Supplementary Material for: Molecular and Functional Heterogeneity of Primary Pancreatic Neuroendocrine Tumors and Metastases

<b><i>Introduction:</i></b> Treatment response to the standard therapy is low for metastatic pancreatic neuroendocrine tumors (PanNETs) mainly due to the tumor heterogeneity. We investigated the heterogeneity between primary PanNETs and metastases to improve the precise treatment. <b><i>Methods:</i></b> The genomic and transcriptomic data of PanNETs were retrieved from the Genomics, Evidence, Neoplasia, Information, Exchange (GENIE), and Gene Expression Omnibus (GEO) database, respectively. Potential prognostic effects of gene mutations enriched in metastases were investigated. Gene set enrichment analysis was performed to investigate the functional difference. Oncology Knowledge Base was interrogated for identifying the targetable gene alterations. <b><i>Results:</i></b> Twenty-one genes had significantly higher mutation rates in metastases which included TP53 (10.3% vs. 16.9%, <i>p</i> = 0.035) and KRAS (3.7% vs. 9.1%, <i>p</i> = 0.016). Signaling pathways related to cell proliferation and metabolism were enriched in metastases, whereas epithelial-mesenchymal transition (EMT) and TGF-β signaling were enriched in primaries. Gene mutations were highly enriched in metastases that had significant unfavorable prognostic effects included mutation of TP53 (<i>p</i> &lt; 0.001), KRAS (<i>p</i> = 0.001), ATM (<i>p</i> = 0.032), KMT2D (<i>p</i> = 0.001), RB1 (<i>p</i> &lt; 0.001), and FAT1 (<i>p</i> &lt; 0.001). Targetable alterations enriched in metastases included mutation of TSC2 (15.5%), ARID1A (9.7%), KRAS (9.1%), PTEN (8.7%), ATM (6.4%), amplification of EGFR (6.0%), MET (5.5%), CDK4 (5.5%), MDM2 (5.0%), and deletion of SMARCB1 (5.0%). <b><i>Conclusion:</i></b> Metastases exhibited a certain extent of genomic and transcriptomic diversity from primary PanNETs. TP53 and KRAS mutation in primary samples might associate with metastasis and contribute to a poorer prognosis. A high fraction of novel targetable alterations enriched in metastases deserves to be validated in advanced PanNETs.

**引言：** 转移性胰腺神经内分泌肿瘤（metastatic pancreatic neuroendocrine tumors, PanNETs）对标准治疗的应答率较低，这主要源于肿瘤异质性（tumor heterogeneity）。本研究旨在探究原发胰腺神经内分泌肿瘤与转移灶之间的异质性，以优化精准治疗方案。**方法：** 分别从基因组学、证据、肿瘤、信息、交换数据库（GENIE）以及基因表达综合数据库（GEO）获取胰腺神经内分泌肿瘤的基因组和转录组数据。探究了转移灶中富集的基因突变的潜在预后影响。通过基因集富集分析（Gene Set Enrichment Analysis）探究二者的功能差异。借助肿瘤学知识库筛选可靶向治疗的基因改变。**结果：** 共有21个基因在转移灶中的突变率显著升高，其中包括TP53（10.3% vs. 16.9%，*p* = 0.035）与KRAS（3.7% vs. 9.1%，*p* = 0.016）。与细胞增殖和代谢相关的信号通路在转移灶中富集，而上皮间质转化（epithelial-mesenchymal transition, EMT）与转化生长因子β（transforming growth factor-β, TGF-β）信号通路则在原发灶中富集。在转移灶中富集且具有显著不良预后影响的基因突变包括TP53（*p* < 0.001）、KRAS（*p* = 0.001）、ATM（*p* = 0.032）、KMT2D（*p* = 0.001）、RB1（*p* < 0.001）以及FAT1（*p* < 0.001）。转移灶中富集的可靶向治疗基因改变包括TSC2突变（15.5%）、ARID1A突变（9.7%）、KRAS突变（9.1%）、PTEN突变（8.7%）、ATM突变（6.4%）、EGFR扩增（6.0%）、MET扩增（5.5%）、CDK4扩增（5.5%）、MDM2扩增（5.0%）以及SMARCB1缺失（5.0%）。**结论：** 转移灶与原发胰腺神经内分泌肿瘤存在一定程度的基因组和转录组差异。原发样本中的TP53与KRAS突变可能与转移发生相关，并会导致较差的预后。转移灶中富集的大量新型可靶向治疗基因改变，值得在晚期胰腺神经内分泌肿瘤中开展验证研究。