Pang, Z., Zhou, G., Ewald, J., Chang, L., Hacariz, O., Basu, N., & Xia, J. (2022). Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nature Protocols, 17, 1735–1761.
Kaiser, H. F. (1960). The application of electronic computers to factor analysis. Educational and Psychological Measurement, 20, 141–151.
Suhr, D. D. (2005). Principal component analysis vs. exploratory factor analysis. SUGI 30 Proceedings, 203, 230.
Nijs, V., 2023. radiant: Business Analytics using R and Shiny. R package version 1.5.0
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57, 289–300.
Saccenti, E., Hendriks, M. H., & Smilde, A. K. (2020). Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models. Scientific Reports, 10, 438.
Camacho, D., De La Fuente, A., & Mendes, P. (2005). The origin of correlations in metabolomics data. Metabolomics, 1, 53–63.
Ramirez, J.-M., Bai, Q., Péquignot, M., Becker, F., Kassambara, A., Bouin, A., Kalatzis, V., Dijon-Grinand, M., & De Vos, J. (2013). Side scatter intensity is highly heterogeneous in undifferentiated pluripotent stem cells and predicts clonogenic self-renewal. Stem Cells and Development, 22, 1851–1860.
Triba, M. N., Le Moyec, L., Amathieu, R., Goossens, C., Bouchemal, N., Nahon, P., Rutledge, D. N., & Savarin, P. (2015). PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters. Molecular BioSystems, 11, 13–19.
Nahm, F. S. (2022). Receiver operating characteristic curve: overview and practical use for clinicians. Korean Journal of Anesthesiology, 75, 25–36.
Desi, N., & Tay, Y. (2019). The butterfly effect of RNA alterations on transcriptomic equilibrium. Cells, 8, 1634.
Mohd Zain, M. Z., Ismail, N. H., Ahmad, N., Sulong, S., Karsani, S. A., & Abdul Majid, N. (2020). Telomerase reverse transcriptase downregulation by RNA interference modulates endoplasmic reticulum stress and mitochondrial energy production. Molecular Biology Reports, 47, 7735–7743.
Fiszer-Kierzkowska, A., Vydra, N., Wysocka-Wycisk, A., Kronekova, Z., Jarząb, M., Lisowska, K. M., & Krawczyk, Z. (2011). Liposome-based DNA carriers may induce cellular stress response and change gene expression pattern in transfected cells. BMC Molecular Biology, 12, 1–9.
Kleefeldt, J. M., Pozarska, A., Nardiello, C., Pfeffer, T., Vadász, I., Herold, S., Seeger, W., & Morty, R. E. (2020). Commercially available transfection reagents and negative control siRNA are not inert. Analytical Biochemistry, 606, 113828.
Yao, Z., Kim, Y. W., Amin, R., Volpe, E., Jogunoori, W., Mishra, L., & Mishra, B. (2008). Telomerase reverse transcriptase regulation by TGF-β signaling through adaptor ELF and Smad3 that is independent of c-Myc. Cancer Research, 68, 3442–3442.
Zhang, K., Zhang, M., Luo, Z., Wen, Z., & Yan, X. (2020). The dichotomous role of TGF-β in controlling liver cancer cell survival and proliferation. Journal of Genetics and Genomics, 47, 497–512.
Cassar, L., Li, H., Jiang, F.-X., & Liu, J.-P. (2010). TGF-β induces telomerase-dependent pancreatic tumor cell cycle arrest. Molecular and Cellular Endocrinology, 320, 97–105.
Farnung, B. O., Brun, C. M., Arora, R., Lorenzi, L. E., & Azzalin, C. M. (2012). Telomerase efficiently elongates highly transcribing telomeres in human cancer cells. PloS One, 7, e35714.
Shen, Y., Zhang, Y.-W., Zhang, Z.-X., Miao, Z.-H., & Ding, J. (2008). hTERT-targeted RNA interference inhibits tumorigenicity and motility of HCT116 cells. Cancer Biology & Therapy, 7, 228–236.
Bakr, M., Abd-Elmawla, M. A., Elimam, H., El-Din, H. G., Fawzy, A., Abulsoud, A. I., & Rizk, S. M. (2023). Telomerase RNA component lncRNA as potential diagnostic biomarker promotes CRC cellular migration and apoptosis evasion via modulation of β-catenin protein level. Non-coding RNA Research, 8, 302–314.
Jirawatnotai, S., Hu, Y., Livingston, D. M., & Sicinski, P. (2012). Proteomic identification of a direct role for cyclin d1 in DNA damage repair. Cancer Research, 72, 4289–4293.
Davies, O., Mendes, P., Smallbone, K., & Malys, N. (2012). Characterisation of multiple substrate-specific (d) ITP/(d) XTPase and modelling of deaminated purine nucleotide metabolism. BMB Reports, 45, 259–264.
Förstermann, U., 2010. Chapter 5 - Uncoupling of Endothelial Nitric Oxide Synthase in Cardiovascular Disease and its Pharmacological Reversal, in: Ignarro, L. J. (Ed.), Nitric Oxide (Second Edition). Academic Press, San Diego, pp. 139–167
Salway, J. G., 2016. Metabolism at a Glance. John Wiley & Sons
Butterworth, P. J. (2005). Lehninger: principles of biochemistry (4th edn) D. L. Nelson and M. C. Cox, W. H. Freeman & Co., New York, 1119 pp (plus 17 pp glossary), ISBN 0-7167-4339-6 (2004). Cell Biochemistry and Function, 23, 293–294.
