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Bao K, Jiang X, Hu HM, Liu T, Zhang J. DEPICT-seq: Single-Cell Transcriptomic Analysis of Rare Cell Subsets Isolated via Nucleic Acid Cytometry. Anal Chem 2024. [PMID: 39287475 DOI: 10.1021/acs.analchem.4c03075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The ability to dive deep into specific rare cell populations is critical for understanding tissue physiology and pathology across various biological domains. As single-cell RNA-seq flourishes, many newly discovered cell subtypes are defined by their transcriptomic markers. However, our ability to retrieve and analyze cells based on their nucleic acid markers remains underdeveloped. Here, we present Double Emulsion PCR-Initiated Cell sorting and Transcriptomic Sequencing (DEPICT-seq), a high-throughput droplet nucleic acid cytometry method that integrates batch cell fixation for cellular information preservation, double emulsion digital PCR-based cell sorting to target nucleic acid markers of interest, and in-depth full-length transcriptomic analyses at single-cell resolution. We utilize DEPICT-seq to isolate and characterize T cell receptor (TCR)-engineered T cells within a mixed population and also demonstrate a variation of the workflow by incorporating an RNase H-dependent PCR step to enrich full-length TCR sequences for paired single-cell TCR sequencing and transcriptomic profiling.
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Affiliation(s)
- Kaixuan Bao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | | | - Hong-Min Hu
- ImmuXell Biotech Ltd., Shanghai 201315, China
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
- Zhejiang Lab, Hangzhou, Zhejiang 311121, China
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2
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Bost P, Drayman N. Dissecting viral infections, one cell at a time, by single-cell technologies. Microbes Infect 2024; 26:105268. [PMID: 38008398 PMCID: PMC11161131 DOI: 10.1016/j.micinf.2023.105268] [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: 10/22/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
The meteoric rise of single-cell genomic technologies, especially of single-cell RNA-sequencing (scRNA-seq), has revolutionized several fields of cellular biology, especially immunology, oncology, neuroscience and developmental biology. While the field of virology has been relatively slow to adopt these technological advances, many works have shed new light on the fascinating interactions of viruses with their hosts using single cell technologies. One clear example is the multitude of studies dissecting viral infections by single-cell sequencing technologies during the recent COVID-19 pandemic. In this review we will detail the advantages of studying viral infections at a single-cell level, how scRNA-seq technologies can be used to achieve this goal and the associated technical limitations, challenges and solutions. We will highlight recent biological discoveries and breakthroughs in virology enabled by single-cell analyses and will end by discussing possible future directions of the field. Given the rate of publications in this exciting new frontier of virology, we have likely missed some important works and we apologize in advance to the researchers whose work we have failed to cite.
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Affiliation(s)
- Pierre Bost
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland; ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093 Switzerland.
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, The Center for Virus Research and The Center for Complex Biological Systems, The University of California, Irvine, CA, 92697, USA
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3
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Ji B, Chen J, Gong H, Li X. Streamlined Full-Length Total RNA Sequencing of Paraformaldehyde-Fixed Brain Tissues. Int J Mol Sci 2024; 25:6504. [PMID: 38928210 PMCID: PMC11204141 DOI: 10.3390/ijms25126504] [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: 04/25/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Paraformaldehyde (PFA) fixation is the preferred method for preserving tissue architecture for anatomical and pathological observations. Meanwhile, PFA reacts with the amine groups of biomolecules to form chemical cross-linking, which preserves RNA within the tissue. This has great prospects for RNA sequencing to characterize the molecular underpinnings after anatomical and pathological observations. However, RNA is inaccessible due to cross-linked adducts forming between RNA and other biomolecules in prolonged PFA-fixed tissue. It is also difficult to perform reverse transcription and PCR, resulting in low sequencing sensitivity and reduced reproducibility. Here, we developed a method to perform RNA sequencing in PFA-fixed tissue, which is easy to use, cost-effective, and allows efficient sample multiplexing. We employ cross-link reversal to recover RNA and library construction using random primers without artificial fragmentation. The yield and quality of recovered RNA significantly increased through our method, and sequencing quality metrics and detected genes did not show any major differences compared with matched fresh samples. Moreover, we applied our method for gene expression analysis in different regions of the mouse brain and identified unique gene expression profiles with varied functional implications. We also find significant dysregulation of genes involved in Alzheimer's disease (AD) pathogenesis within the medial septum (MS)/vertical diagonal band of Broca (VDB) of the 5×FAD mouse brain. Our method can thus increase the performance of high-throughput RNA sequencing with PFA-fixed samples and allows longitudinal studies of small tissue regions isolated by their in situ context.
