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Ahmadzadeh K, Pereira M, Vanoppen M, Bernaerts E, Ko J, Mitera T, Maksoudian C, Manshian BB, Soenen S, Rose CD, Matthys P, Wouters C, Behmoaras J. Multinucleation resets human macrophages for specialized functions at the expense of their identity. EMBO Rep 2023; 24:e56310. [PMID: 36597777 PMCID: PMC9986822 DOI: 10.15252/embr.202256310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Macrophages undergo plasma membrane fusion and cell multinucleation to form multinucleated giant cells (MGCs) such as osteoclasts in bone, Langhans giant cells (LGCs) as part of granulomas or foreign-body giant cells (FBGCs) in reaction to exogenous material. How multinucleation per se contributes to functional specialization of mature mononuclear macrophages remains poorly understood in humans. Here, we integrate comparative transcriptomics with functional assays in purified mature mononuclear and multinucleated human osteoclasts, LGCs and FBGCs. Strikingly, in all three types of MGCs, multinucleation causes a pronounced downregulation of macrophage identity. We show enhanced lysosome-mediated intracellular iron homeostasis promoting MGC formation. The transition from mononuclear to multinuclear state is accompanied by cell specialization specific to each polykaryon. Enhanced phagocytic and mitochondrial function associate with FBGCs and osteoclasts, respectively. Moreover, human LGCs preferentially express B7-H3 (CD276) and can form granuloma-like clusters in vitro, suggesting that their multinucleation potentiates T cell activation. These findings demonstrate how cell-cell fusion and multinucleation reset human macrophage identity as part of an advanced maturation step that confers MGC-specific functionality.
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Affiliation(s)
- Kourosh Ahmadzadeh
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Marie Pereira
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
| | - Margot Vanoppen
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Eline Bernaerts
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Jeong‐Hun Ko
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
| | - Tania Mitera
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Christy Maksoudian
- NanoHealth and Optical Imaging Group, Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Bella B Manshian
- Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Stefaan Soenen
- NanoHealth and Optical Imaging Group, Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Carlos D Rose
- Division of Pediatric Rheumatology Nemours Children's HospitalThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Patrick Matthys
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Carine Wouters
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
- Division Pediatric RheumatologyUZ LeuvenLeuvenBelgium
- European Reference Network for Rare ImmunodeficiencyAutoinflammatory and Autoimmune Diseases (RITA) at University Hospital LeuvenLeuvenBelgium
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational BiologyDuke‐NUS Medical School SingaporeSingaporeSingapore
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2
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Elson A, Anuj A, Barnea-Zohar M, Reuven N. The origins and formation of bone-resorbing osteoclasts. Bone 2022; 164:116538. [PMID: 36028118 DOI: 10.1016/j.bone.2022.116538] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Osteoclasts (OCLs) are hematopoietic cells whose physiological function is to degrade bone. OCLs are key players in the processes that determine and maintain the mass, shape, and physical properties of bone. OCLs adhere to bone tightly and degrade its matrix by secreting protons and proteases onto the underlying surface. The combination of low pH and proteases degrades the mineral and protein components of the matrix and forms a resorption pit; the degraded material is internalized by the cell and then secreted into the circulation. Insufficient or excessive activity of OCLs can lead to significant changes in bone and either cause or exacerbate symptoms of diseases, as in osteoporosis, osteopetrosis, and cancer-induced bone lysis. OCLs are derived from monocyte-macrophage precursor cells whose origins are in two distinct embryonic cell lineages - erythromyeloid progenitor cells of the yolk sac, and hematopoietic stem cells. OCLs are formed in a multi-stage process that is induced by the cytokines M-CSF and RANKL, during which the cells differentiate, fuse to form multi-nucleated cells, and then differentiate further to become mature, bone-resorbing OCLs. Recent studies indicate that OCLs can undergo fission in vivo to generate smaller cells, called "osteomorphs", that can be "re-cycled" by fusing with other cells to form new OCLs. In this review we describe OCLs and discuss their cellular origins and the cellular and molecular events that drive osteoclastogenesis.
