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

摘要和特定目的福尔马林固定是临床实践和临床试验中常用的保存皮肤活检的方法。福尔马林固定，石蜡包埋(FFPE)组织具有良好的组织形态，但DNA和RNA被福尔马林固定降解1。重排T细胞受体基因(HTS)的高通量测序已经改变了皮肤T细胞淋巴瘤(CTCL)2-5患者的诊断、护理和治疗反应的评估。HTS结果在冷冻CTCL皮肤活检中的重复性很高，但在许多临床试验中用于保存皮肤活检的福尔马林会降解DNA并影响HTS测量，可能会导致患者诊断、反应评估和治疗选择的错误。资助母公司U01基金的首要目标是为小型皮肤活检确定一种统一的最佳组织处理方法，以研究CTCL，这种方法将提供准确和可重复性的DNA、RNA和蛋白质测量，保持优秀的组织学，并保存剩余组织用于未来新兴生物标记物的测量。假设：非交联型组织固定剂将在不牺牲组织病理学质量的情况下保持核酸和蛋白质的完整性，对储存的福尔马林固定标本中DNA降解的定量校正将使CTCL患者现有的皮肤活检组织中的HTS测量准确。

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.