异基因造血干细胞移植仍然是高危急性髓系白血病（AML）患者最有效的策略。主要组织相容性复合物 (MHC) 呈递的白血病特异性新抗原被 T 细胞受体 (TCR) 识别，从而引发移植物抗白血病效应。通过复杂的 V(D)J 重排过程生成独特的 TCR 签名，形成能够与肽-MHC 结合的 TCR。生成的 TCR 库会随着疾病进展和治疗而发生动态变化。在这里，我们应用两种不同的计算工具（TRUST4 和 MIXCR）从癌症基因组图谱 (TCGA) 的 RNA-seq 数据中提取 TCR 序列，并检查特征之间的关联成年 AML 患者的 TCR 库及其临床和分子特征。我们发现，两种计算工具仅共享约 30% 的已识别 TCR CDR3。然而，基于从任一工具获得的数据，TCR 与患者临床和分子特征的关联模式是相似的。独特TCR克隆的数量与患者的白细胞计数、骨髓原始细胞百分比和外周血原始细胞百分比高度相关。使用 TRUST4 对具有 AML 患者突变状态的 TCRA 和 TCRB 中位标准化克隆数进行多变量回归，结果显示 TCRA 或 TCRB 与 WT1 突变、WBC 计数、%BM 母细胞和性别（在 TCRB 模型中调整）显着相关。我们观察到 TCRA/B 独特克隆的数量与 T 细胞抑制信号基因（TIGIT、LAG3、CTLA-4）和 Foxp3 的表达之间存在相关性，但与提示 AML 中 T 细胞表型耗尽的 IL2RA、CD69 和 TNFRSF9 无关。需要大量的计算工具来提高所识别克隆的准确性。利用 RNA-seq 数据可以识别高度丰富的 TCR，并将这些克隆与患者的临床和分子特征相关联。这项研究进一步支持了高分辨率 TCR-Seq 分析在表征患者 TCR 库特征方面的价值。版权所有 © 2023 Pospiech、Tamizharasan、Wei、Kumar、Lou、Milstein 和 Alachkar。

Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment.Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics.We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML.Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.Copyright © 2023 Pospiech, Tamizharasan, Wei, Kumar, Lou, Milstein and Alachkar.