Molecular pathological profiling of selected tumors of the central nervous system using the MLPA method

Česká verzia

Authors: Iva Dolinová ¹; Eliška Tvrzníková ¹; Veronika Janoušková ¹; Aleš Vícha ²; Lenka Krsková ³; Tomáš Jirásek ⁴
Authors place of work: Oddělení molekulární genetiky a diagnostiky, Centrum PATOS, Krajská nemocnice Liberec, a. s. ¹; Klinika dětské hematologie a onkologie 2. LF UK a Fakultní nemocnice Motol, Praha ²; Ústav patologie a molekulární medicíny 2. LF UK a Fakultní nemocnice Motol, Praha ³; Oddělení patologie, Centrum PATOS, Krajská nemocnice Liberec, a. s. ⁴
Published in the journal: Čes.-slov. Patol., 58, 2022, No. 3, p. 138-149
Category: Reviews Article

Summary

The current progress and increasing knowledge about the genetic causes of cancer opens up new possibilities for its treatment. However, it is necessary to combine the results obtained using classical pathological methods with sensitive, multiplex molecular pathological methods. The method that meets the required criteria is MLPA based on multiplex PCR reaction. This method detects both changes in gene copy number and DNA methylation and, last but not least, point mutations. The MLPA reaction is applicable to even highly fragmented DNA. At the same time, it is a robust method that can be performed on standard thermocyclers, the fluorescent tip label requires automatic sequencers. Up to 50 genetic markers can be tested in one reaction, a number that allows a diagnostic and prognostic conclusion. All these features lead to the routine use of MLPA analysis not only in diagnosis but also in cancer research. The present article aims to summarize the different types of MLPA reactions, its benefits, but also the potential pitfalls.

Keywords:

Molecular pathology – PCR – MLPA – Tumors of the central nervous system

Zdroje

1. Schouten JP, Cathal JM, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002; 30(12): 57.

2. Hömig-Hölzel C, Savola S. Multiplex ligation- dependent probe amplification (MLPA) in tumor diagnostics and prognostics. Diagn Mol Pathol 2012; 21(4): 189-206.

3. Kozlowski P, Roberts P, Dabora S, et al. Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype- phenotype correlations. Hum Genet 2007; 121: 389-400.

4. MRC-Holland. MS-MLPA General Protocol (One-Tube). 2020; dostupné na www.mlpa.cz.

5. Troxler H, Kleinert P, Schmugge M, Speer O. Advances in hemoglobinopathy detection and identification. Advances in clinical chemistry 2012; 57: 2.

6. Sellner LN, Taylor GR. MLPA and MAPH: New Techniques for Detection of Gene Deletions. Hum Mutat 2004; 23: 413-419.

7. MRC-Holland. MLPA® General information. 2022; dostupné na www.mlpa.cz.

8. Tate JG, Bamford S, Jubb HC, et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic acids Res 2019; 47(D1): D941-D947.

9. Coffa J, Berg J. Analysis of MLPA data using novel softwere Coffalyser. NET by MRC-Holland. In: Eldin, A. B, ed. Modern Approaches to Quality Control. Rijeka, Croatia: In Tech. 2011;125-150.

10. Van Opstal D, Boter M, De Jong D, Van Den Berg C, Brüggenwirth HT, Wildschut HI, Galjaard RJH. Rapid aneuploidy detection with multiplex ligation-dependent probe amplification: a prospective study of 4000 amniotic fluid samples. Eur J Hum Genet 2001; 17(1): 112-121.

11. Sullivan RJ, Flaherty KT. BRAF in melanoma: pathogenesis, diagnosis, inhibition, and resistance. J Skin Cancer 2011. doi. org/10.1155/2011/423239.

12. Eckel-Passow JE, Lachance DH, Molinaro AM, et al. Glioma groups based on 1p/19q, IDH, and TERT promoter mutations in tumors. N Engl J Med 2015; 372(26): 2499-2508.

13. Reis GF, Pekmezci M, Hansen HM, et al. CDKN2A loss is associated with shortened overall survival in lower-grade (World Health Organization Grades II–III) astrocytomas. J Neuropathol E Neurol 2015; 74(5): 442-452.

14. Gillet E, Alentorn A, Doukouré B, et al. TP53 and p53 statuses and their clinical impact in diffuse low grade gliomas. J Neur Onco 2014; 118(1): 131-139.

15. Christensen BC, Smith AA, Zheng S, et al. DNA metylation, isocitrate dehydrogenase mutation, and survival in glioma. J Natl Cancer Inst 2011; 103(2):143-153.

16. Jha P, Sarkar C, Pathak P, Sharma MC, et al. Detection of allelic status of 1p and 19q by microsatellite-based PCR versus FISH: limitations and advantages in application to patient management. Diag Mol Pathol 2011; 20(1): 40-47.

17. Marquez A, Wu R, Zhao J, et al. Evaluation of Epidermal Growth Factor Receptor (EGFR) by Chromogenic In Situ: Hybridization (CISH™) and Immunohistochemistry (IHC) in Archival Gliomas Using Bright-Field Microscopy. Diag Mol Pathol 2004; 13(1): 1-8.

18. Louis DN, Perry A, Reifenberger G, et al. The 2016 World Health Organization classification of tumors of the central nervous system: a summary. Acta neuropathologica 2016; 131(6): 803-820.

19. Stupp R, Mason WP, van den Bent MJ, et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med 2005; 352:987-996.

20. Louis DN, Peery A, Wesseling P, et al. The WHO classification of tumors of the central nervous system: a summary. Neur Oncol 2021; 23(8): 1231-1251.

21. Brat DJ, Aldape K, Bridge JA, et al. Molecular Biomarker Testing for the Diagnosis of Diffuse Gliomas. Arch Pathol Lab Med 2022. doi: 10.5858/arpa.2021-0295-CP.

22. Jones DT, Kocialkowski S, Liu L, et al. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res 2008; 68(21): 8673-8677.

23. Weller M., Felsberg J, Hartmann C, et al. Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J Clin Oncol 2009; 27(34): 5743-5750.

24. Hegi ME, Diserens AC, Gorlia T, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med 2005; 352(10): 997-1003.

25. Pegg A E. Mammalian O6-alkylguanine-DNA alkyltransferase: regulation and importance in response to alkylating carcinogenic and therapeutic agents. Cancer Res 1990; 50(19): 6119-6129.

26. Wick W, Meisner C, Hentsch B, et al. Prognostic or predictive value of MGMT promoter methylation in gliomas depends on IDH1 mutation. Neurology 2013; 81(17): 1515-1522.

27. Molenaar RJ, Verbaan D, Lamba S, et al. The combination of IDH1 mutations and MGMT methylation status predicts survival in glioblastoma better than either IDH1 or MGMT alone. Neur Oncol 2014; 16(9): 1263- 1273.