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Affiliation(s)
- Bingqing Ji
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jiale Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
| | - Xiangning Li
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
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Maizels RJ, Snell DM, Briscoe J. Reconstructing developmental trajectories using latent dynamical systems and time-resolved transcriptomics. Cell Syst 2024; 15:411-424.e9. [PMID: 38754365 DOI: 10.1016/j.cels.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
The snapshot nature of single-cell transcriptomics presents a challenge for studying the dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal information at single-cell level, but current methods have limitations. Here, we present a framework that overcomes these limitations: experimentally, we developed sci-FATE2, an optimized method for metabolic labeling with increased data quality, which we used to profile 45,000 embryonic stem (ES) cells differentiating into neural tube identities. Computationally, we developed a two-stage framework for dynamical modeling: VelvetVAE, a variational autoencoder (VAE) for velocity inference that outperforms all other tools tested, and VelvetSDE, a neural stochastic differential equation (nSDE) framework for simulating trajectory distributions. These recapitulate underlying dataset distributions and capture features such as decision boundaries between alternative fates and fate-specific gene expression. These methods recast single-cell analyses from descriptions of observed data to models of the dynamics that generated them, providing a framework for investigating developmental fate decisions.
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Affiliation(s)
- Rory J Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College, London, UK
| | - Daniel M Snell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Coulter EM, Bewicke-Copley F, Mossner M, Graham TA, Fitzgibbon J, Okosun J. Defining an Optimized Workflow for Enriching and Analyzing Residual Tumor Populations Using Intracellular Markers. J Mol Diagn 2024; 26:245-256. [PMID: 38280422 DOI: 10.1016/j.jmoldx.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/12/2023] [Accepted: 01/11/2024] [Indexed: 01/29/2024] Open
Abstract
Tumor relapse is well recognized to arise from treatment-resistant residual populations. Strategies enriching such populations for in-depth downstream analyses focus on tumor-specific surface markers; however, enrichment using intracellular biomarkers remains challenging. Using B-cell lymphoma as an exemplar, we demonstrate feasibility to enrich B-cell lymphoma 2 (BCL2)high populations, a surrogate marker for t(14;18)+ lymphomas, for use in downstream applications. Different fixation protocols were assessed for impact on antibody expression and RNA integrity; glyoxal fixation demonstrated superior results regarding minimal effects on surface and intracellular expression, and RNA quality, compared with alternative fixatives evaluated. Furthermore, t(14;18)+ B cells were effectively detected using intracellular BCL2 overexpression to facilitate tumor cell enrichment. Tumor cell populations were enriched using the cellenONE F1.4 single-cell sorting platform, which detected and dispensed BCL2high-expressing cells directly into library preparation reagents for transcriptome analyses. Sorted glyoxal-fixed cells generated good quality sequencing libraries, with high concordance between live and fixed single-cell transcriptomic profiles, discriminating cell populations predominantly on B-cell biology. Overall, we successfully developed a proof-of-concept workflow employing a robust cell preparation protocol for intracellular markers combined with cell enrichment using the cellenONE platform, providing an alternative to droplet-based technologies when cellular input is low or requires prior enrichment to detect rare populations. This workflow has wider prognostic and therapeutic potential to study residual cells in a pan-cancer setting.
