Diagnosing post-transplant lymphoproliferative disorder (PTLD) is challenging and often requires invasive procedures. Analyses of cell-free DNA (cfDNA) isolated from plasma is minimally invasive and highly effective for genomic profiling of tumors. We studied the feasibility of using cfDNA to profile PTLD and explore its potential to serve as a screening tool. We included seventeen patients with monomorphic PTLD after solid organ transplantation in this multi-center observational cohort study. We used low-coverage whole genome sequencing (lcWGS) to detect copy number variations (CNVs) and targeted next-generation sequencing (NGS) to identify Epstein-Barr virus (EBV) DNA load and somatic single nucleotide variants (SNVs) in cfDNA from plasma. Seven out of seventeen (41%) patients had EBV-positive tumors, and 13/17 (76%) had stage IV disease. Nine out of seventeen (56%) patients showed CNVs in cfDNA, with more CNVs in EBV-negative cases. Recurrent gains were detected for 3q, 11q, and 18q. Recurrent losses were observed at 6q. The fraction of EBV reads in cfDNA from EBV-positive patients was 3-log higher compared to controls and EBV-negative patients. 289 SNVs were identified, with a median of 19 per sample. SNV burden correlated significantly with lactate dehydrogenase levels. Similar SNV burdens were observed in EBV-negative and EBV-positive PTLD. The most commonly mutated genes were TP53 and KMT2D (41%), followed by SPEN, TET2 (35%), and ARID1A, IGLL5, and PIM1 (29%), indicating DNA damage response, epigenetic regulation, and B-cell signaling/NFkB pathways as drivers of PTLD. Overall, CNVs were more prevalent in EBV-negative lymphoma, while no difference was observed in the number of SNVs. Our data indicated the potential of analyzing cfDNA as a tool for PTLD screening and response monitoring.

中文翻译：

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使用游离 DNA 对移植后淋巴增殖性疾病进行基因组分析

诊断移植后淋巴增殖性疾病 (PTLD) 具有挑战性，并且通常需要侵入性手术。从血浆中分离的游离 DNA (cfDNA) 分析是微创且非常有效的肿瘤基因组分析。我们研究了使用 cfDNA 分析 PTLD 的可行性，并探索其作为筛查工具的潜力。在这项多中心观察性队列研究中，我们纳入了 17 名实体器官移植后患有单形性 PTLD 的患者。我们使用低覆盖率全基因组测序 (lcWGS) 来检测拷贝数变异 (CNV)，并使用靶向下一代测序 (NGS) 来识别来自 cfDNA 的 Epstein-Barr 病毒 (EBV) DNA 负载和体细胞单核苷酸变异 (SNV)等离子体。十七名患者中的七名 (41%) 患有 EBV 阳性肿瘤，13/17 (76%) 患有 IV 期疾病。十七名患者中有九名 (56%) 在 cfDNA 中显示出 CNV，其中 EBV 阴性病例中的 CNV 较多。在第 3 季度、第 11 季度和第 18 季度检测到经常性收益。在第六季度观察到经常性损失。与对照组和 EBV 阴性患者相比，EBV 阳性患者 cfDNA 中 EBV 读数的分数高出 3 个对数。鉴定出 289 个 SNV，每个样本中位数为 19 个。SNV 负荷与乳酸脱氢酶水平显着相关。在 EBV 阴性和 EBV 阳性 PTLD 中观察到类似的 SNV 负担。最常见的突变基因是 TP53 和 KMT2D (41%)，其次是 SPEN、TET2 (35%) 以及 ARID1A、IGLL5 和 PIM1 (29%)，表明 DNA 损伤反应、表观遗传调控和 B 细胞信号传导/ NFkB 通路作为 PTLD 的驱动因素。总体而言，CNV 在 EBV 阴性淋巴瘤中更为常见，而 SNV 的数量没有观察到差异。我们的数据表明分析 cfDNA 作为 PTLD 筛查和反应监测工具的潜力。