DataSheet_2_Well-differentiated G1 and G2 pancreatic neuroendocrine tumors: a meta-analysis of published expanded DNA sequencing data.xlsx

IntroductionWell-differentiated pancreatic neuroendocrine tumors (PNETs) can be non-functional or functional, e.g. insulinoma and glucagonoma. The majority of PNETs are sporadic, but PNETs also occur in hereditary syndromes, primarily multiple endocrine neoplasia type 1 (MEN1). The Knudson hypothesis stated a second, somatic hit in MEN1 as the cause of PNETs of MEN1 syndrome. In the recent years, reports on genetic somatic events in both sporadic and hereditary PNETs have emerged, providing a basis for a more detailed molecular understanding of the pathophysiology. In this systematic review and meta-analysis, we made a collation and statistical analysis of aggregated frequent genetic alterations and potential driver events in human grade G1/G2 PNETs.
MethodsA systematic search was performed in concordance with the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) reporting guidelines of 2020. A search in Pubmed for published studies using whole exome, whole genome, or targeted gene panel (+400 genes) sequencing of human G1/G2 PNETs was conducted at the 25th of September 2023. Fourteen datasets from published studies were included with data on 221 patients and 225 G1/G2 PNETs, which were divided into sporadic tumors, and hereditary tumors with pre-disposing germline variants, and tumors with unknown germline status. Further, non-functioning and functioning PNETs were distinguished into two groups for pathway evaluation. The collated genetical analyses were conducted using the ‘maftools’ R-package.
ResultsSporadic PNETs accounted 72.0% (162/225), hereditary PNETs 13.3% (30/225), unknown germline status 14.7% (33/225). The most frequently altered gene was MEN1, with somatic variants and copy number variations in overall 42% (95/225); hereditary PNETs (germline variations in MEN1, VHL, CHEK2, BRCA2, PTEN, CDKN1B, and/or MUTYH) 57% (16/30); sporadic PNETs 36% (58/162); unknown germline status 64% (21/33). The MEN1 point mutations/indels were distributed throughout MEN1. Overall, DAXX (16%, 37/225) and ATRX-variants (12%, 27/225) were also abundant with missense mutations clustered in mutational hotspots associated with histone binding, and translocase activity, respectively. DAXX mutations occurred more frequently in PNETs with MEN1 mutations, p<0.05. While functioning PNETs shared few variated genes, non-functioning PNETs had more recurrent variations in genes associated with the Phosphoinositide 3-kinase, Wnt, NOTCH, and Receptor Tyrosine Kinase-Ras signaling onco-pathways.
DiscussionThe somatic genetic alterations in G1/G2 PNETs are diverse, but with distinct differences between sporadic vs. hereditary, and functional vs. non-functional PNETs. Increased understanding of the genetic alterations may lead to identification of more drivers and driver hotspots in the tumorigenesis in well-differentiated PNETs, potentially giving a basis for the identification of new drug targets. (Funded by Novo Nordisk Foundation, grant number NNF19OC0057915).

引言

胰腺高分化神经内分泌肿瘤（pancreatic neuroendocrine tumors, PNETs）可分为无功能型与功能型，例如胰岛素瘤与胰高血糖素瘤。大多数PNETs为散发性，但也可发生于遗传性综合征中，以1型多发性内分泌肿瘤综合征（multiple endocrine neoplasia type 1, MEN1）最为常见。克努森假说（Knudson hypothesis）提出，MEN1基因的第二次体细胞击发事件是导致MEN1综合征相关PNETs的病因。近年来，针对散发性与遗传性PNETs体细胞遗传事件的研究陆续发表，为更深入解析其病理生理学的分子机制提供了依据。本项系统综述与荟萃分析旨在整合并统计分析人类G1/G2级PNETs中频发的遗传改变与潜在驱动事件。

方法

本研究严格遵循2020版《系统综述与荟萃分析首选报告条目》(Preferred Reporting Items for Systematic Review and Meta-Analyses, PRISMA)的报告规范开展系统检索。2023年9月25日，我们在PubMed数据库中检索已发表的、针对人类G1/G2级PNETs开展全外显子组测序、全基因组测序或靶向基因面板（≥400个基因）测序的相关研究。最终纳入14项已发表研究的数据集，涵盖221例患者的225个G1/G2级PNETs样本，按来源分为散发性肿瘤、携带易感种系变异的遗传性肿瘤以及未知种系状态的肿瘤。此外，本研究将功能型与无功能型PNETs分为两组以进行通路分析。整合后的遗传分析采用‘maftools’ R包完成。

结果

本研究纳入的样本中，散发性PNETs占72.0%（162/225），遗传性PNETs占13.3%（30/225），未知种系状态的肿瘤占14.7%（33/225）。最常见的发生改变的基因为MEN1，整体存在体细胞变异与拷贝数变异的样本占比为42%（95/225）；其中遗传性PNETs中该比例为57%（16/30），携带的变异包括MEN1、VHL、CHEK2、BRCA2、PTEN、CDKN1B及/或MUTYH的种系变异；散发性PNETs中为36%（58/162）；未知种系状态组为64%（21/33）。MEN1的点突变/插入缺失突变分布于整个基因区域。整体而言，DAXX（16%，37/225）与ATRX变异（12%，27/225）同样频发：DAXX的错义突变聚集于组蛋白结合相关的突变热点区域，而ATRX的变异则集中于与转位酶活性相关的热点区域。DAXX突变在携带MEN1突变的PNETs中更为常见（p<0.05）。功能型PNETs的变异基因较少，而无功能型PNETs在磷脂酰肌醇3-激酶、Wnt、NOTCH及受体酪氨酸激酶-Ras信号通路相关致癌通路基因中存在更多复发性变异。

讨论

G1/G2级PNETs的体细胞遗传改变具有多样性，但散发性与遗传性、功能型与无功能型PNETs之间存在显著差异。加深对这类肿瘤遗传改变的认识，有助于识别高分化PNETs发生发展过程中的更多驱动基因与驱动突变热点，进而为新型药物靶点的筛选提供理论基础。本研究由诺和诺德基金会（Novo Nordisk Foundation）资助，资助编号为NNF19OC0057915。