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Affiliation(s)
- Eve M Coulter
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
| | - Findlay Bewicke-Copley
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom; Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom; Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; AstraZeneca, Waltham, Massachusetts
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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6
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Migalska M, Węglarczyk K, Dudek K, Homa J. Evolutionary trade-offs constraining the MHC gene expansion: beyond simple TCR depletion model. Front Immunol 2024; 14:1240723. [PMID: 38259496 PMCID: PMC10801004 DOI: 10.3389/fimmu.2023.1240723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
The immune system is as much shaped by the pressure of pathogens as it is by evolutionary trade-offs that constrain its structure and function. A perfect example comes from the major histocompatibility complex (MHC), molecules that initiate adaptive immune response by presentation of foreign antigens to T cells. The remarkable, population-level polymorphism of MHC genes is assumed to result mainly from a co-evolutionary arms race between hosts and pathogens, while the limited, within-individual number of functional MHC loci is thought to be the consequence of an evolutionary trade-off between enhanced pathogen recognition and excessive T cell depletion during negative selection in the thymus. Certain mathematical models and infection studies suggest that an intermediate individual MHC diversity would thus be optimal. A recent, more direct test of this hypothesis has shown that the effects of MHC diversity on T-cell receptor (TCR) repertoires may differ between MHC classes, supporting the depletion model only for MHC class I. Here, we used the bank vole (Myodes=Cletronomys glareolus), a rodent species with variable numbers of expressed MHC genes, to test how an individual MHC diversity influences the proportions and TCR repertoires of responding T cell subsets. We found a non-linear relationship between MHC diversity and T cell proportions (with intermediate MHC numbers coinciding with the largest T cell proportions), perhaps reflecting an optimality effect of balanced positive and negative thymic selection. The association was strongest for the relationship between MHC class I and splenic CD8+ T cells. The CD8+ TCR richness alone was unaffected by MHC class I diversity, suggesting that MHC class I expansion may be limited by decreasing T cell counts, rather than by direct depletion of TCR richness. In contrast, CD4+ TCR richness was positively correlated with MHC class II diversity, arguing against a universal TCR depletion. It also suggests that different evolutionary forces or trade-offs may limit the within-individual expansion of the MHC class II loci.
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Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Kazimierz Węglarczyk
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Joanna Homa
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
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Madaci L, Gard C, Nin S, Sarrabay A, Baier C, Venton G, Rihet P, Puthier D, Loriod B, Costello R. Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation. Diseases 2023; 12:1. [PMID: 38275564 PMCID: PMC10814800 DOI: 10.3390/diseases12010001] [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: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION The application of single-cell RNA sequencing has greatly improved our understanding of various cellular and molecular mechanisms involved in physiological and pathophysiological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. MATERIALS AND METHODS In this study, we selected two AML samples that had been fixed in methanol for 12-18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. RESULTS We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. CONCLUSIONS The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effectively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.
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Affiliation(s)
- Lamia Madaci
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Charlyne Gard
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Sébastien Nin
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Alexandre Sarrabay
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Céline Baier
- Advanced BioDesign, Parc Technologique de Lyon, 655 Allée des Parcs, 69800 Saint Priest, France
| | - Geoffroy Venton
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Pascal Rihet
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Denis Puthier
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Béatrice Loriod
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Régis Costello
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
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Labarta-Bajo L, Deng J, Contreras M, Allen NJ. Protocol for the purification and transcriptomic analysis of mouse astrocytes using GFAT. STAR Protoc 2023; 4:102599. [PMID: 37742178 PMCID: PMC10522990 DOI: 10.1016/j.xpro.2023.102599] [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: 06/21/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Astrocytes are glial cells of the central nervous system that modulate neuronal function. Here, we present glyoxal-fixed astrocyte nuclei transcriptomics (GFAT), a protocol for the purification and transcriptomic analysis of astrocyte nuclei from the cortex and cerebellum of adult and aged fresh mouse brain. We describe steps for tissue dissection, glyoxal fixation, homogenization, nuclei isolation, antibody staining, fluorescence-activated cell sorting, and RT-qPCR or bulk RNA sequencing. GFAT does not require transgenic lines or viral injection and allows parallel astrocyte and neuron profiling.
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Affiliation(s)
| | - James Deng
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minerva Contreras
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicola J Allen
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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9
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Hu S, Zhang Q, Ou Z, Dang Y. Particle sorting method based on swirl induction. J Chem Phys 2023; 159:174901. [PMID: 37909455 DOI: 10.1063/5.0170783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023] Open
Abstract
Fluid-based methods for particle sorting demonstrate increasing appeal in many areas of biosciences due to their biocompatibility and cost-effectiveness. Herein, we construct a microfluidic sorting system based on a swirl microchip. The impact of microchannel velocity on the swirl stagnation point as well as particle movement is analyzed through simulation and experiment. Moreover, the quantitative mapping relationship between flow velocity and particle position distribution is established. With this foundation established, a particle sorting method based on swirl induction is proposed. Initially, the particle is captured by a swirl. Then, the Sorting Region into which the particle aims to enter is determined according to the sorting condition and particle characteristic. Subsequently, the velocities of the microchannels are adjusted to control the swirl, which will induce the particle to enter its corresponding Induction Region. Thereafter, the velocities are adjusted again to change the fluid field and drive the particle into a predetermined Sorting Region, hence the sorting is accomplished. We have extensively conducted experiments taking particle size or color as a sorting condition. An outstanding sorting success rate of 98.75% is achieved when dealing with particles within the size range of tens to hundreds of micrometers in radius, which certifies the effectiveness of the proposed sorting method. Compared to the existing sorting techniques, the proposed method offers greater flexibility. The adjustment of sorting conditions or particle parameters no longer requires complex chip redesign, because such sorting tasks can be successfully realized through simple microchannel velocities control.
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Affiliation(s)
- Shuai Hu
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510641, China
| | - Qin Zhang
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510641, China
| | - Zhiming Ou
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yanping Dang
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510641, China
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10
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Bageritz J, Krausse N, Yousefian S, Leible S, Valentini E, Boutros M. Glyoxal as an alternative fixative for single-cell RNA sequencing. G3 (BETHESDA, MD.) 2023; 13:jkad160. [PMID: 37494060 PMCID: PMC10542564 DOI: 10.1093/g3journal/jkad160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
Single-cell RNA sequencing has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms, and understand the heterogeneity in cellular responses. Nevertheless, sample collection and processing remain a severe bottleneck for single-cell RNA sequencing experiments. Cell isolation protocols often lead to significant changes in the transcriptomes of cells, requiring novel methods to preserve cell states. Here, we developed and benchmarked protocols using glyoxal as a fixative for single-cell RNA sequencing applications. Using Drop-seq methodology, we detected a large number of transcripts and genes from glyoxal-fixed Drosophila cells after single-cell RNA sequencing. The effective glyoxal fixation of transcriptomes in Drosophila and human cells was further supported by a high correlation of gene expression data between glyoxal-fixed and unfixed samples. Accordingly, we also found highly expressed genes overlapping to a large extent between experimental conditions. These results indicated that our fixation protocol did not induce considerable changes in gene expression and conserved the transcriptome for subsequent single-cell isolation procedures. In conclusion, we present glyoxal as a suitable fixative for Drosophila cells and potentially cells of other species that allow high-quality single-cell RNA sequencing applications.
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Affiliation(s)
- Josephine Bageritz
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Niklas Krausse
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Schayan Yousefian
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Svenja Leible
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Erica Valentini
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, BioQuant and Medical Faculty Mannheim, German Cancer Research Center (DKFZ), Heidelberg University, D-69120 Heidelberg, Germany
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11
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Channathodiyil P, May K, Segonds-Pichon A, Smith PD, Cook S, Houseley J. Escape from G1 arrest during acute MEK inhibition drives the acquisition of drug resistance. NAR Cancer 2022; 4:zcac032. [PMID: 36267209 PMCID: PMC9575185 DOI: 10.1093/narcan/zcac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/08/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing are poorly understood. Here, we investigate BRAFV600E amplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterized model for reproducible emergence of drug resistance, and show that BRAF amplifications acquired de novo are the primary cause of resistance. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2; however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation, including TIPIN, PLK2 and PLK3, remain at low abundance. This suggests that DNA replication following escape from G1 arrest in drug is more error prone and provides a potential explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that escape from G1 arrest in drug promotes de novo BRAF amplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs through de novo gene amplification and can be suppressed by impeding cell cycle entry in drug.