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Affiliation(s)
- Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anuj Anuj
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maayan Barnea-Zohar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nina Reuven
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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3
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Lone AM, Taskén K. Phosphoproteomics-Based Characterization of Prostaglandin E 2 Signaling in T Cells. Mol Pharmacol 2021; 99:370-382. [PMID: 33674363 DOI: 10.1124/molpharm.120.000170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/01/2021] [Indexed: 12/24/2022] Open
Abstract
Prostaglandin E2 (PGE2) is a key lipid mediator in health and disease and serves as a crucial link between the immune response and cancer. With the advent of cancer therapies targeting PGE2 signaling pathways at different levels, there has been increased interest in mapping and understanding the complex and interconnected signaling pathways arising from the four distinct PGE2 receptors. Here, we review phosphoproteomics studies that have investigated different aspects of PGE2 signaling in T cells. These studies have elucidated PGE2's regulatory effect on T cell receptor signaling and T cell function, the key role of protein kinase A in many PGE2 signaling pathways, the temporal regulation of PGE2 signaling, differences in PGE2 signaling between different T cell subtypes, and finally, the crosstalk between PGE2 signaling pathways elicited by the four distinct PGE2 receptors present in T cells. SIGNIFICANCE STATEMENT: Through the reviewed studies, we now have a much better understanding of PGE2's signaling mechanisms and functional roles in T cells, as well as a solid platform for targeted and functional studies of specific PGE2-triggered pathways in T cells.
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Affiliation(s)
- Anna Mari Lone
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital (A.M.L., K.T.) and Institute for Clinical Medicine, University of Oslo, Oslo, Norway (K.T.)
| | - Kjetil Taskén
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital (A.M.L., K.T.) and Institute for Clinical Medicine, University of Oslo, Oslo, Norway (K.T.)
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4
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The effect of the WKYMVm peptide on promoting mBMSC secretion of exosomes to induce M2 macrophage polarization through the FPR2 pathway. J Orthop Surg Res 2021; 16:171. [PMID: 33658070 PMCID: PMC7927268 DOI: 10.1186/s13018-021-02321-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background When multicystic vesicles (precursors of exosomes) are formed in cells, there are two results. One is decomposition by lysosomes, and the other is the generation of exosomes that are transported out through the transmembrane. On the other hand, M2 macrophages promote the formation of local vascularization and provide necessary support for the repair of bone defects. To provide a new idea for the treatment of bone defects, the purpose of our study was to investigate the effect of WKYMVm (Trp-Lys-Tyr-Met-Val-D-Met-NH2) peptide on the secretion of exosomes from murine bone marrow-derived MSCs (mBMSCs) and the effect of exosomes on the polarization of M2 macrophages. Methods The WKYMVm peptide was used to activate the formyl peptide receptor 2 (FPR2) pathway in mBMSCs. First, we used Cell Counting Kit-8 (CCK-8) to detect the cytotoxic effect of WKYMVm peptide on mBMSCs. Second, we used western blotting (WB) and quantitative real-time polymerase chain reaction (qRT-PCR) to detect the expression of interferon stimulated gene 15 (ISG15) and transcription factor EB (TFEB) in mBMSCs. Then, we detected lysosomal activity using a lysozyme activity assay kit. Third, we used an exosome extraction kit and western blotting to detect the content of exosomes secreted by mBMSCs. Fourth, we used immunofluorescence and western blotting to count the number of polarized M2 macrophages. Finally, we used an inhibitor to block miRNA-146 in exosomes secreted by mBMSCs and counted the number of polarized M2 macrophages. Results We first found that the WKYMVm peptide had no toxic effect on mBMSCs at a concentration of 1 μmol/L. Second, we found that when the FPR2 pathway was activated by the WKYMVm peptide in mBMSCs, ISG15 and TFEB expression was decreased, leading to increased secretion of exosomes. We also found that lysosomal activity was decreased when the FPR2 pathway was activated by the WKYMVm peptide in mBMSCs. Third, we demonstrated that exosomes secreted by mBMSCs promote the polarization of M2 macrophages. Moreover, all these effects can be blocked by the WRWWWW (WRW4, H-Trp-Arg-Trp-Trp-Trp-Trp-OH) peptide, an inhibitor of the FPR2 pathway. Finally, we confirmed the effect of miRNA-146 in exosomes secreted by mBMSCs on promoting the polarization of M2 macrophages. Conclusion Our findings demonstrated the potential value of the WKYMVm peptide in promoting the secretion of exosomes by mBMSCs and eventually leading to M2 macrophage polarization. We believe that our study could provide a research basis for the clinical treatment of bone defects.
