A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.
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DOI：
10.1038/s41598-021-94732-1
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发表时间：
2021-08-04
影响因子：
4.6
通讯作者：
Gunawardane RN
中科院分区：
文献类型：
--
作者：
Grancharova T;Gerbin KA;Rosenberg AB;Roco CM;Arakaki JE;DeLizo CM;Dinh SQ;Donovan-Maiye RM;Hirano M;Nelson AM;Tang J;Theriot JA;Yan C;Menon V;Palecek SP;Seelig G;Gunawardane RN
我们对人类诱导多能干细胞（hiPSC）向心肌细胞分化过程中发生的转录变化进行了全面分析。使用单细胞RNA-seq，我们对来自55个独立样本的bb1020,000个单细胞进行了测序，这些样本代表了两种分化方案和多个hiPSC系。样本包括从未分化的hiPSCs到分化后D90的混合细胞群的实验复制。分化的细胞群按时间点聚类，差异表达分析显示心肌细胞分化和成熟的标志物在D12到D90之间发生变化。接下来，我们进行了一个互补的簇无关稀疏回归分析，以识别和排序基因，最佳分配细胞分化时间点。D12和D24之间排名最高的两个基因（MYH7和MYH6）的准确率为0.84，D24和D90之间排名最高的三个基因（A2M, H19, IGF2）的准确率为0.94，表明低维基因特征可以识别分化心肌细胞的分化或成熟阶段。使用RNA FISH验证所选基因的表达水平。最后，我们在WTC-11背景下研究了两种分化方案、实验重复和三种hiPSC系导致的心脏基因表达差异，以确定这些实验变量的变异来源。
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
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影响因子：
11.8
作者：
DeLaughter, Daniel M.;Bick, Alexander G.;Wakimoto, Hiroko;McKean, David;Gorham, Joshua M.;Kathiriya, Irian S.;Hinson, John T.;Homsy, Jason;Gray, Jesse;Pu, William;Bruneau, Benoit G.;Seidman, J. G.;Seidman, Christine E.
通讯作者：
Seidman, Christine E.
影响因子：
9.3
作者：
Gerbin, Kaytlyn A.;Grancharova, Tanya;Gunawardane, Ruwanthi N.
通讯作者：
Gunawardane, Ruwanthi N.
影响因子：
8.8
作者：
Cui, Yueli;Zheng, Yuxuan;Tang, Fuchou
通讯作者：
Tang, Fuchou
影响因子：
1.2
作者：
Bizy, Alexandra;Guerrero-Serna, Guadalupe;Hu, Bin;Ponce-Balbuena, Daniela;Willis, B. Cicero;Zarzoso, Manuel;Ramirez, Rafael J.;Sener, Michelle F.;Mundada, Lakshmi V.;Klos, Matthew;Devaney, Eric J.;Vikstrom, Karen L.;Herron, Todd J.;Jalife, Jose
通讯作者：
Jalife, Jose
影响因子：
20.1
作者：
Goodyer, William R.;Beyersdorf, Benjamin M.;Wu, Sean M.
通讯作者：
Wu, Sean M.