Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells
Abstract Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Her...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56590-7 |
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| author | John D. Blair Austin Hartman Fides Zenk Philipp Wahle Giovanna Brancati Carol Dalgarno Barbara Treutlein Rahul Satija |
| author_facet | John D. Blair Austin Hartman Fides Zenk Philipp Wahle Giovanna Brancati Carol Dalgarno Barbara Treutlein Rahul Satija |
| author_sort | John D. Blair |
| collection | DOAJ |
| description | Abstract Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify cytoplasmic and nuclear proteins, including those with post-translational modifications, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom neuro-focused antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, alongside both experimental and computational strategies to incorporate transcriptomic measurements. We apply our workflow to cell lines, induced pluripotent stem cells, and months-old retinal and brain organoids to demonstrate its broad applicability. We show that Phospho-seq can provide insights into cellular states and trajectories, shed light on gene regulatory relationships, and help explore the causes and effects of diverse cell signaling in neurodevelopment. |
| format | Article |
| id | doaj-art-421eb8da0574492ab5101f8dad9d0c09 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-421eb8da0574492ab5101f8dad9d0c092025-02-09T12:44:06ZengNature PortfolioNature Communications2041-17232025-02-0116111910.1038/s41467-025-56590-7Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cellsJohn D. Blair0Austin Hartman1Fides Zenk2Philipp Wahle3Giovanna Brancati4Carol Dalgarno5Barbara Treutlein6Rahul Satija7New York Genome CenterNew York Genome CenterETH ZurichETH ZurichETH ZurichNew York Genome CenterETH ZurichNew York Genome CenterAbstract Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify cytoplasmic and nuclear proteins, including those with post-translational modifications, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom neuro-focused antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, alongside both experimental and computational strategies to incorporate transcriptomic measurements. We apply our workflow to cell lines, induced pluripotent stem cells, and months-old retinal and brain organoids to demonstrate its broad applicability. We show that Phospho-seq can provide insights into cellular states and trajectories, shed light on gene regulatory relationships, and help explore the causes and effects of diverse cell signaling in neurodevelopment.https://doi.org/10.1038/s41467-025-56590-7 |
| spellingShingle | John D. Blair Austin Hartman Fides Zenk Philipp Wahle Giovanna Brancati Carol Dalgarno Barbara Treutlein Rahul Satija Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells Nature Communications |
| title | Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells |
| title_full | Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells |
| title_fullStr | Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells |
| title_full_unstemmed | Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells |
| title_short | Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells |
| title_sort | phospho seq integrated multi modal profiling of intracellular protein dynamics in single cells |
| url | https://doi.org/10.1038/s41467-025-56590-7 |
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