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

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.

摘要和具体目标 福尔马林固定是临床实践和临床试验中保存皮肤活检的常用方法。福尔马林固定石蜡包埋 (FFPE) 组织具有良好的组织形态，但福尔马林固定会降解 DNA 和 RNA 1 。重排 T 细胞受体基因 (HTS) 的高通量测序改变了皮肤 T 细胞淋巴瘤 (CTCL)2-5 患者的诊断、护理和治疗反应评估。 HTS 结果在冷冻 CTCL 皮肤活检中具有高度重现性，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，可能导致患者诊断、反应评估和治疗选择的错误。受资助的母公司 U01 资助的总体目标是确定一种统一的最佳组织处理方法，用于小型皮肤活检研究 CTCL，该方法将提供准确且可重复的 DNA、RNA 和蛋白质测量，保持良好的组织学，并保存剩余组织以供将来测量新兴生物标志物。假设：非交联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，并且对储存的福尔马林固定样本中的 DNA 降解进行定量校正将允许在 CTCL 患者的现有皮肤活检中进行准确的 HTS 测量。

项目成果

Tapinarof validates the aryl hydrocarbon receptor as a therapeutic target: A clinical review.

Tapinarof 验证芳烃受体作为治疗靶点：临床回顾。

• 发表时间: 2023-12-27
• 作者: Silverberg, Jonathan I;Boguniewicz, Mark;Quintana, Francisco J;Clark, Rachael A;Gross, Lara;Hirano, Ikuo;Tallman, Anna M;Brown, Philip M;Fredericks, Doral;Rubenstein, David S;McHale, Kimberly A
• 通讯作者: McHale, Kimberly A

Management of relapsed cutaneous T-Cell lymphoma following allogeneic hematopoietic stem cell transplantation: Review with representative patient case.

同种异体造血干细胞移植后复发性皮肤 T 细胞淋巴瘤的治疗：回顾代表性患者病例。

• 发表时间: 2022-07
• 影响因子: 3.6
• 作者: Weiner, David M;Lewis, Daniel J;Spaccarelli, Natalie G;Clark, Rachael A;Nasta, Sunita D;Loren, Alison W;Rook, Alain H;Kim, Ellen J
• 通讯作者: Kim, Ellen J