跨种族群体和基因表达平台的高级别浆液性卵巢癌的分子亚型。
Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms.
发表日期:2024 May 23
作者:
Natalie R Davidson, Mollie E Barnard, Ariel A Hippen, Amy Campbell, Courtney E Johnson, Gregory P Way, Brian K Dalley, Andrew Berchuck, Lucas A Salas, Lauren C Peres, Jeffrey R Marks, Joellen M Schildkraut, Casey S Greene, Jennifer A Doherty
来源:
MOLECULAR & CELLULAR PROTEOMICS
摘要:
高级别浆液性癌 (HGSC) 基因表达亚型与差异生存相关。我们表征了黑人个体中的 HGSC 基因表达,并考虑了自我认定种族的基因表达差异是否可能导致黑人与白人个体中 HGSC 存活率较差。我们纳入了来自黑人和白人个体的新生成的 RNA-Seq 数据,以及基于阵列的基因分型数据来自四项针对白人和日本人的现有研究。我们使用 K 均值聚类(一种没有预定义聚类数量或数据集特定特征的方法)来分配子类型。通过调节的 t 分数总结了簇和数据集特定的基因表达模式。我们通过计算调节 t 分数的汇总向量之间的相关性来比较跨数据集的簇特定基因表达模式。在映射到癌症基因组图谱 (TCGA) 衍生的 HGSC 亚型后,我们使用 Cox 比例风险模型通过数据集估计亚型特异性生存率。簇特异性基因表达在基因表达平台和种族群体中是相似的。将黑人群体与白人群体和日本人群体进行比较,免疫反应性亚型更为常见(39% vs 23%-28%),而分化亚型则不太常见(7% vs 22%-31%)。根据 RNA-Seq 数据,黑人和白人群体的亚型特异性生存模式相似;与间充质病例相比,增殖型和分化型病例的死亡风险相似,而免疫反应性病例的死亡风险较低(黑人群体 HR=0.79 [0.55, 1.13],白人群体 HR=0.86 [0.62, 1.19])。 HGSC 亚型因种族而异,亚型特异性生存率相似。HGSC 亚型可以跨平台和自我识别的种族群体进行一致分配。
High-grade serous carcinoma (HGSC) gene expression subtypes are associated with differential survival. We characterized HGSC gene expression in Black individuals and considered whether gene expression differences by self-identified race may contribute to poorer HGSC survival among Black versus White individuals.We included newly generated RNA-Seq data from Black and White individuals, and array-based genotyping data from four existing studies of White and Japanese individuals. We used K-means clustering, a method with no predefined number of clusters or dataset-specific features, to assign subtypes. Cluster- and dataset-specific gene expression patterns were summarized by moderated t-scores. We compared cluster-specific gene expression patterns across datasets by calculating the correlation between the summarized vectors of moderated t-scores. Following mapping to The Cancer Genome Atlas (TCGA)-derived HGSC subtypes, we used Cox proportional hazards models to estimate subtype-specific survival by dataset.Cluster-specific gene expression was similar across gene expression platforms and racial groups. Comparing the Black population to the White and Japanese populations, the immunoreactive subtype was more common (39% versus 23%-28%) and the differentiated subtype less common (7% versus 22%-31%). Patterns of subtype-specific survival were similar between the Black and White populations with RNA-Seq data; compared to mesenchymal cases, the risk of death was similar for proliferative and differentiated cases and suggestively lower for immunoreactive cases (Black population HR=0.79 [0.55, 1.13], White population HR=0.86 [0.62, 1.19]).While the prevalence of HGSC subtypes varied by race, subtype-specific survival was similar.HGSC subtypes can be consistently assigned across platforms and self-identified racial groups.