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3 months ago 单细胞测序 | 识别肿瘤细胞的4种策略 by 生信控
结论：
1. cluster 分布情况
2. CNV
3. mutation（如果有类似 WES 数据）
4. marker表达（oncogenes）
参考文献：
An atlas of epithelial cell states and plasticity in lung adenocarcinoma
Nature. 2024 Mar;627(8004):656-663. doi: 10.1038/s41586-024-07113-9. Epub 2024 Feb 28.
文中所述：
The following strategies were used to identify malignant cells.
(1) Cluster distribution: owing to the high degree of inter-patient tumour heterogeneity, malignant cells often exhibit distinct cluster distribution compared with normal epithelial cells. Although non-malignant cells derived from different patients are often clustered together by cell type, malignant cells from different patients probably form separate clusters.
(2) CNVs: we applied inferCNV(v.1.3.2) to infer large-scale CNVs in each individual cell with T cells as the reference control. To quantify CNVs at the cell level, CNV scores were aggregated using a previously described strategy. In brief, arm-level CNV scores were computed based on the mean of the squares of CNV values across each chromosomal arm. Arm-level CNV scores were further aggregated across all chromosomal arms by calculating the arithmetic mean value of the arm-level scores using the R function mean.
(3) Marker gene expression: expression of lung epithelial lineage-specific genes and LUAD-related oncogenes was determined in epithelial cell clusters.
(4) Cell-level expression of KRASG12D mutations: as we previously described, BAM files were queried for KRASG12D mutant alleles, which were then mapped to specific cells.
KRASG12D mutations, along with cluster distribution, marker gene expression and inferred CNVs as described above, were used to distinguish malignant cells from non-malignant cells.
可视化方法如下：
a, UMAP distribution of mouse epithelial cell subsets
b, Proportions and average expression levels of select marker genes for mouse normal epithelial cell lineages and malignant cell clusters as defined in panel
c, UMAP plots of alveolar and malignant cells coloured by CNV score, presence of KrasG12D mutation, or expression levels of Kng2 and Meg3
绘图系列·往期精彩
https://mp.weixin.qq.com/s/4UY-JCxwgs4VcaFIJMYJGg