The Vision Center, Children's Hospital Los Angeles, Los Angeles, California, USA.
USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA.
Ophthalmic Genet. 2024 Dec;45(6):646-649. doi: 10.1080/13816810.2024.2374886. Epub 2024 Jul 17.
Heterogeneity can impact biomarker identification. Thus, we investigated the somatic copy number alterations (SCNAs) of individual tumor cells in the vitreous humor of a retinoblastoma patient using single-cell whole-genome profiling and explored the genomic concordance among vitreous and aqueous humor, vitreous seeds, and tumor.
Aqueous humor (AH), vitreous humor (VH), and tumor biopsy were obtained from an enucleated globe with retinoblastoma and vitreous seeding. Micromanipulation was used to manually isolate 39 live single tumor cells from vitreous seeds harvested from the VH. The SCNA profiles of these individual cells were generated via whole-genome sequencing and analyzed alongside profiles from the tumor mass and cell-free DNA (cfDNA) from AH and VH.
Heatmap of VH single-cell SCNA profiles demonstrates heterogeneity among individual vitreous seeds with one clearly dominant subclone (23 of 37 cells). The SCNA profiles from the cells in this subclone demonstrate an average concordance of 98% with cfDNA profiles from acellular AH and VH and with the tumor profile.
Our findings reveal some heterogeneity among single-cell SCNA profiles in individual VH seeds. Despite this heterogeneity, the dominant vitreous subclone exhibits extremely (>98%) high concordance with the SCNA profile from tumor and AH, suggesting AH cfDNA is representative of the dominant genomic subclone. This may facilitate tumoral biomarker identification via the AH. This preliminary work supports the potential of applying single-cell technology to VH seeds in retinoblastoma as a platform to study tumor subclones, which may provide insight into the genomic complexity of disease.
异质性会影响生物标志物的识别。因此，我们使用单细胞全基因组分析技术研究了一名视网膜母细胞瘤患者玻璃体液中单个肿瘤细胞的体细胞拷贝数改变（SCNAs），并探讨了玻璃体液和房水、玻璃体液种子与肿瘤之间的基因组一致性。
从患有视网膜母细胞瘤和玻璃体液播散的眼球中获取房水（AH）、玻璃体液（VH）和肿瘤活检。使用微操作技术从 VH 中收获的玻璃体液种子中手动分离出 39 个活的单个肿瘤细胞。通过全基因组测序生成这些单个细胞的 SCNA 图谱，并与肿瘤组织和 AH 及 VH 中的无细胞 DNA（cfDNA）的图谱进行分析。
VH 单细胞 SCNA 图谱的热图显示，单个玻璃体液种子之间存在异质性，其中一个明显的优势亚克隆（37 个细胞中的 23 个）。该亚克隆中细胞的 SCNA 图谱与无细胞 AH 和 VH 以及肿瘤图谱的 cfDNA 图谱平均一致性为 98%。
我们的研究结果表明，个别 VH 种子中单细胞 SCNA 图谱存在一定程度的异质性。尽管存在这种异质性，但优势玻璃体液亚克隆与肿瘤和 AH 的 SCNA 图谱具有极高的 (>98%)一致性，表明 AH cfDNA 代表了优势基因组亚克隆。这可能通过 AH 促进肿瘤标志物的识别。这项初步研究支持在视网膜母细胞瘤中应用单细胞技术对 VH 种子的潜力，作为研究肿瘤亚克隆的平台，这可能为疾病的基因组复杂性提供深入了解。
