PO.CL01.13 · 临床研究
利用 CosMx 空间分子成像仪对乳腺癌组织进行空间全转录组刻画
Spatial whole transcriptomic profiling of breast cancer tissue with CosMx Spatial Molecular Imager
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
空间转录组学提供了研究基因表达与组织结构之间关系的机会，揭示了对促进肿瘤发生、免疫逃逸及其他疾病机制的细胞间相互作用的新见解。在此，我们采用 CosMx SMI 全转录组检测，对来自 25 个跨分子亚型乳腺癌组织块的组织微阵列（TMA）中的 87 个核心进行刻画。将单张 5 微米切片按照 Bruker 发布的方案（MAN-10184-06）使用人类全转录组面板（WTX）（19K 重）进行染色，利用 37,872 个成像条形码捕获人类蛋白编码转录组中超过 18,000 个基因。我们分析了 154,213 个细胞，总共鉴定出 18,934 个基因，每个细胞平均转录本数为 926，在第 90 百分位处每个细胞鉴定出 2,060 个转录本。对细胞进行质量控制、标准化，并使用 InSituType 结合明确定义的乳腺上皮、基质和免疫细胞参考谱进行细胞分型。我们将 InSituType 分配的癌上皮分子分型与组织学分型进行比较，发现核心水平亚型分配与空间单细胞分配之间总体高度一致。值得注意的是，无论亚型如何，基底细胞类型在所有核心中均以高水平存在，在三阴性、Luminal A、HER2 和 Luminal B 核心中分别占 98%、64%、50% 和 30%。HER2 富集细胞最为独特，占 HER2 核心细胞的约 45%，而在其他核心中占比 <1%。这些结果展示了肿瘤细胞组成的异质性，并强调了在设计靶向治疗时单细胞分辨率在分子分型中的价值。我们接下来研究了所有核心的免疫细胞组成，发现髓系谱系最为主导，其次是 T 细胞和 B 细胞。免疫细胞在不同亚型间组成相似，但其在肿瘤内的空间分布各异，三阴性亚型显示出最高水平的肿瘤浸润。在正在进行的工作中，我们继续刻画核心间和核心内的异质性，以进一步理解局部免疫生态位和周围微环境如何塑造肿瘤发生程序的启动或抑制。
查看英文原文 English abstract
Spatial transcriptomics provides an opportunity to investigate the relationship between gene expression and tissue architecture, revealing new insights into cell-to-cell interactions that promote tumorigenesis, immune evasion, and other disease mechanisms. Here we employ the CosMx SMI Whole Transcriptome assay to profile 87 cores from a tissue microarray (TMA) of 25 breast cancer blocks spanning molecular subtypes. A single 5-micron section was stained following Bruker's published protocol (MAN-10184-06) with the Human Whole Transcriptome Panel (WTX), 19K-plex, utilizing 37,872 imaging barcodes to capture over 18,000 genes in the human protein-coding transcriptome. We analyzed 154,213 cells and identified 18,934 genes overall, with mean transcripts per cell of 926, and in the 90 th percentile identifying 2,060 transcripts per cell. Cells were assessed for quality control, normalized and cell-typed using InSituType with a reference profile of well-defined breast epithelial, stromal, and immune cells. We compared molecular subtyping of the cancer epithelium as assigned by InSituType with subtyping by histology, finding a high overall concordance between core-level subtype assignment and spatial single-cell assignments. Strikingly, basal cell types were present at high levels across all cores regardless of subtype, making up 98%, 64%, 50%, and 30% of triple negative, Luminal A, HER2, and Luminal B cores, respectively. HER2 enriched cells were the most unique, making up ~45% of HER2 core cells and <1% of cells in other cores. These results display the heterogeneity of tumor cell composition and emphasize the value of single-cell resolution in molecular subtyping when designing targeted therapeutics. We next investigated immune cell compositions of all cores and found Myeloid lineages to be the most dominant, followed by T and B cells. Immune cells were similar in composition across different subtypes, however, varied by their spatial distribution in the tumor, with the triple negative subtype displaying the highest level of tumor infiltration. In ongoing work, we continue to characterize inter- and intra- core heterogeneity to further understand how local immune niches and the surrounding microenvironment shape the initiation or suppression of tumorigenic programs.
利益披露 Disclosure
M. Hopkins, None.