Integrated DNA methylation and RNA expression in Small Intestinal neuroendocrine tumors. Homo sapiens

Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival. Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival. Overall design: This study included 97 tumour samples from 85 individuals, this included both primary and metastatic tumour samples. 25 normal small intestinal samples were analysed.

背景与目的 小肠神经内分泌肿瘤（Small intestinal neuroendocrine tumours, SINETs）是小肠最常见的恶性肿瘤，但其潜在致病机制仍未得到充分阐明。全基因组与外显子组测序研究显示，SINETs的突变负荷极低，目前已知的最常见突变仅见于约8%的肿瘤，即细胞周期蛋白依赖性激酶抑制剂1B（cyclin dependent kinase inhibitor 1B, CDKN1B），这提示肿瘤发生可能由其他替代机制驱动。本研究旨在对SINETs进行全基因组范围的分子谱分析，以基于分子特征识别致病驱动因素。本研究是该肿瘤类型中规模最大的无偏倚整合基因组、表观基因组与转录组分析研究。
方法 本文呈现了97例SINETs样本的整合分子分析数据，包括全外显子组或靶向CDKN1B测序（n=29）、Illumina HumanMethylation450 BeadChip芯片谱分析（n=69）、甲基化DNA免疫沉淀测序（n=16）、拷贝数变异分析（n=47）以及Illumina全基因组-DASL表达芯片谱分析（n=43）。
结果 基于分子谱分析，SINETs可被分为3个亚型，这三类亚型在原发肿瘤切除术后的无进展生存期存在显著差异（10年时未达到 vs 56个月 vs 21个月，p=0.04）。表观突变的复发率最高可达85%，本研究共鉴定出21个表观遗传失调基因，包括CDX1（86%）、CELSR3（84%）、FBP1（84%）与GIPR（74%）。
结论 本研究是首个针对SINETs的全面整合分子分析研究。我们证实这类肿瘤存在高度的表观遗传失调。此外，我们鉴定出了对无进展生存期具有显著影响的新型分子亚型。
整体设计 本研究纳入了来自85名个体的97份肿瘤样本，涵盖原发灶与转移灶样本，同时分析了25份正常小肠组织样本。