Utility of Real-time Polymerase Chain Reaction for the Assessment of CDKN2A Homozygous Deletion in Adult-type IDH-mutant Astrocytoma

Overview

Journal Brain Tumor Pathol

Specialties Neurology
Oncology
Pathology

Date 2023 Feb 14

PMID 36788155

Authors

Yuzaburo Shimizu

Mario Suzuki

Osamu Akiyama

Ikuko Ogino

Yuko Matsushita

Kaishi Satomi

Shunsuke Yanagisawa

Makoto Ohno

Masamichi Takahashi

Yasuji Miyakita

Yoshitaka Narita

Koichi Ichimura

Akihide Kondo

Affiliations

Soon will be listed here.

Abstract

The World Health Organization Classification of Tumors of the Central Nervous System 5th Edition (WHO CNS5) introduced a newly defined astrocytoma, IDH-mutant grade 4, for adult diffuse glioma classification. One of the diagnostic criteria is the presence of a CDKN2A/B homozygous deletion (HD). Here, we report a robust and cost-effective quantitative polymerase chain reaction (qPCR)-based test for assessing CDKN2A HD. A TaqMan copy number assay was performed using a probe located within CDKN2A. The linear correlation between the Ct values and relative CDKN2A copy number was confirmed using a serial mixture of DNA from normal blood and U87MG cells. The qPCR assay was performed in 109 IDH-mutant astrocytomas, including 14 tumors with CDKN2A HD, verified either by multiplex ligation-dependent probe amplification (MLPA) or CytoScan HD microarray platforms. Receiver operating characteristic curve analysis indicated that a cutoff value of 0.85 yielded optimal sensitivity (100%) and specificity (99.0%) for determining CDKN2A HD. The assay applies to DNA extracted from frozen or formalin-fixed paraffin-embedded tissue samples. Survival was significantly shorter in patients with than in those without CDKN2A HD, assessed by either MLPA/CytoScan or qPCR. Thus, our qPCR method is clinically applicable for astrocytoma grading and prognostication, compatible with the WHO CNS5.

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References

Brat D, Aldape K, Colman H, Figrarella-Branger D, Fuller G, Giannini C . cIMPACT-NOW update 5: recommended grading criteria and terminologies for IDH-mutant astrocytomas. Acta Neuropathol. 2020; 139(3):603-608. PMC: 8443062. DOI: 10.1007/s00401-020-02127-9. View

Louis D, Perry A, Wesseling P, Brat D, Cree I, Figarella-Branger D . The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol. 2021; 23(8):1231-1251. PMC: 8328013. DOI: 10.1093/neuonc/noab106. View

Appay R, Dehais C, Maurage C, Alentorn A, Carpentier C, Colin C . CDKN2A homozygous deletion is a strong adverse prognosis factor in diffuse malignant IDH-mutant gliomas. Neuro Oncol. 2019; 21(12):1519-1528. PMC: 7145561. DOI: 10.1093/neuonc/noz124. View

Yang R, Shi Z, Zhang Z, Chan A, Aibaidula A, Wang W . IDH mutant lower grade (WHO Grades II/III) astrocytomas can be stratified for risk by CDKN2A, CDK4 and PDGFRA copy number alterations. Brain Pathol. 2019; 30(3):541-553. PMC: 8018138. DOI: 10.1111/bpa.12801. View

Shirahata M, Ono T, Stichel D, Schrimpf D, Reuss D, Sahm F . Novel, improved grading system(s) for IDH-mutant astrocytic gliomas. Acta Neuropathol. 2018; 136(1):153-166. DOI: 10.1007/s00401-018-1849-4. View

Passon N, Pozzo F, Molinis C, Bregant E, Gellera C, Damante G . A simple multiplex real-time PCR methodology for the SMN1 gene copy number quantification. Genet Test Mol Biomarkers. 2009; 13(1):37-42. DOI: 10.1089/gtmb.2008.0084. View

