Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output1, 2, 3, 4, 5, with important functional consequences4, 5. Existing studies of cellular het...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2014
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| Online Access: | http://hdl.handle.net/1721.1/85635 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811098168630181888 |
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| author | Shalek, Alex K. Satija, Rahul Adiconis, Xian Gertner, Rona S. Gaublomme, Jellert T. Raychowdhury, Raktima Schwartz, Schraga Yosef, Nir Malboeuf, Christine Trombetta, John J. Gennert, David Gnirke, Andreas Goren, Alon Hacohen, Nir Levin, Joshua Z. Park, Hongkun Regev, Aviv Lu, Diana, Ph. D. Massachusetts Institute of Technology |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Shalek, Alex K. Satija, Rahul Adiconis, Xian Gertner, Rona S. Gaublomme, Jellert T. Raychowdhury, Raktima Schwartz, Schraga Yosef, Nir Malboeuf, Christine Trombetta, John J. Gennert, David Gnirke, Andreas Goren, Alon Hacohen, Nir Levin, Joshua Z. Park, Hongkun Regev, Aviv Lu, Diana, Ph. D. Massachusetts Institute of Technology |
| author_sort | Shalek, Alex K. |
| collection | MIT |
| description | Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output1, 2, 3, 4, 5, with important functional consequences4, 5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs1, 2 or proteins5, 6 simultaneously, because genomic profiling methods3 could not be applied to single cells until very recently7, 8, 9, 10. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits. |
| first_indexed | 2024-09-23T17:10:57Z |
| format | Article |
| id | mit-1721.1/85635 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T17:10:57Z |
| publishDate | 2014 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/856352022-10-03T10:58:56Z Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Shalek, Alex K. Satija, Rahul Adiconis, Xian Gertner, Rona S. Gaublomme, Jellert T. Raychowdhury, Raktima Schwartz, Schraga Yosef, Nir Malboeuf, Christine Trombetta, John J. Gennert, David Gnirke, Andreas Goren, Alon Hacohen, Nir Levin, Joshua Z. Park, Hongkun Regev, Aviv Lu, Diana, Ph. D. Massachusetts Institute of Technology Massachusetts Institute of Technology. Department of Biology Regev, Aviv Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output1, 2, 3, 4, 5, with important functional consequences4, 5. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs1, 2 or proteins5, 6 simultaneously, because genomic profiling methods3 could not be applied to single cells until very recently7, 8, 9, 10. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits. National Institutes of Health (U.S.) (NIH Postdoctoral Fellowship (1F32HD075541-01)) Charles H. Hood Foundation (Postdoctoral Fellowship) National Institutes of Health (U.S.) (NIH grant U54 AI057159) National Institutes of Health (U.S.) (NIH New Innovator Award (DP2 OD002230)) National Institutes of Health (U.S.) (NIH CEGS Award (1P50HG006193-01)) National Institutes of Health (U.S.) (NIH Pioneer Awards (5DP1OD003893-03)) National Institutes of Health (U.S.) (NIH Pioneer Awards (DP1OD003958-01)) Broad Institute of MIT and Harvard Broad Institute of MIT and Harvard (Klarman Cell Observatory) 2014-03-14T17:23:08Z 2014-03-14T17:23:08Z 2013-05 Article http://purl.org/eprint/type/JournalArticle 0028-0836 1476-4687 http://hdl.handle.net/1721.1/85635 Shalek, Alex K., Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury, Schraga Schwartz, et al. “Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.” Nature 498, no. 7453 (May 19, 2013): 236-240. https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1038/nature12172 Nature Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Nature Publishing Group PMC |
| spellingShingle | Shalek, Alex K. Satija, Rahul Adiconis, Xian Gertner, Rona S. Gaublomme, Jellert T. Raychowdhury, Raktima Schwartz, Schraga Yosef, Nir Malboeuf, Christine Trombetta, John J. Gennert, David Gnirke, Andreas Goren, Alon Hacohen, Nir Levin, Joshua Z. Park, Hongkun Regev, Aviv Lu, Diana, Ph. D. Massachusetts Institute of Technology Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title | Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title_full | Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title_fullStr | Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title_full_unstemmed | Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title_short | Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| title_sort | single cell transcriptomics reveals bimodality in expression and splicing in immune cells |
| url | http://hdl.handle.net/1721.1/85635 https://orcid.org/0000-0001-8567-2049 |
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