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Affiliation(s)
| | - Kieron May
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 4NT, UK
| | | | - Paul D Smith
- Oncology R&D, AstraZeneca CRUK Cambridge Institute, Cambridge, CB2 0AA, UK
| | - Simon J Cook
- Signalling Programme, Babraham Institute, Cambridge, CB22 4NT, UK
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12
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Rossi T, Angeli D, Martinelli G, Fabbri F, Gallerani G. From phenotypical investigation to RNA-sequencing for gene expression analysis: A workflow for single and pooled rare cells. Front Genet 2022; 13:1012191. [PMID: 36452152 PMCID: PMC9703136 DOI: 10.3389/fgene.2022.1012191] [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: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 08/30/2023] Open
Abstract
Combining phenotypical and molecular characterization of rare cells is challenging due to their scarcity and difficult handling. In oncology, circulating tumor cells (CTCs) are considered among the most important rare cell populations. Their phenotypic and molecular characterization is necessary to define the molecular mechanisms underlying their metastatic potential. Several approaches that require cell fixation make difficult downstream molecular investigations on RNA. Conversely, the DEPArray technology allows phenotypic analysis and handling of both fixed and unfixed cells, enabling a wider range of applications. Here, we describe an experimental workflow that allows the transcriptomic investigation of single and pooled OE33 cells undergone to DEPArray analysis and recovery. In addition, cells were tested at different conditions (unfixed, CellSearch fixative (CSF)- and ethanol (EtOH)-fixed cells). In a forward-looking perspective, this workflow will pave the way for novel strategies to characterize gene expression profiles of rare cells, both single-cell and low-resolution input.
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Affiliation(s)
- Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giulia Gallerani
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
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13
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Landscape and age dynamics of immune cells in the Egyptian rousette bat. Cell Rep 2022; 40:111305. [PMID: 36070695 DOI: 10.1016/j.celrep.2022.111305] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/20/2022] [Accepted: 08/10/2022] [Indexed: 01/04/2023] Open
Abstract
Bats harbor high-impact zoonotic viruses often in the absence of disease manifestation. This restriction and disease tolerance possibly rely on specific immunological features. In-depth molecular characterization of cellular immunity and imprinting of age on leukocyte compartments remained unexplored in bats. We employ single-cell RNA sequencing (scRNA-seq) and establish immunostaining panels to characterize the immune cell landscape in juvenile, subadult, and adult Egyptian rousette bats (ERBs). Transcriptomic and flow cytometry data reveal conserved subsets and substantial enrichments of CD79a+ B cells and CD11b+ T cells in juvenile animals, whereas neutrophils, CD206+ myeloid cells, and CD3+ T cells dominate as bats reach adulthood. Despite differing frequencies, phagocytosis of circulating and tissue-resident myeloid cells and proliferation of peripheral and splenic lymphocytes are analogous in juvenile and adult ERBs. We provide a comprehensive map of the immune landscape in ERBs and show age-imprinted resilience progression and find that variability in cellular immunity only partly recapitulates mammalian archetypes.
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14
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Bhowmick R, Lerdrup M, Gadi SA, Rossetti GG, Singh MI, Liu Y, Halazonetis TD, Hickson ID. RAD51 protects human cells from transcription-replication conflicts. Mol Cell 2022; 82:3366-3381.e9. [PMID: 36002000 DOI: 10.1016/j.molcel.2022.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/02/2022] [Accepted: 07/16/2022] [Indexed: 12/16/2022]
Abstract
Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA replication and transcription machineries operating simultaneously at the same loci. One role of the RAD51 recombinase in human cells is to protect replication forks undergoing RS. Here, we have identified a key role for RAD51 in preventing transcription-replication conflicts (TRCs) from triggering replication fork breakage. The genomic regions most affected by RAD51 deficiency are characterized by being replicated and transcribed in early S-phase and show significant overlap with loci prone to cancer-associated amplification. Consistent with a role for RAD51 in protecting against transcription-replication conflicts, many of the adverse effects of RAD51 depletion are ameliorated by inhibiting early S-phase transcription. We propose a model whereby RAD51 suppresses fork breakage and subsequent inadvertent amplification of genomic loci prone to experiencing TRCs.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Sampath Amitash Gadi
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Giacomo G Rossetti
- Department of Molecular Biology, University of Geneva, 30, quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Manika I Singh
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ying Liu
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 30, quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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15
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Thomas S, Sadanandan J, Blackburn SL, McBride DW, Dienel A, Hong S, Zeineddine HA, Thankamani PK. Glyoxal Fixation Is Optimal for Immunostaining of Brain Vessels, Pericytes and Blood-Brain Barrier Proteins. Int J Mol Sci 2022; 23:7776. [PMID: 35887131 PMCID: PMC9317650 DOI: 10.3390/ijms23147776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022] Open
Abstract
Brain vascular staining is very important for understanding cerebrovascular pathologies. 4% paraformaldehyde is considered the gold standard fixation technique for immunohistochemistry and it revolutionized the examination of proteins in fixed tissues. However, this fixation technique produces inconsistent immunohistochemical staining results due to antigen masking. Here, we test a new fixation protocol using 3% glyoxal and demonstrate that this method improves the staining of the brain vasculature, pericytes, and tight junction proteins compared to 4% paraformaldehyde. Use of this new fixation technique will provide more detailed information about vascular protein expressions, their distributions, and colocalizations with other proteins at the molecular level in the brain vasculature.
