Identification of Somatic Changes in Tumors from Fanconi Anemia Patients

This study focused on the identification of genomic signatures present in tumors from Fanconi anemia patients. Fanconi anemia is a rare hereditary disease caused by defects in DNA interstrand crosslink repair. The primary patient phenotypes are bone marrow failure and cancer predisposition. We concentrated on squamous cell carcinomas and used whole genome Illumina sequencing (22 tumor samples and 12 normal samples) , whole exome sequencing (37 tumor samples and 33 normal samples), PacBio long-read whole-genome (nine tumor and four normal samples),10X linked-read whole-genome sequencing, 10x single-cell/nuclei 3’ RNA sequencing (three tumor samples), 10x Visium spatial transcriptomics (one tumor sample), EPIC 850K methylation array (six samples), and bulk RNAseq (six tumor samples) to identify somatic changes present in tumors.
The study aimed to identify changes that drive tumorigenesis in Fanconi anemia, give insight into the early development and aggressive nature of these tumors, and suggest therapeutic avenues for these patients. Another goal was to compare the genomic changes identified in tumors from Fanconi anemia patients with sporadic head and neck cancers.
This study demonstrated that the tumors from Fanconi anemia individuals are generally not driven by HPV. Instead, they acquire mutations in the p53 tumor suppressor. The main characteristic of the tumors is the presence of a high number of structural variants in the form of small deletions, unbalanced translocations, and fold-back inversions, which often form complex rearrangements. These rearrangements result in amplifications and deletions of a multitude of oncogenes and tumor suppressors, respectively. The study also shows that lack of the Fanconi anemia DNA repair pathway leads to an epithelial-to-mesenchymal transition in a mouse model and in human samples that may influence the behavior of tumors in Fanconi anemia. Finally, comparing genomic changes in Fanconi anemia and sporadic tumors of the head and neck, we propose that the structural variants present in sporadic cancer result in a functional deficiency of the Fanconi anemia DNA repair pathway.
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Inclusion Criteria: Individuals diagnosed with Fanconi anemia who had at least one solid tumor that was available for genomic studies.
Exclusion criteria: No special classes of subjects were specifically excluded.

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The International Fanconi Anemia Registry (IFAR) has been active since 1982 when Dr. Auerbach and Dr. Shroeder started it to identify and describe the phenotypic heterogeneity of individuals with Fanconi anemia. In 2003, Kutler DI et al., based on the data from the registry, reported that Fanconi anemia patients had a 700-fold increased risk of developing head and neck cancer. In 2011, Dr. Smogorzewska became the principal investigator of the registry. After initially identifying causative genes mutated in Fanconi anemia individuals, she focused on gathering tumor samples for the present study. The registry gathered fresh and archival material for the study through collaboration with multiple physicians and working with the enrolled individuals and their families. The normal/germline samples in the form of blood and fibroblast cultures were gathered in parallel or were already available through the registry. The Fanconi Anemia Research Fund has been fundamental in identifying individuals eligible for this study. ]]>

本研究聚焦于范科尼贫血（Fanconi anemia）患者肿瘤中存在的基因组特征鉴定。范科尼贫血是一种罕见的遗传性疾病，由DNA链间交联修复缺陷引发。患者的主要表型为骨髓衰竭及癌症易感性。本研究聚焦于鳞状细胞癌，采用了多组学测序与芯片技术：全基因组Illumina测序（22份肿瘤样本、12份正常样本）、全外显子测序（37份肿瘤样本、33份正常样本）、PacBio长读长全基因组测序（9份肿瘤、4份正常样本）、10X链接读长全基因组测序、10x单细胞/细胞核3’ RNA测序（3份肿瘤样本）、10x Visium空间转录组测序（1份肿瘤样本）、EPIC 850K甲基化芯片（6份样本）及批量RNA测序（6份肿瘤样本），以鉴定肿瘤中的体细胞变异。

本研究旨在识别驱动范科尼贫血相关肿瘤发生的变异，解析此类肿瘤的早期发生与侵袭性特征，并为该类患者提出治疗方向。另一项核心目标是将范科尼贫血患者肿瘤中的基因组变异与散发性头颈部癌症进行对比分析。

本研究证实，范科尼贫血患者的肿瘤通常并非由HPV驱动，而是通过p53肿瘤抑制基因的突变致癌。此类肿瘤的主要特征为存在大量以小缺失、不平衡易位及反向折叠倒位形式存在的结构变异，这些变异常形成复杂重排。这类重排分别导致大量癌基因扩增与肿瘤抑制基因缺失。研究还显示，范科尼贫血DNA修复通路的缺失会在小鼠模型及人类样本中引发上皮间质转化（epithelial-to-mesenchymal transition），这可能影响范科尼贫血相关肿瘤的生物学行为。最后，通过对比范科尼贫血与散发性头颈部肿瘤的基因组变异，我们提出：散发性癌症中存在的结构变异会导致范科尼贫血DNA修复通路的功能缺陷。

纳入标准：确诊为范科尼贫血且至少存在1份可用于基因组研究的实体瘤的个体。
排除标准：未特别排除任何特定类别的受试者。

国际范科尼贫血注册库（International Fanconi Anemia Registry, IFAR）自1982年起投入运行，由Auerbach博士与Shroeder博士创立，旨在识别并描述范科尼贫血患者的表型异质性。2003年，Kutler DI等人基于该注册库的数据报道称，范科尼贫血患者患头颈部癌症的风险升高700倍。2011年，Smogorzewska博士成为该注册库的首席研究员。在最初鉴定出范科尼贫血患者的致病基因突变后，她着手为本次研究收集肿瘤样本。本研究通过与多名临床医师合作，并对接入注册库的患者及其家属开展工作，收集了研究所需的新鲜样本与存档样本。正常/生殖系样本（以血液及成纤维细胞培养物形式存在）可通过同期收集或注册库已有的资源获取。范科尼贫血研究基金会（Fanconi Anemia Research Fund）在筛选符合本研究入组条件的患者方面发挥了核心作用。