Phylogenetic inference from single-cell RNA-seq data.
Phylogenetic inference from single-cell RNA-seq data.
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DOI：
10.1038/s41598-023-39995-6
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发表时间：
2023-08-08
影响因子：
4.6
通讯作者：
中科院分区：
文献类型：
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作者：
Tumors are comprised of subpopulations of cancer cells that harbor distinct genetic profiles and phenotypes that evolve over time and during treatment. By reconstructing the course of cancer evolution, we can understand the acquisition of the malignant properties that drive tumor progression. Unfortunately, recovering the evolutionary relationships of individual cancer cells linked to their phenotypes remains a difficult challenge. To address this need, we have developed PhylinSic, a method that reconstructs the phylogenetic relationships among cells linked to their gene expression profiles from single cell RNA-sequencing (scRNA-Seq) data. This method calls nucleotide bases using a probabilistic smoothing approach and then estimates a phylogenetic tree using a Bayesian modeling algorithm. We showed that PhylinSic identified evolutionary relationships underpinning drug selection and metastasis and was sensitive enough to identify subclones from genetic drift. We found that breast cancer tumors resistant to chemotherapies harbored multiple genetic lineages that independently acquired high K-Ras and β-catenin, suggesting that therapeutic strategies may need to control multiple lineages to be durable. These results demonstrated that PhylinSic can reconstruct evolution and link the genotypes and phenotypes of cells across monophyletic tumors using scRNA-Seq.
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DOI：
10.1093/bioinformatics/btac254
发表时间：
2022-06-24
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
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影响因子：
64.8
作者：
Choi, Junhong;Chen, Wei;Minkina, Anna;Chardon, Florence M.;Suiter, Chase C.;Regalado, Samuel G.;Domcke, Silvia;Hamazaki, Nobuhiko;Lee, Choli;Martin, Beth;Daza, Riza M.;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
5.8
作者：
Liberzon, Arthur;Subramanian, Aravind;Mesirov, Jill P.
通讯作者：
Mesirov, Jill P.
单细胞数据的树推断。
影响因子：
12.3
作者：
Jahn K;Kuipers J;Beerenwinkel N
通讯作者：
Beerenwinkel N
影响因子：
64.8
作者：
Greaves, Mel;Maley, Carlo C.
通讯作者：
Maley, Carlo C.