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5
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Pereira M, Ko JH, Logan J, Protheroe H, Kim KB, Tan ALM, Croucher PI, Park KS, Rotival M, Petretto E, Bassett JD, Williams GR, Behmoaras J. A trans-eQTL network regulates osteoclast multinucleation and bone mass. eLife 2020; 9:55549. [PMID: 32553114 PMCID: PMC7351491 DOI: 10.7554/elife.55549] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Functional characterisation of cell-type-specific regulatory networks is key to establish a causal link between genetic variation and phenotype. The osteoclast offers a unique model for interrogating the contribution of co-regulated genes to in vivo phenotype as its multinucleation and resorption activities determine quantifiable skeletal traits. Here we took advantage of a trans-regulated gene network (MMnet, macrophage multinucleation network) which we found to be significantly enriched for GWAS variants associated with bone-related phenotypes. We found that the network hub gene Bcat1 and seven other co-regulated MMnet genes out of 13, regulate bone function. Specifically, global (Pik3cb-/-, Atp8b2+/-, Igsf8-/-, Eml1-/-, Appl2-/-, Deptor-/-) and myeloid-specific Slc40a1 knockout mice displayed abnormal bone phenotypes. We report opposing effects of MMnet genes on bone mass in mice and osteoclast multinucleation/resorption in humans with strong correlation between the two. These results identify MMnet as a functionally conserved network that regulates osteoclast multinucleation and bone mass.
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Affiliation(s)
- Marie Pereira
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom.,Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Jeong-Hun Ko
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom.,Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - John Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Hayley Protheroe
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
| | | | - Peter I Croucher
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of NewSouth Wales Medicine, Sydney, Australia
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, United States
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Centre National de la Recherche Scientifique, UMR 2000, Paris, France
| | | | - Jh Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith Hospital, Imperial College London, London, United Kingdom
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6
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Ng AYH, Li Z, Jones MM, Yang S, Li C, Fu C, Tu C, Oursler MJ, Qu J, Yang S. Regulator of G protein signaling 12 enhances osteoclastogenesis by suppressing Nrf2-dependent antioxidant proteins to promote the generation of reactive oxygen species. eLife 2019; 8:e42951. [PMID: 31490121 PMCID: PMC6731062 DOI: 10.7554/elife.42951] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/28/2019] [Indexed: 02/06/2023] Open
Abstract
Regulators of G-protein Signaling are a conserved family of proteins required in various biological processes including cell differentiation. We previously demonstrated that Rgs12 is essential for osteoclast differentiation and its deletion in vivo protected mice against pathological bone loss. To characterize its mechanism in osteoclastogenesis, we selectively deleted Rgs12 in C57BL/6J mice targeting osteoclast precursors using LyzM-driven Cre mice or overexpressed Rgs12 in RAW264.7 cells. Rgs12 deletion in vivo led to an osteopetrotic phenotype evidenced by increased trabecular bone, decreased osteoclast number and activity but no change in osteoblast number and bone formation. Rgs12 overexpression increased osteoclast number and size, and bone resorption activity. Proteomics analysis of Rgs12-depleted osteoclasts identified an upregulation of antioxidant enzymes under the transcriptional regulation of Nrf2, the master regulator of oxidative stress. We confirmed an increase of Nrf2 activity and impaired reactive oxygen species production in Rgs12-deficient cells. Conversely, Rgs12 overexpression suppressed Nrf2 through a mechanism dependent on the 26S proteasome, and promoted RANKL-induced phosphorylation of ERK1/2 and NFκB, which was abrogated by antioxidant treatment. Our study therefore identified a novel role of Rgs12 in regulating Nrf2, thereby controlling cellular redox state and osteoclast differentiation.
