PO.MCB06.04 · 分子与细胞生物学
采用多组学方法为沙特多形性胶质母细胞瘤识别新型生物标志物
Identifying novel biomarkers for Saudi glioblastoma multiform using multi-omics approach
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摘要 Abstract
中文摘要
背景：多形性胶质母细胞瘤（GBM）是一种高级别侵袭性脑胶质瘤，约占中枢神经系统恶性肿瘤的一半。根据最新的《沙特癌症发病率报告》，GBM是全国最常见的中枢神经系统肿瘤，诊断后生存期约为15个月。
目的：需要识别能够提高诊断准确性并提供更可靠预后预测的新型分子生物标志物，特别是针对沙特GBM患者。
方法：本研究从利雅得国民卫队卫生事务部（MNGHA）的阿卜杜勒阿齐兹国王医疗城招募了30名知情同意的GBM患者，方案编号为RC13/258/R。在手术当天采集切除的脑肿瘤组织并立即速冻。DNA和RNA提取按标准方案进行。按照制造商方案制备了用于Illumina全基因组测序、Illumina RNA测序和MGI全基因组亚硫酸氢盐测序的文库。分析流程包括：1）序列读长质量检查，2）修剪，3）比对到参考基因组（注释），4）生成命中计数，5）成对比较/富集分析，以及6）通路分析。
结果：两个试验性GBM样本的初步RNA测序数据分别产生了19k和21k个2×150的双端序列读长。大多数序列读长（87%）质量良好（Phred分值>30），且大多数具有唯一的基因组比对（占序列读长的70%）。分析揭示了19,007个标准化计数，两个样本具有高度相关性（Spearman相关系数r = 0.787，P < 0.001）。此外，分析识别出904个差异表达基因（DEG），其中上调和下调基因分别为434个和470个。预计将生成更多测序数据，并进行完整的多组学整合分析。
结论：本研究首次探究了尚未开发的沙特GBM的多组学特征，并进一步识别和验证人群特异性的新型生物标志物，以指导GBM的临床诊断和预后。
查看英文原文 English abstract
Background: Glioblastoma Multiform (GBM) is a high grade aggressive glioma of the brain and it accounts for almost half of malignant tumours of the central nervous system. As per the latest Saudi Cancer Incidence Report, GBM is the most common central nervous system tumour nationally with about 15 months survival following diagnosis.
Aims: There is a need to identify new molecular biomarkers that can improve diagnostic accuracy and provide a more reliable prognostic prediction, especially for Saudi GBM patients.
Methods: The study recruited 30 consented GBM patients from King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA) hospitals, Riyadh, under protocol No. RC13/258/R. Resected brain tumour tissues were collected on surgery day and immediately were snap-frozen. DNA and RNA extraction were conducted as per standard protocols. Libraries for Illumina Whole Genome Sequencing, Illumina RNA Sequencing and MGI Whole Genome Bisulfite Sequencing were prepared as per manufacturer's protocols. Analysis pipeline included: 1) quality check of sequence reads, 2) trimming, 3) mapping to reference genome (annotation), 4) generating hit counts, 5) pairwise comparison/enrichment analysis, and 6) pathway analysis.
Results: Preliminary RNA sequencing data of two trial GBM samples has generated 19k and 21k paired end 2 x 150 sequence reads. Majority of the sequence reads (87%) had good quality (Phred Score > 30) and majority had a unique genome mapping (70% of sequence reads). The analysis revealed 19,007 normalised counts and the two samples had high correlation (Spearman's correlation r = 0.787, P < 0.001). Additionally, the analysis identified 904 Differentially Expressed Genes (DEG), of which 434 and 470 upregulated and downregulated genes, respectively. Additional sequencing data are expected to be generated with full multi-omics integration analysis to be done.
Conclusion: This study marks the first to investigate the GBM multi-omics profile of the untapped Saudi GBM and to further identify and validate novel biomarkers that are population-specific to guide clinical diagnosis and prognosis for GBM.
利益披露 Disclosure
A. A. Alsaleh, None..
A. Aloraidi, None..
B. M. Alrfaei, None.