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Chow A, Lareau CA. Concepts and new developments in droplet-based single cell multi-omics. Trends Biotechnol 2024:S0167-7799(24)00184-7. [PMID: 39095258 DOI: 10.1016/j.tibtech.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/31/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
Single cell sequencing technologies have become a fixture in the molecular profiling of cells due to their ease, flexibility, and commercial availability. In particular, partitioning individual cells inside oil droplets via microfluidic reactions enables transcriptomic or multi-omic measurements for thousands of cells in parallel. Complementing the multitude of biological discoveries from genomics analyses, the past decade has brought new capabilities from assay baselines to enable a deeper understanding of the complex data from single cell multi-omics. Here, we highlight four innovations that have improved the reliability and understanding of droplet microfluidic assays. We emphasize new developments that further orient principles of technology development and guidelines for the design, benchmarking, and implementation of new droplet-based methodologies.
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Affiliation(s)
- Arthur Chow
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caleb A Lareau
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Metzner E, Southard KM, Norman TM. Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605307. [PMID: 39091800 PMCID: PMC11291144 DOI: 10.1101/2024.07.26.605307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding that ARID1A and SUZ12 knockdowns induce programs enriched for developmental features. Pseudotime analysis of perturbations connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state.
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Affiliation(s)
- Eli Metzner
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Kaden M. Southard
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas M. Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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3
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Feng AC, Thomas BJ, Purbey PK, de Melo FM, Liu X, Daly AE, Sun F, Lo JHH, Cheng L, Carey MF, Scumpia PO, Smale ST. The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling. Immunity 2024; 57:462-477.e9. [PMID: 38430908 PMCID: PMC10984581 DOI: 10.1016/j.immuni.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.
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Affiliation(s)
- An-Chieh Feng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon J Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA 98195, USA
| | - Prabhat K Purbey
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Filipe Menegatti de Melo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Allison E Daly
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fei Sun
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jerry Hung-Hao Lo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lijing Cheng
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Philip O Scumpia
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Gao C, Welch JD. Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580655. [PMID: 38464242 PMCID: PMC10925154 DOI: 10.1101/2024.02.16.580655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Recent experimental developments enable single-cell multimodal epigenomic profiling, which measures multiple histone modifications and chromatin accessibility within the same cell. Such parallel measurements provide exciting new opportunities to investigate how epigenomic modalities vary together across cell types and states. A pivotal step in using this type of data is integrating the epigenomic modalities to learn a unified representation of each cell, but existing approaches are not designed to model the unique nature of this data type. Our key insight is to model single-cell multimodal epigenome data as a multi-channel sequential signal. Based on this insight, we developed ConvNet-VAEs, a novel framework that uses 1D-convolutional variational autoencoders (VAEs) for single-cell multimodal epigenomic data integration. We evaluated ConvNet-VAEs on nano-CT and scNTT-seq data generated from juvenile mouse brain and human bone marrow. We found that ConvNet-VAEs can perform dimension reduction and batch correction better than previous architectures while using significantly fewer parameters. Furthermore, the performance gap between convolutional and fully-connected architectures increases with the number of modalities, and deeper convolutional architectures can increase performance while performance degrades for deeper fully-connected architectures. Our results indicate that convolutional autoencoders are a promising method for integrating current and future single-cell multimodal epigenomic datasets.
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Affiliation(s)
- Chao Gao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI 48109, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI 48109, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor MI 48109, USA
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Piran Z, Cohen N, Hoshen Y, Nitzan M. Disentanglement of single-cell data with biolord. Nat Biotechnol 2024:10.1038/s41587-023-02079-x. [PMID: 38225466 DOI: 10.1038/s41587-023-02079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/30/2023] [Indexed: 01/17/2024]
Abstract
Biolord is a deep generative method for disentangling single-cell multi-omic data to known and unknown attributes, including spatial, temporal and disease states, used to reveal the decoupled biological signatures over diverse single-cell modalities and biological systems. By virtually shifting cells across states, biolord generates experimentally inaccessible samples, outperforming state-of-the-art methods in predictions of cellular response to unseen drugs and genetic perturbations. Biolord is available at https://github.com/nitzanlab/biolord .
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Affiliation(s)
- Zoe Piran
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | - Niv Cohen
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | - Yedid Hoshen
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel.
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel.
- Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
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