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Affiliation(s)
- Andrew Ying Hui Ng
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Ziqing Li
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Megan M Jones
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
| | - Shuting Yang
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Chunyi Li
- Department of Oral BiologySchool of Dental Medicine, University at BuffaloBuffaloUnited States
| | - Chuanyun Fu
- Department of StomatologyShandong Provincial Hospital Affiliated to Shandong UniversityJinanChina
| | - Chengjian Tu
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical SciencesUniversity at BuffaloBuffaloUnited States
| | - Merry Jo Oursler
- Division of Endocrinology, Metabolism, Nutrition & DiabetesMayo ClinicRochesterUnited States
| | - Jun Qu
- New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Department of Pharmaceutical Science, School of Pharmacy and Pharmaceutical SciencesUniversity at BuffaloBuffaloUnited States
| | - Shuying Yang
- Department of Anatomy and Cell BiologySchool of Dental Medicine, University of PennsylvaniaPhiladelphiaUnited States
- The Penn Center for Musculoskeletal DisordersSchool of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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7
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Liu GT, Jiang JF, Liu XN, Jiang JZ, Sun L, Duan W, Li RM, Wang Y, Lecourieux D, Liu CH, Li SH, Wang LJ. New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses. HORTICULTURE RESEARCH 2019; 6:100. [PMID: 31666961 PMCID: PMC6804945 DOI: 10.1038/s41438-019-0183-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 °C, 40 °C, and 45 °C in comparison with the proteome profiles of plants grown at 25 °C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.
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Affiliation(s)
- Guo-Tian Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jian-Fu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xin-Na Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jin-Zhu Jiang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Rui-Min Li
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - David Lecourieux
- Universite´ de Bordeaux, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
- INRA, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Chong-Huai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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8
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Engelmann BW, Hsiao CJ, Blischak JD, Fourne Y, Khan Z, Ford M, Gilad Y. A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. Sci Rep 2018; 8:12106. [PMID: 30108239 PMCID: PMC6092387 DOI: 10.1038/s41598-018-30587-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/17/2018] [Indexed: 11/12/2022] Open
Abstract
Phosphorylation of proteins on serine, threonine, and tyrosine residues is a ubiquitous post-translational modification that plays a key part of essentially every cell signaling process. It is reasonable to assume that inter-individual variation in protein phosphorylation may underlie phenotypic differences, as has been observed for practically any other molecular regulatory phenotype. However, we do not know much about the extent of inter-individual variation in phosphorylation because it is quite challenging to perform a quantitative high throughput study to assess inter-individual variation in any post-translational modification. To test our ability to address this challenge with SILAC-based mass spectrometry, we quantified phosphorylation levels for three genotyped human cell lines within a nested experimental framework, and found that genetic background is the primary determinant of phosphoproteome variation. We uncovered multiple functional, biophysical, and genetic associations with germline driven phosphopeptide variation. Variants affecting protein levels or structure were among these associations, with the latter presenting, on average, a stronger effect. Interestingly, we found evidence that is consistent with a phosphopeptide variability buffering effect endowed from properties enriched within longer proteins. Because the small sample size in this 'pilot' study may limit the applicability of our genetic observations, we also undertook a thorough technical assessment of our experimental workflow to aid further efforts. Taken together, these results provide the foundation for future work to characterize inter-individual variation in post-translational modification levels and reveal novel insights into the nature of inter-individual variation in phosphorylation.
