Evaluation of DNA Microarray in Biomarker Detection in Cell-free DNA from Colorectal Cancer Cell Lines: A Proof-of-Concept Study

Yıl 2023, Cilt: 13 Sayı: 2, 86 - 92, 18.09.2023

Hasan Huseyin Kazan , Ceyhan Pırıl Karahan , Ekin Çelik , Ahmet Çağlar Özketen , Duygu Birgücü-çağıl Mehmet Ali Ergun

https://doi.org/10.26650/experimed.1260973

Öz

Objective: DNA microarray is a powerful method to identify genomic anomalies including small insertions, duplications and/or deletions. This method is widely used in routine genetic screening for explaining the genetic background of certain phenotypes, for example, cancer. Cell-free DNA (cfDNA), which is an approach that may give information about the somatic tissues in peripheral blood, is another popular method used in routine genetic screening to understand the background of particular phenotypes, one of which is cancer. There is limited available research that investigates the involvement of these two approaches to decipher novel cancer biomarkers in the literature. However, detection of cancer biomarkers, especially non-invasive types, has been of great interest to research groups.
Materials and Methods: In the present study, we used colorectal cancer as a model tumor to figure out whether we could determine definite biomarkers from cfDNA using DNA microarray methodology. We isolated cfDNA from the cell-free mediums of the cultures of colorectal cancer cell lines in the presence of the control group which was the healthy epithelial colon cell line.
Results: Our results underlined significant alterations that were deletions and/or duplications in some of the genomic regions in a cell line-specific manner.
Conclusion: We propose that DNA microarray be used to assess the sub-types of certain cancers in a non-invasive manner using cfDNA approaches.

