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利用单细胞转录组数据对干细胞身份进行从头预测。

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.

作者信息

Grün Dominic, Muraro Mauro J, Boisset Jean-Charles, Wiebrands Kay, Lyubimova Anna, Dharmadhikari Gitanjali, van den Born Maaike, van Es Johan, Jansen Erik, Clevers Hans, de Koning Eelco J P, van Oudenaarden Alexander

机构信息

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands.

出版信息

Cell Stem Cell. 2016 Aug 4;19(2):266-277. doi: 10.1016/j.stem.2016.05.010. Epub 2016 Jun 23.

DOI:10.1016/j.stem.2016.05.010
PMID:27345837
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4985539/
Abstract

Adult mitotic tissues like the intestine, skin, and blood undergo constant turnover throughout the life of an organism. Knowing the identity of the stem cell is crucial to understanding tissue homeostasis and its aberrations upon disease. Here we present a computational method for the derivation of a lineage tree from single-cell transcriptome data. By exploiting the tree topology and the transcriptome composition, we establish StemID, an algorithm for identifying stem cells among all detectable cell types within a population. We demonstrate that StemID recovers two known adult stem cell populations, Lgr5+ cells in the small intestine and hematopoietic stem cells in the bone marrow. We apply StemID to predict candidate multipotent cell populations in the human pancreas, a tissue with largely uncharacterized turnover dynamics. We hope that StemID will accelerate the search for novel stem cells by providing concrete markers for biological follow-up and validation.

摘要

像肠道、皮肤和血液这样的成体有丝分裂组织在生物体的整个生命过程中都经历着持续的更新。了解干细胞的身份对于理解组织稳态及其在疾病时的异常情况至关重要。在这里，我们提出了一种从单细胞转录组数据推导谱系树的计算方法。通过利用树的拓扑结构和转录组组成，我们建立了StemID，这是一种用于在群体中所有可检测细胞类型中识别干细胞的算法。我们证明StemID可以识别出两个已知的成体干细胞群体，即小肠中的Lgr5 +细胞和骨髓中的造血干细胞。我们将StemID应用于预测人类胰腺中候选多能细胞群体，胰腺是一种周转动态很大程度上未被表征的组织。我们希望StemID将通过为生物学后续研究和验证提供具体标记，加速对新型干细胞的搜索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/26abe38f4e5e/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/e795281491b2/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/44c43eae7319/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/0bb46301d379/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/eb66051f5a4a/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/b1162e9c9669/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/73028e402991/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/7a7ed67875f0/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/26abe38f4e5e/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/e795281491b2/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/44c43eae7319/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/0bb46301d379/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/eb66051f5a4a/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/b1162e9c9669/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/73028e402991/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/7a7ed67875f0/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed08/4985539/26abe38f4e5e/gr7.jpg

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2
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Cell. 2015 Dec 17;163(7):1663-77. doi: 10.1016/j.cell.2015.11.013. Epub 2015 Nov 25.
3
Entropy, Ergodicity, and Stem Cell Multipotency.熵、遍历性与干细胞多能性
Sci Rep. 2025 Jun 6;15(1):19975. doi: 10.1038/s41598-025-03956-y.
4
Scale up manufacturing approach for production of human induced pluripotent stem cell-derived islets using Vertical Wheel® bioreactors.使用Vertical Wheel®生物反应器扩大生产人诱导多能干细胞衍生胰岛的制造方法。
NPJ Regen Med. 2025 May 29;10(1):24. doi: 10.1038/s41536-025-00409-y.
5
Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.将动态系统建模与时空单细胞RNA测序数据分析相结合。
Entropy (Basel). 2025 Apr 22;27(5):453. doi: 10.3390/e27050453.
6
Alternative lengthening of telomeres confers favorable prognosis in chondrosarcomas.端粒的替代性延长赋予软骨肉瘤良好的预后。
J Transl Med. 2025 May 12;23(1):536. doi: 10.1186/s12967-025-06539-7.
7
ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction.ScAGCN：用于单细胞RNA测序数据降维的具有自适应聚合机制的图卷积网络
Interdiscip Sci. 2025 Apr 25. doi: 10.1007/s12539-025-00702-w.
8
Live-cell omics with Raman spectroscopy.基于拉曼光谱的活细胞组学
Microscopy (Oxf). 2025 Jun 26;74(3):189-200. doi: 10.1093/jmicro/dfaf020.
9
Zero-shot evaluation reveals limitations of single-cell foundation models.零样本评估揭示了单细胞基础模型的局限性。
Genome Biol. 2025 Apr 18;26(1):101. doi: 10.1186/s13059-025-03574-x.
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Brief Bioinform. 2025 Mar 4;26(2). doi: 10.1093/bib/bbaf138.
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4
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