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Affiliation(s)
- Brett W Engelmann
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
- AbbVie, North Chicago, Illinois, USA.
| | | | - John D Blischak
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Yannick Fourne
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Zia Khan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Genentech, South San Francisco, California, USA
| | - Michael Ford
- MS Bioworks, LLC, 3950, Varsity Drive, Ann Arbor, Michigan, USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.
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9
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Ng AY, Tu C, Shen S, Xu D, Oursler MJ, Qu J, Yang S. Comparative Characterization of Osteoclasts Derived From Murine Bone Marrow Macrophages and RAW 264.7 Cells Using Quantitative Proteomics. JBMR Plus 2018; 2:328-340. [PMID: 30460336 PMCID: PMC6237207 DOI: 10.1002/jbm4.10058] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/26/2018] [Accepted: 05/07/2018] [Indexed: 12/29/2022] Open
Abstract
Osteoclasts are bone-resorbing cells differentiated from macrophage/monocyte precursors in response to macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL). In vitro models are principally based on primary bone marrow macrophages (BMMs), but RAW 264.7 cells are frequently used because they are widely available, easy to culture, and more amenable to genetic manipulation than primary cells. Increasing evidence, however, has shown that the vastly different origins of these two cell types may have important effects on cell behavior. In particular, M-CSF is a prerequisite for the differentiation of BMMs, by promoting survival and proliferation and priming the cells for RANKL induction. RAW 264.7 cells readily form osteoclasts in the presence of RANKL, but M-CSF is not required. Based on these key differences, we sought to understand their functional implications and how it might affect osteoclast differentiation and related signaling pathways. Using a robust and high-throughput proteomics strategy, we quantified the global protein changes in osteoclasts derived from BMMs and RAW 264.7 cells at 1, 3, and 5 days of differentiation. Data are available via ProteomeXchange with the identifier PXD009610. Correlation analysis of the proteomes demonstrated low concordance between the two cell types (R2 ≈ 0.13). Bioinformatics analysis indicate that RANKL-dependent signaling was intact in RAW 264.7 cells, but biological processes known to be dependent on M-CSF were significantly different, including cell cycle control, cytoskeletal organization, and apoptosis. RAW 264.7 cells exhibited constitutive activation of Erk and Akt that was dependent on the activity of Abelson tyrosine kinase, and the timing of Erk and Akt activation was significantly different between BMMs and RAW 264.7 cells. Our findings provide the first evidence for major discrepancies between BMMs and RAW 264.7 cells, indicating that careful consideration is needed when using the RAW 264.7 cell line for studying M-CSF-dependent signaling and functions. © 2018 American Society for Bone and Mineral Research. © 2018 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Andrew Yh Ng
- Department of Anatomy and Cell Biology School of Dental Medicine University of Pennsylvania Philadelphia PA USA.,Department of Oral Biology School of Dental Medicine University at Buffalo Buffalo NY USA.,New York State Center of Excellence in Bioinformatics and Life Sciences Buffalo NY USA
| | - Chengjian Tu
- New York State Center of Excellence in Bioinformatics and Life Sciences Buffalo NY USA.,Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences University at Buffalo NY USA
| | - Shichen Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences Buffalo NY USA.,Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences University at Buffalo NY USA
| | - Ding Xu
- Department of Oral Biology School of Dental Medicine University at Buffalo Buffalo NY USA
| | - Merry J Oursler
- Division of Endocrinology Metabolism, Nutrition, and Diabetes Mayo Clinic Rochester MN USA
| | - Jun Qu
- New York State Center of Excellence in Bioinformatics and Life Sciences Buffalo NY USA.,Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences University at Buffalo NY USA
| | - Shuying Yang
- Department of Anatomy and Cell Biology School of Dental Medicine University of Pennsylvania Philadelphia PA USA
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10
