Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling.
Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling.
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神经母细胞瘤分子风险-通过无细胞循环肿瘤DNA分析进行DNA拷贝数分层和ALK基因分型。
DOI：
10.3390/cancers13133365
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发表时间：
2021-07-05
期刊：
影响因子：
5.2
通讯作者：
Karpelowsky J
中科院分区：
文献类型：
--
作者：
Kahana-Edwin S;Cain LE;McCowage G;Darmanian A;Wright D;Mullins A;Saletta F;Karpelowsky J
神经母细胞瘤是由几个分子亚型，与不同的结果。这些亚型的风险分类在诊断时进行常规评估，并基于对肿瘤DNA中明确定义的染色体变化的评价，这需要组织活检。然而，目前的临床实践限制了可用于分子诊断的肿瘤组织的量。肿瘤通常会将细胞和亚细胞成分脱落到体液中。液体活检是一种新兴的方法来检测血液中的这种癌症生物分子，并为个性化医疗带来了巨大的希望。在这里，我们提出了使用液体活检提供神经母细胞瘤的分子分类，是独立于组织活检，并可能被用作一个伴侣诊断测试，以减少组织的要求。我们还将讨论在临床环境中成功应用这种方法的分析前的考虑因素。背景资料：MYCN扩增（MNA）、节段性染色体畸变（SCA）和ALK激活突变是神经母细胞瘤风险组分层和靶向治疗的生物标志物，目前均通过组织活检进行评估。用于神经母细胞瘤诊断的肿瘤基因检测需求的增加对当前实践构成了挑战，因为获得的小尺寸芯针活检需要用于多种分子检测。我们评估了在循环中检测这些生物标志物的效用。方法：测试各种预分析条件以优化循环肿瘤DNA（ctDNA）拷贝数变化评估。使用目前用于神经母细胞瘤诊断的单核苷酸多态性（SNP）阵列方法评估来自10名诊断为神经母细胞瘤的患者的血浆样本的SCA和MNA，使用数字液滴PCR（ddPCR）独立评估MNA状态。3例患者（1例与前10例相同）使用ddPCR检测ALK激活突变p.F1174L和p.F1245I。结果如下：拷贝数检测受血液样本的物理扰动（模拟次优样本运输）的影响很大，这可以使用专用的防腐剂收集管来克服。在SNP染色体微阵列处理之前对ctDNA的预分析DNA修复程序提高了SCA和MNA的检测下限，分别定义为20%和10%。我们使用SNP阵列在10/10（100%）患者中检测到SCA，其中7例还呈现MNA。循环游离DNA（cfDNA）和匹配的肿瘤DNA图谱通常相同。使用ddPCR在7/7（100%）MNA和0/12（0%）非MNA病例中检测到MNA。分别在来自4名和3名患者（1名患者同时患有两种疾病）的纵向样本中评估了MNA和ALK突变动态变化，准确反映了6/6例（100%）病例的治疗应答和5/6例（83%）病例的疾病复发。在ALK抑制剂Lorlatinib靶向治疗前和治疗6-8周采集的样本显示，根据治疗应答，ALK变体减少/增加。结论：这些结果证明了ctDNA分析用于分子风险分层的可行性，以及在临床相关时间范围内的治疗监测，以及减少目前嵌入神经母细胞瘤管理中的新鲜组织要求的潜力。
Neuroblastoma is composed of several molecular subtypes that are associated with distinct outcomes. Risk classification into these subtypes is routinely assessed at diagnosis and is based on the evaluation of well-defined chromosomal changes found in the tumor DNA which requires a tissue biopsy. However, current clinical practice limits the amount of tumor tissue available for molecular diagnostics. Tumors often shed cells and subcellular components into body fluids. Liquid biopsy is an emerging method to detect such cancer biomolecules in the bloodstream and holds great promise for personalized medicine. Here, we present the use of liquid biopsy to provide molecular classification for neuroblastoma that is independent to tissue biopsy and can potentially be used as a companion diagnostic test to reduce tissue requirements. We will also discuss the pre-analytical considerations for the successful application of this approach in the clinical setting. Background: MYCN amplification (MNA), segmental chromosomal aberrations (SCA) and ALK activating mutations are biomarkers for risk-group stratification and for targeted therapeutics for neuroblastoma, both of which are currently assessed on tissue biopsy. Increase in demand for tumor genetic testing for neuroblastoma diagnosis is posing a challenge to current practice, as the small size of the core needle biopsies obtained are required