High-resolution 400K oligonucleotide array comparative genomic hybridization analysis of neurofibromatosis type 1-associated cutaneous neurofibromas Akiko Asai a,b,1 , Sivasundaram Karnan a,1 , Akinobu Ota a, ⁎ ,1 , Miyuki Takahashi a,c , Lhagvasuren Damdindorj a , Yuko Konishi a , Ekhtear Hossain a , Hiroyuki Konishi a , Ayako Nagata d , Kazuhisa Yokoo b , Yoshitaka Hosokawa a a Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi, Japan b Department of Plastic & Reconstructive Surgery, Aichi Medical University School of Medicine, Nagakute, Aichi, Japan c Department of Internal Medicine Division of Hematology, Aichi Medical University School of Medicine, Nagakute, Aichi, Japan d Department of Plastic & Reconstructive Surgery, Daiyukai Daiichi Hospital, Ichinomiya, Aichi, Japan abstract article info Article history: Received 5 September 2014 Received in revised form 18 December 2014 Accepted 28 December 2014 Available online 3 January 2015 Keywords: Oligo-array CGH Neurofibromatosis type 1 Cutaneous neurofibroma Tumor-related gene Gene expression Neurofibromatosis type 1 (NF1) is a genetic disorder where affected individuals develop benign or malignant nervous system tumors. To date, NF1 is caused by mutations in the NF1 tumor suppressor gene located at chro- mosome band 17q11.2. In this study, we aimed to characterize novel recurrent regional chromosomal imbalances and tumor-related candidate genes in NF1-associated cutaneous neurofibromas. Nine cutaneous neurofibromas from NF1 patients were screened for recurrent chromosomal imbalances using high-resolution 400K oligonucle- otide array comparative genomic hybridization (aCGH). All the cases exhibited at least one sub-microscopic ab- normality. Regions of recurrent chromosomal imbalances in a least one third of cases were loss of 1q13.2 (33%, FAM19A3), 1q21.1 (44%, RABGAP1L), 2q37.1 (56%, INPP5D), 3p25.1 (67%, CHCHD4), 4p15.32 (56%, FGFBP1), 5q11.2 (56%, ARL15), 6q22.31 (56%, NKAIN2), 6q22.33 (67%, ARHGAP18), 6q25.1 (67%, UST), 7q13 (56%, ADCY1), 12q13.13 (44%, KRT71), 19q13.32 (56%, GRLF1), and 20p11.21 (56%, NLP) and gain of 2p23.3 (76%, C2orf53), 8q22.3 (44%, ODF1) and 8q24.3 (67%, ARC). Several chromosomal imbalances, including loss of 7q11.23, 13q14.1, 14q32.13, 17p12, and 17q11.2 were detected at a lower frequency. We also confirmed that these chromosomal imbalances were not detected in the patient-matched lymphocyte DNAs. Amongst the 6 tumor-related candidate genes (RABGAP1L, ADCY1, SLIT2, GRLF1, UST, and ARC) identified in the regions of recur- rent chromosomal imbalances, the gene expression changes of UST (down-regulation) and ARC (up-regulation) were found to be significantly associated with copy number alterations. The novel recurrent chromosomal imbalances and the altered expression levels of the tumor-related candidate genes may be associated with the development of NF1-associated benign cutaneous neurofibromas. © 2014 Elsevier B.V. All rights reserved. 1. Introduction Neurofibromatosis type 1 (NF1), also called von Recklinghausen dis- ease, is an autosomal dominant genetic disorder which occurs in ap- proximately 1 in 2500–3000 live births throughout the world (Ferner et al., 2007; Gottfried et al., 2006; Huson et al., 1989; Jouhilahti et al., 2011a; Miller et al., 2006). NF1 patients have defects in neural crest- derived tissues, leading to a wide spectrum of clinical presentations, in- cluding developmental, pigment and neoplastic aberrations (Le and Parada, 2007). The main clinical features of NF1 include café-au-lait spots (6 or more café-au-lait macules measuring at least 5 mm and 15 mm in diameter in prepubertal and postpubertal individuals respec- tively), freckling in the axillary or inguinal region, cognitive impairment, and neurofibromas (two or more types or plexiform neurofibroma) (National Institutes of Health Consensus Development Conference Statement Neurofibromatosis, 1988; Riccardi, 1991). NF1-associated cutaneous neurofibromas are complex tumors com- posed of multiple cell types with the genotype NF1 +/- including Schwann cells, fibroblasts, epithelial cells, and mast cells (Jouhilahti et al., 2011a). Neurofibroma is thought to be initiated by “second-hit” somatic mutation or loss of the inherited wild-type NF1 allele in Gene 558 (2015) 220–226 Abbreviations: NF1, neurofibromatosis type 1; RT-PCR, reverse transcription polymer- asechain reaction;BAC,bacterialartificial chromosome; CGH, comparative genomic hybrid- ization; pNFs, plexiform neurofibromas; MPNST, malignant peripheral nerve sheath tumors; aCGH, array CGH; SNP, single-nucleotide polymorphism; LOH, loss of heterozygos- ity;CNN-LOH, copynumber neutral-LOH; CNAs, copynumberaberrations; CNVs,copynum- ber variations; UST, uronyl-2-sulfotransferase; AMPARs, AMPA-type glutamate receptors; MRI, magnetic resonance imaging. ⁎ Corresponding author at: Department of Biochemistry, Aichi Medical University School of Medicine 1-1 Yazako Karimata, Building #2, Room 362, Nagakute, Aichi 480- 1195, Japan. E-mail address: aota@aichi-med-u.ac.jp (A. Ota). 1 Akiko Asai, Sivasundaram Karnan, and Akinobu Ota contributed equally to this work. http://dx.doi.org/10.1016/j.gene.2014.12.064 0378-1119/© 2014 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene