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Wang S, Jiménez-Gracia L, De Amaral AA, Vlachos IS, Plummer J, Heyn H, Martelotto LG. FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays. Bio Protoc 2024; 14:e5063. [PMID: 39315321 PMCID: PMC11417608 DOI: 10.21769/bioprotoc.5063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/25/2024] Open
Abstract
The quality of standard single-cell experiments often depends on the immediate processing of cells or tissues post-harvest to preserve fragile and vulnerable cell populations, unless the samples are adequately fixed and stored. Despite the recent rise in popularity of probe-based and aldehyde-fixed RNA assays, these methods face limitations in species and target availability and are not suitable for immunoprofiling or assessing chromatin accessibility. Recently, a reversible fixation strategy known as FixNCut has been successfully deployed to separate sampling from downstream applications in a reproducible and robust manner, avoiding stress or necrosis-related artifacts. In this article, we present an optimized and robust practical guide to the FixNCut protocol to aid the end-to-end adaptation of this versatile method. This protocol not only decouples tissue or cell harvesting from single-cell assays but also enables a flexible and decentralized workflow that unlocks the potential for single-cell analysis as well as unconventional study designs that were previously considered unfeasible. Key features • Reversible fixation: Preserves cellular and molecular structures with the option to later reverse the fixation for downstream applications, maintaining cell integrity • Compatibility with single-cell assays: Supports single-cell genomic assays such as scRNA-seq and ATAC-seq, essential for high-resolution analysis of cell function and gene expression • Flexibility in sample handling: Allows immediate fixation post-collection, decoupling sample processing from analysis, beneficial in settings where immediate processing is impractical • Preservation of RNA and DNA integrity: Effectively preserves RNA and DNA, reducing degradation to ensure accurate transcriptomic and genomic profiling • Suitability for various biological samples: Applicable to a wide range of biological samples, including tissues and cell suspensions, whether freshly isolated or post-dissociated • Enables multi-center studies: Facilitates collaborative research across multiple centers by allowing sample fixation at the point of collection, enhancing research scale and diversity • Avoidance of artifacts: Minimizes stress or necrosis-related artifacts, preserving the natural cellular physiology for accurate genomic and transcriptomic analysis.
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Affiliation(s)
- Shuoshuo Wang
- Spatial Technologies, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Jiménez-Gracia
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Antonella Arruda De Amaral
- Spatial Technologies, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioannis S. Vlachos
- Spatial Technologies, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jasmine Plummer
- Center for Spatial Omics, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Cellular and Molecular Biology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Comprehensive Cancer Center, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
- Omniscope, Barcelona, Spain
| | - Luciano G. Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
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Briney CA, Henriksen JC, Lin C, Jones LA, Benner L, Rains AB, Gutierrez R, Gafken PR, Rissland OS. Muskelin acts as a substrate receptor of the highly regulated Drosophila CTLH E3 ligase during the maternal-to-zygotic transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601265. [PMID: 39005399 PMCID: PMC11244905 DOI: 10.1101/2024.06.28.601265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The maternal-to-zygotic transition (MZT) is a conserved developmental process where the maternally-derived protein and mRNA cache is replaced with newly made zygotic gene products. We have previously shown that in Drosophila the deposited RNA-binding proteins ME31B, Cup, and Trailer Hitch (TRAL) are ubiquitylated by the CTLH E3 ligase and cleared. However, the organization and regulation of the CTLH complex remain poorly understood in flies. In particular, Drosophila lacks an identifiable substrate adaptor, and the mechanisms restricting degradation of ME31B and its cofactors to the MZT are unknown. Here, we show that the developmental specificity of the CTLH complex is mediated by multipronged regulation, including transcriptional control by the transcription factor OVO and autoinhibition of the E3 ligase. One major regulatory target is the subunit Muskelin, which we demonstrate acts as a substrate adaptor for the Drosophila CTLH complex. Although conserved, Muskelin has structural roles in other species, suggesting a surprising functional plasticity. Finally, we find that Muskelin has few targets beyond the three known RNA binding proteins, showing exquisite target specificity. Thus, multiple levels of integrated regulation restrict the activity of the embryonic CTLH complex to early embryogenesis, seemingly with the goal of regulating three important RNA binding proteins.
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Affiliation(s)
- Chloe A Briney
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Jesslyn C Henriksen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Chenwei Lin
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109
| | - Lisa A Jones
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109
| | - Leif Benner
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Addison B Rains
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Roxana Gutierrez
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Philip R Gafken
- Proteomics & Metabolomics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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Torres HM, Fang F, May DG, Bosshardt P, Hinojosa L, Roux KJ, Tao J. Comprehensive analysis of the proximity-dependent nuclear interactome for the oncoprotein NOTCH1 in live cells. J Biol Chem 2024; 300:105522. [PMID: 38043798 PMCID: PMC10788534 DOI: 10.1016/j.jbc.2023.105522] [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: 05/31/2023] [Revised: 10/25/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023] Open
Abstract
Notch signaling plays a critical role in cell fate decisions in all cell types. Furthermore, gain-of-function mutations in NOTCH1 have been uncovered in many human cancers. Disruption of Notch signaling has recently emerged as an attractive disease treatment strategy. However, the nuclear interaction landscape of the oncoprotein NOTCH1 remains largely unexplored. We therefore employed here a proximity-dependent biotin identification approach to identify in vivo protein associations with the nuclear Notch1 intracellular domain in live cells. We identified a large set of previously reported and unreported proteins that associate with NOTCH1, including general transcription and elongation factors, DNA repair and replication factors, coactivators, corepressors, and components of the NuRD and SWI/SNF chromatin remodeling complexes. We also found that Notch1 intracellular domain associates with protein modifiers and components of other signaling pathways that may influence Notch signal transduction and protein stability such as USP7. We further validated the interaction of NOTCH1 with histone deacetylase 1 or GATAD2B using protein network analysis, proximity-based ligation, in vivo cross-linking and coimmunoprecipitation assays in several Notch-addicted cancer cell lines. Through data mining, we also revealed potential drug targets for the inhibition of Notch signaling. Collectively, these results provide a valuable resource to uncover the mechanisms that fine-tune Notch signaling in tumorigenesis and inform therapeutic targets for Notch-addicted tumors.
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Affiliation(s)
- Haydee M Torres
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA
| | - Fang Fang
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Paige Bosshardt
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Leetoria Hinojosa
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jianning Tao
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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