Characterization and comparison of genomic profiles between primary cancer cell lines and parent atypical meningioma tumors

(2020) 20:345 Kim et al. Cancer Cell Int https://doi.org/10.1186/s12935-020-01438-x PRIMARY RESEARCH Cancer Cell International Open Access Characterization and comparison of genomic profiles between primary cancer cell lines and parent atypical meningioma tumors Eunhye Kim1,2, Mirae Kim1,2, Kyungha So1,2, Young Seok Park3, Chang Gok Woo4 and Sang‑Hwan Hyun1,2* Abstract Background: Meningiomas are the second most common primary tumors of the central nervous system. However, there is a paucity of data on meningioma biology due to the lack of suitable preclinical in vitro and in vivo models. In this study, we report the establishment and characterization of patient-derived, spontaneously immortalized cancer cell lines derived from World Health Organization (WHO) grade I and atypical WHO grade II meningiomas. Methods: We evaluated high-resolution 3T MRI neuroimaging findings in meningioma patients which were followed by histological analysis. RT-qPCR and immunostaining analyses were performed to determine the expression levels of meningioma-related factors. Additionally, flow cytometry and sorting assays were conducted to investigate and isolate the CD133 and CD44 positive cells from primary atypical meningioma cells. Further, we compared the gene expression profiles of meningiomas and cell lines derived from them by performing whole-exome sequencing of the blood and tumor samples from the patients, and the primary cancer cell lines established from the meningioma tumor. Results: Our results were consistent with earlier studies that reported mutations in NF2, SMO, and AKT1 genes in atypical meningiomas, and we also observed mutations in MYBL2, a gene that was recently discovered. Significantly, the genomic signature was consistent between the atypical meningioma cancer cell lines and the tumor and blood samples from the patient. Conclusion: Our results lead us to conclude that established meningioma cell lines with a genomic signature identi‑ cal to tumors might be a valuable tool for understanding meningioma tumor biology, and for screening therapeutic agents to treat recurrent meningiomas. Keywords: Atypical meningioma, Primary cancer cell line, Whole-exome sequencing, Stem cell Background Meningiomas are the second most common primary intracranial tumors of the central nervous system, comprising nearly 30% of all primary brain tumors with *Correspondence: 1 Laboratory of Veterinary Embryology and Biotechnology (VETEMBIO), Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, 1 Chungdae‑ro, Seowon‑gu, Cheongju 28644, Republic of Korea Full list of author information is available at the end of the article annual incidence rates ranging from 1.3 to 7.8 and age-standardized mortality rate around 0.3 deaths per 100,000 individuals [1–3]. According to the World Health Organization (WHO) classification criteria, meningiomas are histologically classified into three main subtypes: benign (grade I, low-grade), atypical (grade II), and malignant meningiomas (grade III, high-grade) [4]. Surgical resection of low-grade meningiomas offers a better survival to patients; however, up to 18% of benign meningiomas, 40% of atypical meningiomas, and 80% of malignant meningioma recur within 5 years of complete © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativeco mmons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Kim et al. Cancer Cell Int (2020) 20:345 excision [5–7]. Chemotherapeutic interventions have largely been unsuccessful for meningioma therapy, and refractory or recurring meningiomas are instead treated with surgery and radiotherapy [8, 9]. Here is an urgent need for novel therapeutic approaches based on effective molecular targets in order to improve long-term control of meningioma. Lack of sufficient clinical predictive power remains one of the most critical obstacles in the development of novel study models [10]. Over recent years, patient-derived xenograft (PDX) models, which are created by grafting of patient-derived cancer cells into immunodeficient mice [11], have emerged as important tools for translational research. Efforts are underway to establish xenograft models in benign and malignant meningiomas [12, 13]. The success of xenograft models depends on reliable and biologically relevant primary cancer cell lines. Most of the well-characterized cell lines are derived from malignant meningiomas (grade III) [14–16]; however, there is a paucity of cell lines derived from grade I [17, 18] and grade II [19] meningiomas. The available atypical meningioma cell lines have been artificially-immortalized by viral transduction to induce in vivo expression of the human telomerase reverse transcriptase gene (hTERT), human papillomavirus E6/E7 oncogenes, or SV40 large T antigen. However, the use of these cell lines as a meningioma model comes with the caveat that it is difficult to know how artificial immortalization might impact the biology of these tumors. Over the past decade, novel methods of high-throughput DNA sequencing, termed as next-generation sequencing (NGS), have been developed. These technologies have provided new insights into the genomic characterization of tumors, and the complex processes that occur throughout cancer progression [20–23]. In meningioma, an inactivating mutation of a tumor suppressor gene, the neurofibromatosis type 2 (NF2) gene, is a well-known genetic alteration [24]. NF2 is thought to be involved in meningioma initiation rather than progression [4]. In addition, recent genomic analyses of meningioma using next-generation sequencing have identified mutations in the TNF receptor-associated factor 7 (TRAF7), the Kruppel-like factor 4 (KLF4), the v-Akt murine thymoma viral oncogene homolog 1 (AKT1), and the smoothened (SMO) gene [25, 26]. Interestingly, such mutations were found to be associated with tumorigenesis and progression of NF2 independent meningiomas [7]. The TRAF7 and KLF4 are transcription factors thought to drive tumor initiation, induction of (...truncated)