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Affiliation(s)
| | | | | | | | | | | | | | - Peeyush Kumar Thankamani
- The Vivian L. Smith Department of Neurosurgery, University of Texas Health Science Center, 6431 Fannin St. MSB 7.147, Houston, TX 77030, USA; (S.T.); (J.S.); (S.L.B.); (D.W.M.); (A.D.); (S.H.); (H.A.Z.)
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16
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Kleino I, Nowlan K, Kotimaa J, Kekäläinen E. Optimising protein detection with fixable custom oligo-labelled antibodies for single-cell multi-omics approaches. Biotechnol J 2022; 17:e2100213. [PMID: 35174641 DOI: 10.1002/biot.202100213] [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: 04/23/2021] [Revised: 02/06/2022] [Accepted: 02/12/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND AND AIM Single-cell RNA sequencing (scRNA-seq) is a powerful method utilising transcriptomic data for detailed characterisation of heterogeneous cell populations. The use of oligonucleotide-labelled antibodies for targeted proteomics addresses the shortcomings of the scRNA-seq-only based approach by improving detection of low expressing targets. However, optimisation of large antibody panels is challenging and depends on the availability of co-functioning oligonucleotide-labelled antibodies. MAIN METHODS AND RESULTS We present here a simple adjustable oligonucleotide-antibody conjugation method which enables desired level of oligo-conjugation per antibody. The mean labelling in the produced antibody batches varied from 1 to 6 oligos per antibody. In the scRNA-seq multimodal experiment, the highest sensitivity was seen with moderate antibody labelling as the high activation and/or labelling was detrimental to antibody performance. The conjugates were also tested for compatibility with the fixation and freeze storage protocols. The oligo-antibody signal was stable in fixed cells indicating feasibility of the stain, fix, store, and analyse later type of workflow for multimodal scRNA-seq. CONCLUSIONS AND IMPLICATIONS Optimised oligo-labelling will improve detection of weak protein targets in scRNA-seq multimodal experiments and reduce sequencing costs due to a more balanced amplification of different antibody signals in CITE-seq libraries. Furthermore, the use of a pre-stain, fix, run later protocol will allow for flexibility, facilitate sample pooling, and ease logistics in scRNA-seq multimodal experiments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Iivari Kleino
- Translational Immunology Research Program, University of Helsinki
| | - Kirsten Nowlan
- Doctoral Programme in Biomedicine, University of Helsinki
| | - Juha Kotimaa
- Complement Group, University of Helsinki, Department of Bacteriology and Immunology
| | - Eliisa Kekäläinen
- Dept. of Bacteriology and Immunology, University of Helsinki, and Helsinki University Hospital
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17
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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18
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Machado L, Relaix F, Mourikis P. Stress relief: emerging methods to mitigate dissociation-induced artefacts. Trends Cell Biol 2021; 31:888-897. [PMID: 34074577 DOI: 10.1016/j.tcb.2021.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022]
Abstract
The rapid progress of single-cell RNA-sequencing (scRNA-seq) at large scales has led to what seemed impossible until recently: the generation of comprehensive transcriptional maps of nearly all cells in multicellular tissues. We pinpoint three key elements as being critical to the production of these maps: scalability, spatial information, and accuracy of the transcriptome of the individual cells. Here, we discuss the ramifications of traditional cell-isolation protocols when capturing the transcriptional signature of cells as they exist in their native tissue context, the methods that have been developed to avoid these distortions, and the biological processes that have unraveled on account of these upgraded methodological approaches.
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Affiliation(s)
- Léo Machado
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France
| | - Frederic Relaix
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France; EnvA, IMRB, F-94700 Maisons-Alfort, France; Etablissement Français du Sang (EFS), IMRB, F-94010 Creteil, France; Assistance Publique-Hôpitaux de Paris, Hopital Mondor, Service d'Histologie, F-94010 Creteil, France.
| | - Philippos Mourikis
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France.
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