Kelley, E. E., Khoo, N. K., Hundley, N. J., Malik, U. Z., Freeman, B. A., & Tarpey, M. M. (2010). Hydrogen peroxide is the major oxidant product of xanthine oxidase. Free Radical Biology and Medicine, 48, 493–498.
Ko, E., Seo, H. W., & Jung, G. (2018). Telomere length and reactive oxygen species levels are positively associated with a high risk of mortality and recurrence in hepatocellular carcinoma. Hepatology, 67, 1378–1391.
Li, P., Wu, M., Wang, J., Sui, Y., Liu, S., & Shi, D. (2016). NAC selectively inhibit cancer telomerase activity: a higher redox homeostasis threshold exists in cancer cells. Redox Biology, 8, 91–97.
Trachana, V., Petrakis, S., Fotiadis, Z., Siska, E. K., Balis, V., Gonos, E. S., Kaloyianni, M., & Koliakos, G. (2017). Human mesenchymal stem cells with enhanced telomerase activity acquire resistance against oxidative stress-induced genomic damage. Cytotherapy, 19, 808–820.
Pérez-Rivero, G., Ruiz-Torres, M. P., Díez-Marqués, M. L., Canela, A., López-Novoa, J. M., Rodríguez-Puyol, M., Blasco, M. A., & Rodríguez-Puyol, D. (2008). Telomerase deficiency promotes oxidative stress by reducing catalase activity. Free Radical Biology and Medicine, 45, 1243–1251.
Mouilleron, H., Delcourt, V., & Roucou, X. (2015). Death of a dogma: eukaryotic mRNAs can code for more than one protein. Nucleic Acids Res, 44, 14–23.
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011). Global quantification of mammalian gene expression control. Nature, 473, 337–342.
Li, J., Huang, X., Xie, X., Wang, J., & Duan, M. (2011). Human telomerase reverse transcriptase regulates cyclin D1 and G1/S phase transition in laryngeal squamous carcinoma. Acta Oto-laryngologica, 131, 546–551.
Liu, A.-Q., Ge, L.-Y., Lu, X.-L., Luo, X.-L., Cai, Y.-L., Ye, X.-Q., & Geng, F.-F. (2014). Silencing of the hTERT gene by shRNA inhibits colon cancer SW480 cell growth in vitro and in vivo. PloS One, 9, e107019–e107019.
Shi, Y.-A., Zhao, Q., Zhang, L.-H., Du, W., Wang, X.-Y., He, X., Wu, S., & Li, Y.-L. (2014). Knockdown of hTERT by siRNA inhibits cervical cancer cell growth in vitro and in vivo. International Journal of Oncology, 45, 1216–1224.
Neurohr, G. E., Terry, R. L., Lengefeld, J., Bonney, M., Brittingham, G. P., Moretto, F., Miettinen, T. P., Vaites, L. P., Soares, L. M., & Paulo, J. A. (2019). Excessive cell growth causes cytoplasm dilution and contributes to senescence. Cell, 176, 1083–1097.e1018.
Gavia-García, G., Rosado-Pérez, J., Arista-Ugalde, T. L., Aguiñiga-Sánchez, I., Santiago-Osorio, E., & Mendoza-Núñez, V. M. (2021). Telomere length and oxidative stress and its relation with metabolic syndrome components in the aging. Biology, 10, 253.
Von Zglinicki, T. (2002). Oxidative stress shortens telomeres. Trends in Biochemical Sciences, 27, 339–344.
Acknowledgements
The authors thank Universiti Malaya, Malaysia for the facilities and financial support (RP030C-15AFR) provided.
Funding
This research was funded by Universiti Malaya (RP030C-15AFR).
Author information
Authors and Affiliations
Contributions
J.S.Y., N.A.M. and M.A.S. conceived and designed the experiment(s). M.A.S. conducted the experiments, collected the data and performed the statistical analysis. J.S.Y., M.Z.S., N.A.M. and S.A.K. advised on the preparation of materials. J.S.Y., M.Z.S. and M.A.S. contributed reagents/materials. J.S.Y. and M.Z.S. advised on the metabolomics section. J.S.Y., M.Z.S. and S.A.K. provided the facilities for analysis, M.A.S. wrote the manuscript. J.S.Y., M.Z.S. and N.A.M. read and edited the manuscript. All authors approved the final manuscript. All authors have read and agreed to the published version of the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Samad, M.A., Saiman, M.Z., Abdul Majid, N. et al. Berberine and RNAi-Targeting Telomerase Reverse Transcriptase (TERT) and/or Telomerase RNA Component (TERC) Caused Oxidation in Colorectal Cancer Cell Line, HCT 116: An Integrative Approach using Molecular and Metabolomic Studies. Cell Biochem Biophys 82, 153–173 (2024). https://doi.org/10.1007/s12013-023-01210-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12013-023-01210-8