A prognostic mRNA immune signature for resected stage II-III melanoma

切除的 II-III 期黑色素瘤的预后 mRNA 免疫特征

• 批准号: 10412153
• 负责人: Yvonne Margaret Saenger
• 金额: $ 40.23万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-13 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10412153
• 关键词: Adjuvant; Adjuvant Study; Adjuvant Therapy; Algorithmic Analysis; Binding; Biological Assay; Biological Markers; Biopsy; Biotechnology; British Columbia; CD8B1 gene; CLIA certified; Cessation of life; Clinical; Clinical Trials; Collaborations; Comprehensive Cancer Center; Data; Data Set; Diagnosis; Eastern Cooperative Oncology Group; Ensure; Environment; Excision; Exposure to; Face; Follow-Up Studies; Formalin; Future; Genes; Goals; Herbert Irving Comprehensive Cancer Center; Immune; Immune checkpoint inhibitor; Immunofluorescence Immunologic; Immunologic Markers; Immunology procedure; Immunotherapy; Impairment; Interferons; Interobserver Variability; Laboratories; Manuals; Messenger RNA; Methodology; Methods; Migration Assay; Morphology; New York; Operative Surgical Procedures; Outcome; Paraffin Embedding; Pathologic; Patient Selection; Patients; Phase; Pilot Projects; Placebos; Polymerase Chain Reaction; Population; Procedures; Process; Prognosis; Prognostic Marker; Program Evaluation; Publishing; RNA; Randomized; Recurrence; Regulator Genes; Relapse; Reporter; Reproducibility; Research; Resected; Retrospective Studies; Risk; Risk Assessment; Roswell Park Cancer Institute; Sampling; Sensitivity and Specificity; Specimen; Staging; System; Technology; Testing; Time; Tissue Embedding; Tissues; Training; Tumor-Infiltrating Lymphocytes; Universities; Validation; autoimmune toxicity; base; biomarker development; biomarker signature; clinical application; clinical diagnostics; clinical practice; clinical prognostic; cohort; density; experimental study; genetic signature; health care settings; high risk; immune activation; immunotherapy clinical trials; improved; indexing; instrumentation; melanoma; mortality; nano-string; patient biomarkers; patient population; patient stratification; predicting response; prevent; prognostic; prognostic value; prospective; sample fixation; tool; transcriptome sequencing; trial design; tumor; tumor-immune system interactions

We propose to develop a prognostic mRNA immune signature for resected stage II-III melanoma, in order to stratify these patients, who have a recurrence risk of ~50%. There is an urgent need to define accurate prognostic markers for stage II-III melanoma patients because adjuvant immunotherapy to prevent recurrence is both toxic and expensive. Unfortunately, conventional staging does not allow for accurate assessment of risk and many “low risk” patients in fact progress. Further, while the immune tumor micro- environment is a key determinant of outcomes, standard pathologic assessment of tumor infiltrating lymphocytes (TILs) is subjective and not applicable to general clinical practice. In order to better stratify patients for adjuvant immunotherapy, we seek to validate a previously defined 53-gene signature. This signature employs NanoString, a probe based technology well suited to the analysis of the partially degraded RNA typically recovered from clinical grade FFPE tissue sections. We initially defined this signature in a training set and then validated these findings in an independent test set [Sivendran, et al. (2014) J. Invest. Dermatol. 134:2202-11]. As both training and test sets populations are retrospective, the next step to develop a clinically applicable assay is to test the signature on prospectively gathered samples. Given the fact that melanomas can recur years after resection in these early stage patients, prospective validation would be lengthy, and thus we opted to use the prospective retrospective analysis [PRA] approach whereby samples are collected and annotated prospectively but analyzed retrospectively. For this purpose we use samples from the Eastern Cooperative Group (ECOG) E1697 study of adjuvant interferon randomized vs placebo in stage II-III resected melanoma. Patients in this study have been maintained on study follow-up since they were randomized between 1998 and 2010. This project is collaboration between the Herbert Irving Comprehensive Cancer Center (HICCC) at Columbia University, the Roswell Park Comprehensive Cancer Center (RPCCC), the University of British Columbia and Omniseq, a commercial biotech spin-off that is majority owned by RPCCC. In Aim 1 (UH2 phase), we perform the analytical validation of the assay including validation of gene reference controls, RNA extraction quality, and reporter binding density. The milestone for moving to the UH3 phase (Aim 2) will be submission to the NYS Clinical Laboratory Evaluation Program. In the UH3 clinical validation phase, we first evaluate two additional retrospective sample populations (from HICCC and RPCCC). As part of this study we will also correlate the 53-gene signature with state of the art immune indices including quantitative multiplex immunofluorescence (qmIF) to assess CD8 to CD68 ratio, a metric recently defined (by our group) to correlate with survival. We then perform the definitive PRA analysis using the E1697 samples.

我们建议为切除的II-III期黑色素瘤开发一种预测预后的mrna免疫标志，依次为 对这些复发风险约为50%的患者进行分层。迫切需要准确地定义 II-III期黑色素瘤患者的预后标记物，因为辅助免疫治疗可以预防 复发既有毒，又代价高昂。不幸的是，传统的分期不能提供准确的 风险评估和许多“低风险”患者事实上都在进步。此外，虽然免疫肿瘤微观- 环境是决定预后的关键因素，肿瘤浸润性的标准病理评估 淋巴细胞(TIL)是主观的，不适用于一般临床实践。为了更好地分层 对于接受辅助免疫治疗的患者，我们寻求验证先前定义的53基因签名。这 Signature采用了纳米串，这是一种基于探针的技术，非常适合分析部分 降解的RNA通常从临床级FFPE组织切片中恢复。我们最初定义的是 在训练集中签名，然后在独立测试集中验证这些发现[Sivenran等人。 (2014)J.Invest。皮肤素。134：2202-11]。由于训练和测试集人口都具有追溯性， 开发一种临床适用的检测方法的下一步是测试预期收集的签名 样本。鉴于这些早期患者的黑色素瘤可能在切除后数年内复发， 前瞻性验证将是漫长的，因此我们选择使用前瞻性回顾分析 [PRA]对样本进行前瞻性收集和注释，但进行分析的方法 追溯。为此，我们使用来自东部合作组织(ECOG)E1697的样本 II-III期切除黑色素瘤的随机辅助性干扰素与安慰剂对照研究。这里的病人 自1998年至2010年随机进行研究以来，一直对研究的后续行动进行研究。 该项目是赫伯特·欧文综合癌症中心(HICCC)在 哥伦比亚大学罗斯威尔公园综合癌症中心(RPCCC)，英国大学 哥伦比亚和Omniseq，后者是一家商业生物技术公司，由RPCCC持有多数股权。目标1(UH2 阶段)，我们执行分析验证，包括验证基因参考对照， RNA提取质量和报告结合密度。迈向超高浓缩铀阶段的里程碑(目标2) 将提交给纽约临床实验室评估计划。在UH3临床验证中 阶段，我们首先评估另外两个回溯性样本总体(来自HICCC和RPCCC)。AS 作为这项研究的一部分，我们还将把53个基因的签名与最新的免疫指标联系起来 包括定量多重免疫荧光(QmIF)来评估CD8与CD68的比率，这是一项指标 最近定义(由我们的小组)与生存相关。然后，我们执行最终的PRA分析 使用E1697样本。