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Jeong S, Chang H, Hong SH. Protocol for differentiation of functional macrophages from human induced pluripotent stem cells. STAR Protoc 2024; 5:102925. [PMID: 38421862 PMCID: PMC10910355 DOI: 10.1016/j.xpro.2024.102925] [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: 12/22/2023] [Revised: 01/16/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived macrophages provide a valuable tool for disease modeling and drug discovery. Here, we present a protocol to generate functional macrophages from hiPSCs using a feeder-free hematopoietic differentiation technique. We describe steps for preparing hiPSCs, mesodermal differentiation, hematopoietic commitment, and macrophage differentiation and expansion. We then detail assays to characterize their phenotype, polarization, and phagocytic functions. The functional macrophages generated here could be used to generate organoids for disease modeling and drug discovery studies. For complete details on the use and execution of this protocol, please refer to Jeong et al.1 and Heo et al.2.
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Affiliation(s)
- Suji Jeong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | | | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea; KW-Bio Co., Ltd., Chuncheon, Republic of Korea.
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2
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Yao M, Mao X, Zhang Z, Cui F, Shao S, Mao B. Communication molecules (ncRNAs) mediate tumor-associated macrophage polarization and tumor progression. Front Cell Dev Biol 2024; 12:1289538. [PMID: 38523627 PMCID: PMC10957787 DOI: 10.3389/fcell.2024.1289538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding RNAs play important roles in tumor cells and macrophages and participate in their communication as messengers. Non-coding RNAs have an impact in tumor cell proliferation, migration, and apoptosis, and they also regulate the differentiation and regulation of immune cells. In macrophages, they stimulate the polarization of macrophages into M1 or M2 by regulating proteins related to signaling pathways; in tumor cells, non-coding RNAs can enter macrophages through exosomes and affect the latter polarization. The polarization of macrophages further regulates the biological functions of cancer cells. The direction of macrophage polarization determines tumor progression, angiogenesis and drug resistance. This often creates a feedback loop. Non-coding RNAs act as bridges between tumor cells and macrophages to regulate the balance of the tumor microenvironment. We reviewed the signaling pathways related to macrophage polarization and the regulatory mechanisms of non-coding RNA in tumor-associated macrophages M1 and M2, and discussed the potential applications and prospects of exosome engineering.
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Affiliation(s)
- Min Yao
- The Affiliated Yixing Hospital of Jiangsu University, WuXi, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xuhua Mao
- The Affiliated Yixing Hospital of Jiangsu University, WuXi, China
| | - Zherui Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Feilun Cui
- The Affiliated Taizhou Second People`s Hospital of Yangzhou University, Taizhou, Jiangsu, China
| | - Shihe Shao
- The Affiliated Yixing Hospital of Jiangsu University, WuXi, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Boneng Mao
- The Affiliated Yixing Hospital of Jiangsu University, WuXi, China
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3
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Wang Y. Erdr1 orchestrates macrophage polarization and determines cell fate via dynamic interplay with YAP1 and Mid1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.17.557960. [PMID: 37781614 PMCID: PMC10541097 DOI: 10.1101/2023.09.17.557960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Erythroid differentiation regulator 1 (Erdr1) is a stress-induced, widely distributed, extremely conserved secreted factor found in both humans and mice. Erdr1 is highly linked with the Hippo-YAP1 signaling. Initially identified as an inducer of hemoglobin synthesis, it has emerged as a multifunctional protein, especially in immune cells. Although Erdr1 has been implicated in T cells and NK cell function, its role in macrophage remains unclear. This study aims to explore the function and mechanism of Erdr1 in IL-1β production in macrophages. Data manifest Erdr1 could play an inhibition role in IL-1β production, which also has been reported by previous research. What significance is we discovered Erdr1 can promote IL-1β production which is associated with Erdr1 dose and cell density. We observed that Erdr1 was inhibited in pro-inflammatory (M1) macrophages but was upregulated in anti-inflammatory (M2) macrophages compared to naive macrophages. We hypothesized that Erdr1 dual drives and modulates IL-1β production by binding with distinct adaptors via concentration change. Mechanistically, we demonstrated that Erdr1 dual regulates IL-1β production by dynamic interaction with YAP1 and Mid1 by distinct domains. Erdr1-YAP1 interplay mediates macrophage M2 polarization by promoting an anti-inflammatory response, enhancing catabolic metabolism, and leading to sterile cell death. Whereas, Erdr1-Mid1 interplay mediates macrophage M1 polarization by initiating a pro-inflammatory response, facilitating anabolic metabolism, and causing inflammatory cell death. This study highlights Erdr1 orchestrates macrophage polarization and determines cell date by regulating YAP1 through non-classical Hippo pathway.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA (Current)
