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Brüggenthies JB, Dittmer J, Martin E, Zingman I, Tabet I, Bronner H, Groetzner S, Sauer J, Dehghan Harati M, Scharnowski R, Bakker J, Riegger K, Heinzelmann C, Ast B, Ries R, Fillon SA, Bachmayr-Heyda A, Kitt K, Grundl MA, Heilker R, Humbeck L, Schuler M, Weigle B. Insights into the Identification of iPSC- and Monocyte-Derived Macrophage-Polarizing Compounds by AI-Fueled Cell Painting Analysis Tools. Int J Mol Sci 2024; 25:12330. [PMID: 39596395 PMCID: PMC11595184 DOI: 10.3390/ijms252212330] [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: 10/18/2024] [Revised: 11/08/2024] [Accepted: 11/13/2024] [Indexed: 11/28/2024] Open
Abstract
Macrophage polarization critically contributes to a multitude of human pathologies. Hence, modulating macrophage polarization is a promising approach with enormous therapeutic potential. Macrophages are characterized by a remarkable functional and phenotypic plasticity, with pro-inflammatory (M1) and anti-inflammatory (M2) states at the extremes of a multidimensional polarization spectrum. Cell morphology is a major indicator for macrophage activation, describing M1(-like) (rounded) and M2(-like) (elongated) states by different cell shapes. Here, we introduced cell painting of macrophages to better reflect their multifaceted plasticity and associated phenotypes beyond the rigid dichotomous M1/M2 classification. Using high-content imaging, we established deep learning- and feature-based cell painting image analysis tools to elucidate cellular fingerprints that inform about subtle phenotypes of human blood monocyte-derived and iPSC-derived macrophages that are characterized as screening surrogate. Moreover, we show that cell painting feature profiling is suitable for identifying inter-donor variance to describe the relevance of the morphology feature 'cell roundness' and dissect distinct macrophage polarization signatures after stimulation with known biological or small-molecule modulators of macrophage (re-)polarization. Our novel established AI-fueled cell painting analysis tools provide a resource for high-content-based drug screening and candidate profiling, which set the stage for identifying novel modulators for macrophage (re-)polarization in health and disease.
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Affiliation(s)
- Johanna B. Brüggenthies
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
| | - Jakob Dittmer
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim RCV GmbH & Co. KG, 1121 Vienna, Austria; (J.D.); (A.B.-H.)
| | - Eva Martin
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Igor Zingman
- Global Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (I.Z.); (M.A.G.); (L.H.)
| | - Ibrahim Tabet
- ScreeningHub und ValueData GmbH, 70563 Stuttgart, Germany; (I.T.); (C.H.); (B.A.)
| | - Helga Bronner
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Sarah Groetzner
- Department Immunology and Respiratory, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (S.G.); (J.S.)
| | - Julia Sauer
- Department Immunology and Respiratory, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (S.G.); (J.S.)
| | - Mozhgan Dehghan Harati
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Rebekka Scharnowski
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
| | - Julia Bakker
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
| | - Katharina Riegger
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
| | - Caroline Heinzelmann
- ScreeningHub und ValueData GmbH, 70563 Stuttgart, Germany; (I.T.); (C.H.); (B.A.)
| | - Birgit Ast
- ScreeningHub und ValueData GmbH, 70563 Stuttgart, Germany; (I.T.); (C.H.); (B.A.)
| | - Robert Ries
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Sophie A. Fillon
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA;
| | - Anna Bachmayr-Heyda
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim RCV GmbH & Co. KG, 1121 Vienna, Austria; (J.D.); (A.B.-H.)
| | - Kerstin Kitt
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
| | - Marc A. Grundl
- Global Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (I.Z.); (M.A.G.); (L.H.)
| | - Ralf Heilker
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Lina Humbeck
- Global Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (I.Z.); (M.A.G.); (L.H.)
| | - Michael Schuler
- Global Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (E.M.); (H.B.); (M.D.H.); (R.R.); (R.H.); (M.S.)
| | - Bernd Weigle
- Department Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach a.d. Riss, Germany; (J.B.B.); (R.S.); (J.B.); (K.R.); (K.K.)
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Macrophage Phenotyping in Atherosclerosis by Proteomics. Int J Mol Sci 2023; 24:ijms24032613. [PMID: 36768933 PMCID: PMC9917096 DOI: 10.3390/ijms24032613] [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: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Macrophages are heterogeneous and plastic cells, able to adapt their phenotype and functions to changes in the microenvironment. They are involved in several homeostatic processes and also in many human diseases, including atherosclerosis, where they participate in all the stages of the disease. For these reasons, macrophages have been studied extensively using different approaches, including proteomics. Proteomics, indeed, may be a powerful tool to better understand the behavior of these cells, and a careful analysis of the proteome of different macrophage phenotypes can help to better characterize the role of these phenotypes in atherosclerosis and provide a broad view of proteins that might potentially affect the course of the disease. In this review, we discuss the different proteomic techniques that have been used to delineate the proteomic profile of macrophage phenotypes and summarize some results that can help to elucidate the roles of macrophages and develop new strategies to counteract the progression of atherosclerosis and/or promote regression.
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iPSC-Derived Macrophages: The Differentiation Protocol Affects Cell Immune Characteristics and Differentiation Trajectories. Int J Mol Sci 2022; 23:ijms232416087. [PMID: 36555728 PMCID: PMC9781144 DOI: 10.3390/ijms232416087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The generation of human macrophages from induced pluripotent stem cells (iMacs) is a rapidly developing approach used to create disease models, screen drugs, study macrophage-pathogen interactions and develop macrophage-based cell therapy. To generate iMacs, different types of protocols have been suggested, all thought to result in the generation of similar iMac populations. However, direct comparison of iMacs generated using different protocols has not been performed. We have compared the productivity, the differentiation trajectories and the characteristics of iMacs generated using two widely used protocols: one based on the formation of embryoid bodies and the induction of myeloid differentiation by only two cytokines, interleukin-3 and macrophage colony-stimulating factor, and the other utilizing multiple exogenous factors for iMac generation. We report inter-protocol differences in the following: (i) protocol productivity; (ii) dynamic changes in the expression of genes related to inflammation and lipid homeostasis following iMac differentiation and (iii) the transcriptomic profiles of terminally differentiated iMacs, including the expression of genes involved in inflammatory response, antigen presentation and lipid homeostasis. The results document the dependence of fine iMac characteristics on the type of differentiation protocol, which is important for further development of the field, including the development of iMac-based cell therapy.
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