Zhang X, Huang M, Wu X, Kadlubar S, Lin J, Yu X . GSTM1 copy number and promoter haplotype as predictors for risk of recurrence and/or second primary tumor in patients with head and neck cancer. Pharmgenomics Pers Med. 2013; 6:9-17. PMC: 3596140. DOI: 10.2147/PGPM.S35949. View

Satomi K, Ohno M, Matsushita Y, Takahashi M, Miyakita Y, Narita Y . Utility of methylthioadenosine phosphorylase immunohistochemical deficiency as a surrogate for CDKN2A homozygous deletion in the assessment of adult-type infiltrating astrocytoma. Mod Pathol. 2020; 34(4):688-700. DOI: 10.1038/s41379-020-00701-w. View

Arita H, Narita Y, Matsushita Y, Fukushima S, Yoshida A, Takami H . Development of a robust and sensitive pyrosequencing assay for the detection of IDH1/2 mutations in gliomas. Brain Tumor Pathol. 2014; 32(1):22-30. DOI: 10.1007/s10014-014-0186-0. View

10.

Luchman H, Stechishin O, Dang N, Blough M, Chesnelong C, Kelly J . An in vivo patient-derived model of endogenous IDH1-mutant glioma. Neuro Oncol. 2011; 14(2):184-91. PMC: 3266388. DOI: 10.1093/neuonc/nor207. View

11.

Setoodeh R, Schwartz S, Papenhausen P, Zhang L, Sagatys E, Moscinski L . Double-hit mantle cell lymphoma with MYC gene rearrangement or amplification: a report of four cases and review of the literature. Int J Clin Exp Pathol. 2013; 6(2):155-67. PMC: 3544229. View

12.

Kamb A, Gruis N, Liu Q, Harshman K, Tavtigian S, STOCKERT E . A cell cycle regulator potentially involved in genesis of many tumor types. Science. 1994; 264(5157):436-40. DOI: 10.1126/science.8153634. View

13.

Suzuki H, Aoki K, Chiba K, Sato Y, Shiozawa Y, Shiraishi Y . Mutational landscape and clonal architecture in grade II and III gliomas. Nat Genet. 2015; 47(5):458-68. DOI: 10.1038/ng.3273. View

14.

Reis G, Pekmezci M, Hansen H, Rice T, Marshall R, Molinaro A . CDKN2A loss is associated with shortened overall survival in lower-grade (World Health Organization Grades II-III) astrocytomas. J Neuropathol Exp Neurol. 2015; 74(5):442-52. PMC: 4397174. DOI: 10.1097/NEN.0000000000000188. View

15.

Korshunov A, Casalini B, Chavez L, Hielscher T, Sill M, Ryzhova M . Integrated molecular characterization of IDH-mutant glioblastomas. Neuropathol Appl Neurobiol. 2018; 45(2):108-118. DOI: 10.1111/nan.12523. View

16.

Aoki K, Nakamura H, Suzuki H, Matsuo K, Kataoka K, Shimamura T . Prognostic relevance of genetic alterations in diffuse lower-grade gliomas. Neuro Oncol. 2017; 20(1):66-77. PMC: 5761527. DOI: 10.1093/neuonc/nox132. View

17.

Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P . Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell. 2022; 185(12):2184-2199.e16. PMC: 9189056. DOI: 10.1016/j.cell.2022.04.038. View

18.

Kocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Sulman E . Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nat Genet. 2021; 53(7):1088-1096. PMC: 8483261. DOI: 10.1038/s41588-021-00874-3. View

19.

Barthel F, Johnson K, Varn F, Moskalik A, Tanner G, Kocakavuk E . Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019; 576(7785):112-120. PMC: 6897368. DOI: 10.1038/s41586-019-1775-1. View

20.

Schmidt E, Ichimura K, Reifenberger G, Collins V . CDKN2 (p16/MTS1) gene deletion or CDK4 amplification occurs in the majority of glioblastomas. Cancer Res. 1994; 54(24):6321-4. View