Supplementary Material for: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms

Introduction:
Pseudomyxoma peritonei (PMP) is a disease characterized by progressive accumulation of intraperitoneal mucinous ascites produced by neoplasms in the abdominal cavity. Since the prognosis of patients with PMP remain unsatisfactory, the development of effective therapeutic drug(s) is a matter of pressing concern. Genetic analyses of PMP have clarified the frequent activation of GNAS and/or KRAS. However, the involvement of global epigenetic alterations in PMPs has not been reported.

Methods:
To clarify the genetic background of the 15 PMP tumors, we performed genetic analysis using AmpliSeq Cancer HotSpot Panel v2. We further investigated global DNA methylation in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes.

Results:
This is the first report of comprehensive DNA methylation profiles of PMPs in the world. We clarified that the 15 PMPs could be classified into at least two epigenotypes, unique methylation epigenotype (UME) and normal-like methylation epigenotype (NLME), and that genes associated with neuronal development and synaptic signaling may be involved in the development of PMPs. In addition, we identified a set of hypermethylation marker genes such as HOXD1 and TSPYL5 in the 15 PMPs.

Conclusions:
These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.

引言：
腹膜假性黏液瘤（Pseudomyxoma peritonei, PMP）是一种以腹腔内肿瘤产生的黏液性腹水进行性积聚为特征的疾病。由于PMP患者的预后仍不理想，开发有效的治疗药物是亟待解决的重要课题。对PMP的遗传分析已明确GNAS和/或KRAS基因的频繁激活，但目前尚未有全局表观遗传改变参与PMP发生发展的相关报道。

方法：
为阐明15例PMP肿瘤的遗传背景，本研究采用AmpliSeq癌症热点面板v2（AmpliSeq Cancer HotSpot Panel v2）进行遗传分析。此外，本研究利用包含总计865,918个探针的甲基化EPIC阵列芯片（Infinium 850k），对15例PMP肿瘤及8例非癌性结肠上皮细胞开展全基因组DNA甲基化检测。

结果：
本研究为全球首项针对PMP的全基因组DNA甲基化谱研究。研究表明15例PMP可至少分为两种表观亚型：独特甲基化表观亚型（unique methylation epigenotype, UME）与正常样甲基化表观亚型（normal-like methylation epigenotype, NLME）；同时发现神经元发育与突触信号相关基因可能参与PMP的发生发展。此外，本研究在15例PMP中鉴定出HOXD1、TSPYL5等一组高甲基化标记基因。

结论：
上述研究结果有助于加深对PMP分子机制的理解，并可为这一致命性疾病的治疗策略开发提供参考。