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Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569494. [PMID: 38076932 PMCID: PMC10705493 DOI: 10.1101/2023.11.30.569494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
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Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Jon Bezney
- Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Stöberl N, Maguire E, Salis E, Shaw B, Hall-Roberts H. Human iPSC-derived glia models for the study of neuroinflammation. J Neuroinflammation 2023; 20:231. [PMID: 37817184 PMCID: PMC10566197 DOI: 10.1186/s12974-023-02919-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
Neuroinflammation is a complex biological process that plays a significant role in various brain disorders. Microglia and astrocytes are the key cell types involved in inflammatory responses in the central nervous system. Neuroinflammation results in increased levels of secreted inflammatory factors, such as cytokines, chemokines, and reactive oxygen species. To model neuroinflammation in vitro, various human induced pluripotent stem cell (iPSC)-based models have been utilized, including monocultures, transfer of conditioned media between cell types, co-culturing multiple cell types, neural organoids, and xenotransplantation of cells into the mouse brain. To induce neuroinflammatory responses in vitro, several stimuli have been established that can induce responses in either microglia, astrocytes, or both. Here, we describe and critically evaluate the different types of iPSC models that can be used to study neuroinflammation and highlight how neuroinflammation has been induced and measured in these cultures.
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Affiliation(s)
- Nina Stöberl
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff, CF10 3AT UK
| | - Emily Maguire
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff, CF10 3AT UK
| | - Elisa Salis
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff, CF10 3AT UK
| | - Bethany Shaw
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff, CF10 3AT UK
| | - Hazel Hall-Roberts
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff, CF10 3AT UK
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Ruder AV, Temmerman L, van Dommelen JM, Nagenborg J, Lu C, Sluimer JC, Goossens P, Biessen EA. Culture density influences the functional phenotype of human macrophages. Front Immunol 2023; 14:1078591. [PMID: 36969194 PMCID: PMC10036771 DOI: 10.3389/fimmu.2023.1078591] [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: 10/24/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Macrophages (MΦ) are commonly cultured in vitro as a model of their biology and functions in tissues. Recent evidence suggests MΦ to engage in quorum sensing, adapting their functions in response to cues about the proximity of neighboring cells. However, culture density is frequently overlooked in the standardization of culture protocols as well as the interpretation of results obtained in vitro. In this study, we investigated how the functional phenotype of MΦ was influenced by culture density. We assessed 10 core functions of human MΦ derived from the THP-1 cell line as well as primary monocyte-derived MΦ. THP-1 MΦ showed increasing phagocytic activity and proliferation with increasing density but decreasing lipid uptake, inflammasome activation, mitochondrial stress, and secretion of cytokines IL-10, IL-6, IL-1β, IL-8, and TNF-α. For THP-1 MΦ, the functional profile displayed a consistent trajectory with increasing density when exceeding a threshold (of 0.2 x 103 cells/mm2), as visualized by principal component analysis. Culture density was also found to affect monocyte-derived MΦ, with functional implications that were distinct from those observed in THP-1 MΦ, suggesting particular relevance of density effects for cell lines. With increasing density, monocyte-derived MΦ exhibited progressively increased phagocytosis, increased inflammasome activation, and decreased mitochondrial stress, whereas lipid uptake was unaffected. These different findings in THP-1 MΦ and monocyte-derived MΦ could be attributed to the colony-forming growth pattern of THP-1 MΦ. At the lowest density, the distance to the closest neighboring cells showed greater influence on THP-1 MΦ than monocyte-derived MΦ. In addition, functional differences between monocyte-derived MΦ from different donors could at least partly be attributed to differences in culture density. Our findings demonstrate the importance of culture density for MΦ function and demand for awareness of culture density when conducting and interpreting in vitro experiments.
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Affiliation(s)
- Adele V. Ruder
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Lieve Temmerman
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Joep M.A. van Dommelen
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Jan Nagenborg
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Chang Lu
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Judith C. Sluimer
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
- BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Pieter Goossens
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
| | - Erik A.L. Biessen
- Cardiovascular Research Institute Maastricht (CARIM), Department of Pathology, Maastricht University Medical Center (UMC), Maastricht, Netherlands
- Institute for Molecular Cardiovascular Research, RWTH Aachen University, Aachen, Germany
- *Correspondence: Erik A.L. Biessen,
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