Hypermutation and malignant progression in an expanded cohort of TMZ treated LGG patients from different molecular subgroups

来自不同分子亚组的接受 TMZ 治疗的 LGG 患者扩大队列中的超突变和恶性进展

• 批准号: 9252225
• 负责人: Matthew R Grimmer
• 金额: $ 5.63万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9252225
• 关键词: 19q; ATRX gene; Adjuvant Therapy; Algorithms; Alkylating Agents; Aneuploidy; Astrocytoma; Automobile Driving; Cell Line; Cells; ChIP-seq; Chromatin; Chromatin Remodeling Factor; Clone Cells; DNA Repair; DNA lesion; Data; Data Set; Endonuclease I; Engineering; Epigenetic Process; Event; Evolution; FRAP1 gene; Family; Future; GTP-Binding Protein alpha Subunits, Gs; Gene Dosage; Gene Family; Genes; Genetic; Genomics; Glioma; Growth; Guide RNA; Histologic; Histone-Lysine N-Methyltransferase; Histones; Image; Label; MLL gene; MLL2 gene; Malignant - descriptor; Malignant Neoplasms; Measures; Mediating; Methyltransferase; Mismatch Repair; Molecular; Monitor; Mus; Mutate; Mutation; NOD/SCID mouse; Oligodendroglioma-Astrocytoma; Pathway Analysis; Pathway interactions; Patients; Pharmaceutical Preparations; Primary Neoplasm; Proteins; Proto-Oncogene Proteins c-akt; Recurrence; Recurrent tumor; Reporting; Resistance; Role; SMARCA4 gene; Science; Subgroup; Surveys; TP53 gene; Testing; The Cancer Genome Atlas; Therapeutic Intervention; Tumor Burden; Xenograft procedure; actionable mutation; clinical practice; cohort; cytotoxic; epigenome; epigenomics; exome; in vivo; molecular subtypes; mutant; oligodendroglioma; outcome forecast; promoter; public health relevance; response; targeted sequencing; temozolomide; transcriptome sequencing; tumor

 DESCRIPTION (provided by applicant): Low-grade glioma (LGG) represents a histologically and genetically heterogeneous group of slow-growing and invasive tumors, including oligodendroglioma (molecularly defined as 1p/19q/IDH1 mutant) and astrocytoma (TP53/ATRX/IDH1 mutant). The most prevalent anti-glioma drug, temozolomide (TMZ), extends overall survival for high-grade glioma (HGG) patients, but can drive genetic hypermutation (HM) and malignant progression in LGG. We recently reported genetic HM in 6 of 10 recurrent astrocytomas upon TMZ treatment, with all hypermutant recurrences progressing to HGG and harboring TMZ-related mutations in the RB and AKT-mTOR pathways, all of which are drivers of HGG. We have recently expanded our TMZ-treated LGG cohort to include paired primary and recurrent tumors from 24 astrocytomas and 13 oligodendrogliomas, allowing a deeper survey of HM, tumor evolution, and malignant progression in two distinct LGG subtypes. Our preliminary analyses show that 7 of 13 TMZ-treated, initially low-grade oligodendrogliomas hypermutated upon recurrence, with the majority of hypermutant recurrences progressing to HGG and harboring TMZ-related mutations in the p53 (common in pretreatment astrocytoma) and AKT-mTOR pathways. These results suggest a genetic convergence of astrocytoma and oligodendroglioma upon TMZ-induced HM and malignant progression. Initial pathway analysis yields chromatin modifiers as a top-ranked gene class common to HM in both LGG subtypes, with MLL methyltransferases and the SWI/SNF chromatin remodeling complex being the most frequent. Deleterious mutations in each of these families are driving events in an array of cancers, including HGG. The hypothesis of this proposal is 1) TMZ-induced hypermutation pushes initially distinct low grade astrocytomas and oligodendrogliomas down a convergent path to malignant progression and 2) the convergence is mediated, in part, by recurrent mutations in chromatin modifier genes. First, genetic pathways or gene families most associated with TMZ-induced HM in both LGG subtypes will be determined from exome mutation calls from initial and recurrent LGG tumors. Importantly, HM- associated candidate tumor driver pathways will be explored by comprehensive pathway enrichment analysis. Next, I will determine the functional role of 2 candidate driver mutations (CDMs) in a chromatin modifier gene (eg. MLL3) by engineering CDMs in 1p/19q/IDH1 mutant oligoastrocytoma cells. The consequence of the CDMs will be tested by ChIP-seq for CDM protein and CDM-related histone marks (eg. H3K4me1), as well as subsequent genomic expression changes by RNA-seq. Finally, the role of the CDMs on malignant progression will be investigated in vivo. These functional studies serve to expand our understanding of convergent LGG evolution, as well as genetic and epigenetic drivers of malignant progression in the context of TMZ-induced HM.

 描述（由适用提供）：低度神经胶质瘤（LGG）代表了一个组织学和遗传性异构的缓慢增长和浸润性肿瘤的组，包括少突胶质瘤（分子定义为1P/19Q/IDH1突变体）和星形瘤（TP53/ATRX/IDH1突变体）。最普遍的抗神经胶质瘤药物替莫唑胺（TMZ）扩展了高级神经胶质瘤（HGG）患者的总生存期，但可以驱动LGG中的遗传性超孕（HM）和恶性进展。我们最近报道了TMZ处理后的10个复发性星形胶质细胞瘤中的6个遗传HM，所有超重物复发均逐渐发展为HGG，并在RB和AKT-MTOR途径中携带与TMZ相关的突变，所有这些途径均为HGG驱动因素。最近，我们扩展了经过TMZ处理的LGG队列，包括来自24个星形胶质细胞瘤和13个少突胶质瘤的成对的原发性和复发性肿瘤，从而可以对两个不同LGG亚型的HM，肿瘤进化和恶性进展进行更深入的调查。我们的初步分析表明，在复发后，有13个TMZ治疗的，最初的低级别寡糖瘤过度过多，大多数过度突然复发发展为HGG，并在P53中携带了TMZ相关的突变（在P53中（常见于预处理Astrolocytoma中常见）和Akt-Mtor pathorey）。这些结果表明，在TMZ诱导的HM和恶性进展时，星形细胞瘤和少突胶质瘤的遗传收敛。初始途径分析产生的染色质修饰剂是两个LGG亚型中HM共有的顶级基因类别，其中MLL甲基转移酶和SWI/SNF染色质重塑络合物是最频繁的。这些家庭中每个家庭中的有害突变都在包括HGG在内的一系列癌症中驱动事件。该提案的假设是1）TMZ诱导的超突变推动最初不同的低级星形胶质瘤和少突胶质瘤，沿染色质模质基因中的复发突变介导了融合到恶性进展的融合途径。首先，在两个LGG亚型中与TMZ诱导的HM最相关的遗传途径或基因家族将由来自初始和复发性LGG肿瘤的外部突变调用确定。重要的是，将通过全面的途径富集分析来探索HM相关的候选肿瘤驱动器途径。接下来，我将通过1P/19Q/IDH1突变体寡聚群瘤细胞中的CDMS来确定2个候选驱动器突变（CDM）在染色质修饰剂基因（例如MLL3）中的功能作用。 CDM的结果将通过CHIP-SEQ测试CDM蛋白和与CDM相关的组蛋白标记（例如H3K4ME1），以及随后的基因组表达随RNA-Seq的变化而变化。最后，将在体内研究CDM在恶性进展中的作用。这些功能研究旨在扩展我们对收敛性LGG演化的理解，以及在TMZ诱导的HM背景下，恶性进展的遗传和表观遗传驱动因素。