Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type.

作者: Miri Adler , Yael Korem Kohanim , Avichai Tendler , Avi Mayo , Uri Alon

DOI: 10.1016/J.CELS.2018.12.008

关键词:

摘要: Summary Single-cell gene expression reveals the diversity within a differentiated cell type. Often, cells of same type show continuum gene-expression patterns. The origin such patterns is unclear. To address this, we develop theory to understand how provides division labor in tissue which collectively contribute several tasks. We find that optimal when there are spatial gradients affect performance each task. bounded inside polyhedron whose vertices profiles at test this using single-cell for intestinal villi and liver hepatocytes, form curved 1D trajectory full 3D tetrahedron space, respectively. infer tasks both types characterize zonation task-specialist cells. This approach can be generally applied other tissues.

参考文章(63)
Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi Mayo, Michael E. Rothenberg, Tomer Kalisky, Uri Alon, Geometry of the Gene Expression Space of Individual Cells PLOS Computational Biology. ,vol. 11, pp. e1004224- ,(2015) , 10.1371/JOURNAL.PCBI.1004224
P.B. Lazarow, Rat liver peroxisomes catalyze the beta oxidation of fatty acids. Journal of Biological Chemistry. ,vol. 253, pp. 1522- 1528 ,(1978) , 10.1016/S0021-9258(17)34897-4
Joseph M. JEZ, Melanie J. BENNETT, Brian P. SCHLEGEL, Mitchell LEWIS, Trevor M. PENNING, Comparative anatomy of the aldo-keto reductase superfamily. Biochemical Journal. ,vol. 326, pp. 625- 636 ,(1997) , 10.1042/BJ3260625
Dominic Grün, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden, Single-cell messenger RNA sequencing reveals rare intestinal cell types Nature. ,vol. 525, pp. 251- 255 ,(2015) , 10.1038/NATURE14966
William E. Van Nostrand, The influence of the amyloid ß-protein and its precursor in modulating cerebral hemostasis. Biochimica et Biophysica Acta. ,vol. 1862, pp. 1018- 1026 ,(2016) , 10.1016/J.BBADIS.2015.10.020
Guoyao Wu, Yun-Zhong Fang, Sheng Yang, Joanne R. Lupton, Nancy D. Turner, Glutathione Metabolism and Its Implications for Health Journal of Nutrition. ,vol. 134, pp. 489- 492 ,(2004) , 10.1093/JN/134.3.489
R W Mahley, T L Innerarity, S C Rall, K H Weisgraber, Plasma lipoproteins: apolipoprotein structure and function. Journal of Lipid Research. ,vol. 25, pp. 1277- 1294 ,(1984) , 10.1016/S0022-2275(20)34443-6
Hee-Bum Kang, Jun Fan, Ruiting Lin, Shannon Elf, Quanjiang Ji, Liang Zhao, Lingtao Jin, Jae Ho Seo, Changliang Shan, Jack L. Arbiser, Cynthia Cohen, Daniel Brat, Henry M. Miziorko, Eunhee Kim, Omar Abdel-Wahab, Taha Merghoub, Stefan Fröhling, Claudia Scholl, Pablo Tamayo, David A. Barbie, Lu Zhou, Brian P. Pollack, Kevin Fisher, Ragini R. Kudchadkar, David H. Lawson, Gabriel Sica, Michael Rossi, Sagar Lonial, Hanna J. Khoury, Fadlo R. Khuri, Benjamin H. Lee, Titus J. Boggon, Chuan He, Sumin Kang, Jing Chen, Metabolic Rewiring by Oncogenic BRAF V600E Links Ketogenesis Pathway to BRAF-MEK1 Signaling Molecular Cell. ,vol. 59, pp. 345- 358 ,(2015) , 10.1016/J.MOLCEL.2015.05.037
Patrick Tso, Min Liu, Theodore John Kalogeris, Alan BR Thomson, THE ROLE OF APOLIPOPROTEIN A-IV IN THE REGULATION OF FOOD INTAKE Annual Review of Nutrition. ,vol. 21, pp. 231- 254 ,(2001) , 10.1146/ANNUREV.NUTR.21.1.231