Abstract：
Alveolar soft part sarcoma (ASPS) is a rare subtype of soft tissue sarcoma characterized by an unbalanced translocation, resulting in ASPSCR1-TFE3 fusion that transcriptionally upregulates MET expression. The European Organization for Research and Treatment of Cancer (EORTC) 90101 \"CREATE\" phase II trial evaluated the MET inhibitor crizotinib in ASPS patients, achieving only limited antitumor activity. We performed a comprehensive molecular analysis of ASPS tissue samples collected in this trial to identify potential biomarkers correlating with treatment outcome. A tissue microarray containing 47 ASPS cases was used for the characterization of the tumor microenvironment using multiplex immunofluorescence. DNA isolated from 34 available tumor samples was analyzed to detect recurrent gene copy number alterations (CNAs) and mutations by low-coverage whole-genome sequencing and whole-exome sequencing. Pathway enrichment analysis was used to identify diseased-associated pathways in ASPS sarcomagenesis. Kaplan-Meier estimates, Cox regression, and the Fisher\'s exact test were used to correlate histopathological and molecular findings with clinical data related to crizotinib treatment, aiming to identify potential factors associated with patient outcome. Tumor microenvironment characterization showed the presence of PD-L1 and CTLA-4 in 10 and 2 tumors, respectively, and the absence of PD-1 in all specimens. Apart from CD68, other immunological markers were rarely expressed, suggesting a low level of tumor-infiltrating lymphocytes in ASPS. By CNA analysis, we detected a number of broad and focal alterations. The most common alteration was the loss of chromosomal region 1p36.32 in 44% of cases. The loss of chromosomal regions 1p36.32, 1p33, 1p22.2, and 8p was associated with shorter progression-free survival. Using whole-exome sequencing, 13 cancer-associated genes were found to be mutated in at least three cases. Pathway enrichment analysis identified genetic alterations in NOTCH signaling, chromatin organization, and SUMOylation pathways. NOTCH4 intracellular domain dysregulation was associated with poor outcome, while inactivation of the beta-catenin/TCF complex correlated with improved outcome in patients receiving crizotinib. ASPS is characterized by molecular heterogeneity. We identify genetic aberrations potentially predictive of treatment outcome during crizotinib therapy and provide additional insights into the biology of ASPS, paving the way to improve treatment approaches for this extremely rare malignancy.
摘要：
肺泡软组织部分肉瘤（ASPS）是一种罕见的软组织肉瘤亚型，其特征是不平衡的易位。导致ASPSCR1-TFE3融合蛋白在转录上上调MET表达。欧洲癌症研究和治疗组织（EORTC）90101“CREATE”II期试验评估了MET抑制剂克唑替尼在ASPS患者中的应用，仅实现有限的抗肿瘤活性。我们对该试验中收集的ASPS组织样本进行了全面的分子分析，以确定与治疗结果相关的潜在生物标志物。包含47例ASPS病例的组织微阵列用于使用多重免疫荧光表征肿瘤微环境。分析从34个可用肿瘤样品中分离的DNA，以通过低覆盖率全基因组测序和全外显子组测序检测复发的基因拷贝数改变（CNAs）和突变。通路富集分析用于鉴定ASPS肉瘤发生中的疾病相关通路。Kaplan-Meier估计,Cox回归,Fisher精确检验用于将组织病理学和分子检查结果与克唑替尼治疗相关的临床数据相关联，旨在确定与患者预后相关的潜在因素。肿瘤微环境表征显示在10个和2个肿瘤中存在PD-L1和CTLA-4,分别,所有标本中都没有PD-1。除CD68外，其他免疫标志物很少表达，提示ASPS中肿瘤浸润淋巴细胞水平较低。通过CNA分析,我们发现了一些广泛和局灶性的改变。最常见的改变是44％的病例中染色体区域1p36.32的丢失。染色体区域1p36.32、1p33、1p22.2和8p的缺失与更短的无进展生存期相关。使用全外显子组测序，在至少3个病例中发现13个癌症相关基因发生了突变。通路富集分析确定了NOTCH信号中的遗传改变，染色质组织，和磺酰化途径。NOTCH4细胞内结构域失调与不良预后相关，而在接受克唑替尼的患者中,β-连环蛋白/TCF复合物的失活与预后改善相关.ASPS的特征在于分子异质性。我们确定了在克唑替尼治疗期间可能预测治疗结果的遗传畸变，并提供了对ASPS生物学的更多见解。为改善这种极为罕见的恶性肿瘤的治疗方法铺平了道路。
