Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia.
Department of Radiology, University of Virginia, Charlottesville, Virginia.
Cancer Res. 2021 Apr 1;81(7):1840-1852. doi: 10.1158/0008-5472.CAN-20-1034. Epub 2021 Feb 2.
The heterogeneous composition of solid tumors is known to impact disease progression and response to therapy. Malignant cells coexist in different regulatory states that can be accessed transcriptomically by single-cell RNA sequencing, but these methods have many caveats related to sensitivity, noise, and sample handling. We revised a statistical fluctuation analysis called stochastic profiling to combine with 10-cell RNA sequencing, which was designed for laser-capture microdissection (LCM) and extended here for immuno-LCM. When applied to a cohort of late-onset, early-stage luminal breast cancers, the integrated approach identified thousands of candidate regulatory heterogeneities. Intersecting the candidates from different tumors yielded a relatively stable set of 710 recurrent heterogeneously expressed genes (RHEG), which were significantly variable in >50% of patients. RHEGs were not strongly confounded by dissociation artifacts, cell-cycle oscillations, or driving mutations for breast cancer. Rather, RHEGs were enriched for epithelial-to-mesenchymal transition genes and, unexpectedly, the latest pan-cancer assembly of driver genes across cancer types other than breast. These findings indicate that heterogeneous transcriptional regulation conceivably provides a faster, reversible mechanism for malignant cells to evaluate the effects of potential oncogenes or tumor suppressors on cancer hallmarks. SIGNIFICANCE: Profiling intratumor heterogeneity of luminal breast carcinoma cells identifies a recurrent set of genes, suggesting sporadic activation of pathways known to drive other types of cancer..
肿瘤的异质性组成已知会影响疾病的进展和对治疗的反应。恶性细胞共存于不同的调节状态，可以通过单细胞 RNA 测序在转录组水平上进行检测，但这些方法存在许多与灵敏度、噪声和样本处理相关的问题。我们修改了一种称为随机分布分析的统计波动分析方法，将其与 10 细胞 RNA 测序相结合，该方法专为激光捕获显微切割 (LCM) 设计，并在此基础上进行了免疫 LCM 的扩展。当应用于一组晚发性早期阶段 luminal 乳腺癌队列时，该综合方法鉴定了数千个候选调节异质性。对来自不同肿瘤的候选基因进行交集，产生了一组相对稳定的 710 个反复表达的基因 (RHEG)，这些基因在超过 50%的患者中存在显著差异。RHEG 不受解离伪影、细胞周期波动或乳腺癌驱动突变的强烈干扰。相反，RHEG 富含上皮间质转化基因，出乎意料的是，在除乳腺癌以外的其他癌症类型中，最新的泛癌症驱动基因组合也存在这些基因。这些发现表明，异质性转录调控可能为恶性细胞提供了一种更快、更可逆的机制，以评估潜在的致癌基因或肿瘤抑制基因对癌症特征的影响。意义：分析 luminal 乳腺癌细胞的肿瘤内异质性，确定了一组反复出现的基因，表明已知驱动其他类型癌症的途径偶尔会被激活。
