Optimizing pre-analytic sample handling for high throughput TCR sequencing in cutaneous T cell lymphoma

优化皮肤 T 细胞淋巴瘤高通量 TCR 测序的分析前样品处理

• 批准号: 10814026
• 负责人: Rachael Ann Clark
• 金额: $ 4.38万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10814026
• 关键词: Affect; Age; Biological Markers; Biopsy; Caring; Clinical Trials; Cutaneous Lymphoma; Cutaneous T-cell lymphoma; DNA; Diagnosis; Fixatives; Formalin; Freezing; Funding; Future; Goals; Grant; High-Throughput Nucleotide Sequencing; Histology; Link; Measurement; Methods; Morphology; Nucleic Acids; Paraffin Embedding; Parents; Patients; Proteins; RNA; Reproducibility; Sampling; Skin; Skin Tissue; Specimen; T cell receptor repertoire sequencing; T-Cell Receptor Genes; Techniques; Testing; Tissue Embedding; Tissues; cancer type; clinical practice; preservation; response; sample fixation; tissue processing; treatment response; Affect; Age; Biological Markers; Biopsy; Caring; Clinical Trials; Cutaneous Lymphoma; Cutaneous T-cell lymphoma; DNA; Diagnosis; Fixatives; Formalin; Freezing; Funding; Future; Goals; Grant; High-Throughput Nucleotide Sequencing; Histology; Link; Measurement; Methods; Morphology; Nucleic Acids; Paraffin Embedding; Parents; Patients; Proteins; RNA; Reproducibility; Sampling; Skin; Skin Tissue; Specimen; T cell receptor repertoire sequencing; T-Cell Receptor Genes; Techniques; Testing; Tissue Embedding; Tissues; cancer type; clinical practice; preservation; response; sample fixation; tissue processing; treatment response

ABSTRACT AND SPECIFIC AIMS Formalin fixation is a common method used to preserve skin biopsies in both clinical practice and clinical trials. Formalin-fixed, paraffin-embedded (FFPE) tissues have excellent tissue morphology, but DNA and RNA are degraded by formalin fixation 1 . High throughput sequencing of the rearranged T cell receptor genes (HTS) has transformed the diagnosis, care and assessment of therapeutic responses in patients with cutaneous T cell lymphoma (CTCL)2-5. HTS results are highly reproducible in frozen CTCL skin biopsies but the formalin used to preserve skin biopsies in many clinical trials degrades DNA and affects HTS measurements, potentially causing errors in patient diagnosis, assessment of responses and choices of therapy. The overarching goal of the funded parent U01 grant is to identify a single uniform optimal tissue processing approach for small skin biopsies to study CTCL that will give accurate and reproducible DNA, RNA and protein measurements, maintain excellent histology, and preserve remaining tissue for future measurement of emerging biomarkers. Hypothesis: Non-cross-linking tissue fixatives will maintain nucleic acid and protein integrity without sacrificing histopathologic quality and quantitative corrections for DNA degradation in banked formalin-fixed specimens will allow accurate HTS measurements in existing skin biopsies from patients with CTCL.

摘要和具体目的福尔马林固定是一种常见方法，用于在临床实践和临床试验中保存皮肤活检。福尔马林固定，石蜡包裹的（FFPE）组织具有出色的组织形态，但DNA和RNA被福尔马林固定降解1。重排的T细胞受体基因（HTS）的高通量测序已转化了皮肤T细胞淋巴瘤（CTCL）患者治疗反应的诊断，护理和评估2-5。 HTS结果在冷冻的CTCL皮肤活检中高度可重复，但是在许多临床试验中用于保留皮肤活检的福尔马林降解并影响HTS测量，可能导致患者诊断，评估反应和治疗选择。资助的父级U01赠款的总体目标是确定小型皮肤活检的单一均匀最佳组织加工方法研究CTCL，该方法将提供准确且可重现的DNA，RNA和蛋白质测量值，维持出色的组织学，并保留剩余的组织，以使其未来的生物标志物的未来测量。假设：非跨链接组织固定剂将维持核酸和蛋白质完整性，而无需牺牲组织病理学质量和定量校正，以验证福尔马林固定标本中的DNA降解，将允许从患有CTCL患者的现有皮肤生物群体中准确的HTS测量。