for multiple molecular tests. We evaluated the utility of detecting these biomarkers in the circulation. Methods: Various pre-analytical conditions tested to optimize circulating-tumor DNA (ctDNA) copy number changes evaluations. Plasma samples from 10 patients diagnosed with neuroblastoma assessed for SCA and MNA using single nucleotide polymorphism (SNP) array approach currently used for neuroblastoma diagnosis, with MNA status assessed independently using digital-droplet PCR (ddPCR). Three patients (one in common with the previous 10) tested for ALK activating mutations p.F1174L and p.F1245I using ddPCR. Results: Copy number detection is highly affected by physical perturbations of the blood sample (mimicking suboptimal sample shipment), which could be overcome using specialized preservative collection tubes. Pre-analytical DNA repair procedures on ctDNA before SNP chromosome microarray processing improved the lower limit of detection for SCA and MNA, defined as 20% and 10%, respectively. We detected SCA in 10/10 (100%) patients using SNP array, 7 of which also presented MNA. Circulating-free DNA (cfDNA) and matched tumor DNA profiles were generally identical. MNA was detected using ddPCR in 7/7 (100%) of MNA and 0/12 (0%) non-MNA cases. MNA and ALK mutation dynamic change was assessed in longitudinal samples from 4 and 3 patients (one patient with both), respectively, accurately reflected response to treatment in 6/6 (100%) and disease recurrence in 5/6 (83%) of cases. Samples taken prior to targeted treatment with the ALK inhibitor Lorlatinib and 6–8 weeks on treatment showed reduction/increase in ALK variants according to response to treatment. Conclusions: These results demonstrate the feasibility of ctDNA profiling for molecular risk-stratification, and treatment monitoring in a clinically relevant time frame and the potential to reduce fresh tissue requirements currently embedded in the management of neuroblastoma.
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影响因子：
4.1
作者：
Peitz, Constantin;Spruessel, Annika;Lodrini, Marco
通讯作者：
Lodrini, Marco
影响因子：
4
作者：
Combaret, Valerie;Iacono, Isabelle;Bellini, Angela;Brejon, Stephanie;Bernard, Virginie;Marabelle, Aurelien;Coze, Carole;Pierron, Gaelle;Lapouble, Eve;Schleiermacher, Gudrun;Blay, Jean Yves
通讯作者：
Blay, Jean Yves
通过碎片尺寸分析增强了循环肿瘤DNA的检测。
影响因子：
17.1
作者：
Mouliere F;Chandrananda D;Piskorz AM;Moore EK;Morris J;Ahlborn LB;Mair R;Goranova T;Marass F;Heider K;Wan JCM;Supernat A;Hudecova I;Gounaris I;Ros S;Jimenez-Linan M;Garcia-Corbacho J;Patel K;Østrup O;Murphy S;Eldridge MD;Gale D;Stewart GD;Burge J;Cooper WN;van der Heijden MS;Massie CE;Watts C;Corrie P;Pacey S;Brindle KM;Baird RD;Mau-Sørensen M;Parkinson CA;Smith CG;Brenton JD;Rosenfeld N
通讯作者：
Rosenfeld N
影响因子：
12.3
作者：
Koboldt DC
通讯作者：
Koboldt DC
影响因子：
9.3
作者：
Huggett, Jim F.;Foy, Carole A.;Bustin, Stephen A.
通讯作者：
Bustin, Stephen A.