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Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
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Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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Fourneaux C, Racine L, Koering C, Dussurgey S, Vallin E, Moussy A, Parmentier R, Brunard F, Stockholm D, Modolo L, Picard F, Gandrillon O, Paldi A, Gonin-Giraud S. Differentiation is accompanied by a progressive loss in transcriptional memory. BMC Biol 2024; 22:58. [PMID: 38468285 PMCID: PMC10929117 DOI: 10.1186/s12915-024-01846-9] [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: 04/05/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Cell differentiation requires the integration of two opposite processes, a stabilizing cellular memory, especially at the transcriptional scale, and a burst of gene expression variability which follows the differentiation induction. Therefore, the actual capacity of a cell to undergo phenotypic change during a differentiation process relies upon a modification in this balance which favors change-inducing gene expression variability. However, there are no experimental data providing insight on how fast the transcriptomes of identical cells would diverge on the scale of the very first two cell divisions during the differentiation process. RESULTS In order to quantitatively address this question, we developed different experimental methods to recover the transcriptomes of related cells, after one and two divisions, while preserving the information about their lineage at the scale of a single cell division. We analyzed the transcriptomes of related cells from two differentiation biological systems (human CD34+ cells and T2EC chicken primary erythrocytic progenitors) using two different single-cell transcriptomics technologies (scRT-qPCR and scRNA-seq). CONCLUSIONS We identified that the gene transcription profiles of differentiating sister cells are more similar to each other than to those of non-related cells of the same type, sharing the same environment and undergoing similar biological processes. More importantly, we observed greater discrepancies between differentiating sister cells than between self-renewing sister cells. Furthermore, a progressive increase in this divergence from first generation to second generation was observed when comparing differentiating cousin cells to self renewing cousin cells. Our results are in favor of a gradual erasure of transcriptional memory during the differentiation process.
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Affiliation(s)
- Camille Fourneaux
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Laëtitia Racine
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Catherine Koering
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Sébastien Dussurgey
- Plateforme AniRA-Cytométrie, Université Claude Bernard Lyon 1, CNRS UAR3444, Inserm US8, ENS de Lyon, SFR Biosciences, Lyon, F-69007, France
| | - Elodie Vallin
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Alice Moussy
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Romuald Parmentier
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Fanny Brunard
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Daniel Stockholm
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Franck Picard
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Olivier Gandrillon
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France
- Inria Center, Grenoble Rhone-Alpes, Equipe Dracula, Villeurbanne, F69100, France
| | - Andras Paldi
- Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France
| | - Sandrine Gonin-Giraud
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
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