Anahtar Kelimeler

cfDNA, carcinogenesis, colorectal cancer, DNA microarray, biomarker

Destekleyen Kurum

None

Proje Numarası

None

Teşekkür

None

Kaynakça

• 1. Ferlay J, Ervik M, Lam F, Colombet M, Mery L, Pineros M, et al. Global cancer observatory: Cancer today. Lyon, France: International Agency for Research on Cancer 2020. Available from: https://gco. iarc.fr/today, accessed 01 February 2023 google scholar
• 2. Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: Cancer J Clin 2021; 71(3): 209-49. google scholar
• 3. Colorectal cancer facts & figures. American Cancer Society 20202022. Published online, 48. google scholar
• 4. Petit J, Carroll G, Gould T, Pockney P, Dun M, Scott RJ. Cell-free DNA as a diagnostic blood-based biomarker for colorectal cancer: a systematic review. J Surg Res 2019; 236: 184-97. google scholar
• 5. Osborne JM, Wilson C, Moore V, Gregory T, Flight I, Young GP. Sample preference for colorectal cancer screening tests: blood or stool? Open J Prev Med 2012; 02(03): 326-31. google scholar
• 6. Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. Biomol Detect Quantif 2019; 17: 100087. google scholar
• 7. Alborelli I, Generali D, Jermann P, Cappelletti MR, Ferrero G, Scaggiante B, et al. Cell-free DNA analysis in healthy individuals by next-generation sequencing: a proof of concept and technical validation study. Cell Death Dis 2019; 10(7): 534. google scholar
• 8. Seki Y, Fujiwara Y, Kohno T, Takai E, Sunami K, Goto Y, et al. Picoliter-droplet digital polymerase chain reaction-based analysis of cell-free plasma DNA to assess EGFR mutations in lung adenocarcinoma that confer resistance to tyrosine-kinase inhibitors. Oncologist 2016; 21(2): 156-64. google scholar
• 9. Palande V, Shay DR, Frenkel-Morgenstern MI. Detection of cell-free DNA in blood plasma samples of cancer patients. JoVE 2020; 9(163): e61449. google scholar
• 10. Selvaraj S, Natarajan J. Microarray data analysis and mining tools. Bioinformation 2011; 6(3): 95. google scholar
• 11. Miller MB, Tang YW. Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 2009; 22(4): 611-33. google scholar
• 12. Costa P, Novoradovskaya N, Basehore S, Fulmer-Smentek S. Single cell copy number screening using the GenetiSure Pre-Screen kit. Application Note. Agilent Technologies, Inc. 2014. USA, 5991-5325EN. google scholar
• 13. Xi Y, Xu P. Global colorectal cancer burden in 2020 and projections to 2040. Transl Oncol 2021; 14(10): 101174. google scholar
• 14. Yan YY, Guo QR, Wang FH, Adhikari R, Zhu ZY, Zhang HY, et al. Cell-free DNA: hope and potential application in cancer. Front Cell Dev Biol 202; 9: 639233. google scholar
• 15. Cisneros-Villanueva M, Hidalgo-Perez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, et al. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126(3): 391-400. google scholar
• 16. Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, et al. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6(3): 232-45. google scholar
• 17. Barault L, Amatu A, Siravegna G, Ponzetti A, Moran S, Cassingena A, et al. Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. Gut 2018; 67(11): 1995-2005. google scholar
• 18. Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 2011; 32(4): 177. google scholar
• 19. Taylor BS, Barretina J, Socci ND, DeCarolis P, Ladanyi M, Meyerson M, et al. Functional copy-number alterations in cancer. PloS One 2008; 3(9): e3179. google scholar
• 20. Azad AA, Volik SV, Wyatt AW, Haegert A, Le Bihan S, Bell RH, et al. Androgen receptor gene aberrations in circulating cell-free DNA: Biomarkers of therapeutic resistance in castration-resistant prostate CancerAR gene aberrations in circulating cell-free DNA. Clin Cancer Res 2015; 21(10): 2315-24. google scholar
• 21. Mathivanan S, Ji H, Tauro BJ, Chen YS, Simpson RJ. Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry. J Proteomics 2012; 76: 141-9. google scholar
• 22. Cevenini A, Orru S, Imperlini E. Secretome proteomic approaches for biomarker discovery: an update on colorectal cancer. Medicina 2020; 56(9): 443. google scholar
• 23. Dache ZA, Otandault A, Tanos R, Pastor B, Meddeb R, Sanchez C, et al. Blood contains circulating cell-free respiratory competent mitochondria. FASEB J 2020; 34(3): 3616-30. google scholar
• 24. Yatsenko SA, Shaw CA, Ou Z, Pursley AN, Patel A, Bi W, et al. Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA. J Mol Diagn 2009; 11(3): 226-37. google scholar
• 25. Kleivi K,Teixeira MR, Ekn«s M, DiepCB,Jakobsen KS, Hamelin R,et al. Genome signatures of colon carcinoma cell lines. Cancer Genet Cytogenet 2004; 155(2): 119-31. google scholar
• 26. Williams CS, Bernard JK, Demory Beckler M, Almohazey D, Washington MK, Smith JJ, et al. ERBB4 is over-expressed in human colon cancer and enhances cellular transformation. Carcinogenesis 2015; 36(7): 710-8. google scholar
• 27. Doyle BT, O’Neill AJ, Fitzpatrick JM, Watson RW. Differentiation-induced HL-60 cell apoptosis: a mechanism independent of mitochondrial disruption? Apoptosis 2004; 9: 345-52. google scholar
• 28. Bell RA, Megeney LA. Evolution of caspase-mediated cell death and differentiation: Twins separated at birth. Cell Death Differ 2017; 24(8): 1359-68. google scholar
• 29. Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, et al. The reactome pathway knowledgebase 2022. Nucleic Acids Res 2022; 50(D1): D687-92. google scholar
• 30. Chung C, Cho HJ, Lee C, Koo J. Odorant receptors in cancer. BMB Rep 2022; 55(2): 72. google scholar
• 31. Matsuda Y, Ueda J, Ishiwata T. Fibroblast growth factor receptor 2: expression, roles, and potential as a novel molecular target for colorectal cancer. Pathol Res Int 2012: 1-8. google scholar
• 32. Tokar EJ, Benbrahim-Tallaa L, Waalkes MP. Metal ions in human cancer development. Met Ions Life Sci 2011; 8: 375-401. google scholar
• 33. Spindler KL, Boysen AK, Pallisgârd N, Johansen JS, Tabernero J, S0rensen MM, et al. Cell-free DNA in metastatic colorectal cancer: a systematic review and meta-analysis. Oncologist 2017; 22(9): 1049-55. google scholar
• 34. Strickler JH, Loree JM, Ahronian LG, Parikh AR, Niedzwiecki D, Pereira AA, et al. Genomic landscape of cell-free DNA in patients with colorectal cancercell-free dna sequencing in colorectal cancer. Cancer Discov 2018; 8(2): 164-73. google scholar
• 35. Vymetalkova V, Cervena K, Bartu L, Vodicka P. Circulating cell-free DNA and colorectal cancer: a systematic review. Int J Mol Sci 2018; 19(11): 3356. google scholar