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Pereira M, Petretto E, Gordon S, Bassett JHD, Williams GR, Behmoaras J. Common signalling pathways in macrophage and osteoclast multinucleation. J Cell Sci 2018; 131:131/11/jcs216267. [PMID: 29871956 DOI: 10.1242/jcs.216267] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macrophage cell fusion and multinucleation are fundamental processes in the formation of multinucleated giant cells (MGCs) in chronic inflammatory disease and osteoclasts in the regulation of bone mass. However, this basic cell phenomenon is poorly understood despite its pathophysiological relevance. Granulomas containing multinucleated giant cells are seen in a wide variety of complex inflammatory disorders, as well as in infectious diseases. Dysregulation of osteoclastic bone resorption underlies the pathogenesis of osteoporosis and malignant osteolytic bone disease. Recent reports have shown that the formation of multinucleated giant cells and osteoclast fusion display a common molecular signature, suggesting shared genetic determinants. In this Review, we describe the background of cell-cell fusion and the similar origin of macrophages and osteoclasts. We specifically focus on the common pathways involved in osteoclast and MGC fusion. We also highlight potential approaches that could help to unravel the core mechanisms underlying bone and granulomatous disorders in humans.
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Affiliation(s)
- Marie Pereira
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City 33302, Taiwan.,Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, London W12 0NN, UK
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11
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Surdziel E, Clay I, Nigsch F, Thiemeyer A, Allard C, Hoffman G, Reece-Hoyes JS, Phadke T, Gambert R, Keller CG, Ludwig MG, Baumgarten B, Frederiksen M, Schübeler D, Seuwen K, Bouwmeester T, Fodor BD. Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization. PLoS One 2017; 12:e0183679. [PMID: 28837623 PMCID: PMC5570424 DOI: 10.1371/journal.pone.0183679] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 01/05/2023] Open
Abstract
Macrophages are key cell types of the innate immune system regulating host defense, inflammation, tissue homeostasis and cancer. Within this functional spectrum diverse and often opposing phenotypes are displayed which are dictated by environmental clues and depend on highly plastic transcriptional programs. Among these the 'classical' (M1) and 'alternative' (M2) macrophage polarization phenotypes are the best characterized. Understanding macrophage polarization in humans may reveal novel therapeutic intervention possibilities for chronic inflammation, wound healing and cancer. Systematic loss of function screening in human primary macrophages is limited due to lack of robust gene delivery methods and limited sample availability. To overcome these hurdles we developed cell-autonomous assays using the THP-1 cell line allowing genetic screens for human macrophage phenotypes. We screened 648 chromatin and signaling regulators with a pooled shRNA library for M1 and M2 polarization modulators. Validation experiments confirmed the primary screening results and identified OGT (O-linked N-acetylglucosamine (GlcNAc) transferase) as a novel mediator of M2 polarization in human macrophages. Our approach offers a possible avenue to utilize comprehensive genetic tools to identify novel candidate genes regulating macrophage polarization in humans.
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Affiliation(s)
- Ewa Surdziel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ieuan Clay
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Anke Thiemeyer
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Cyril Allard
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Gregory Hoffman
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - John S. Reece-Hoyes
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - Tanushree Phadke
- Novartis Institutes for Biomedical Research, Cambridge, United States of America
| | - Romain Gambert
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | | | | | | | - Dirk Schübeler
- Friedrich Miescher Institute for BioMedical Research, Basel, Switzerland
| | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Barna D. Fodor
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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12
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Papathanassiu AE, Ko JH, Imprialou M, Bagnati M, Srivastava PK, Vu HA, Cucchi D, McAdoo SP, Ananieva EA, Mauro C, Behmoaras J. BCAT1 controls metabolic reprogramming in activated human macrophages and is associated with inflammatory diseases. Nat Commun 2017; 8:16040. [PMID: 28699638 PMCID: PMC5510229 DOI: 10.1038/ncomms16040] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
Branched-chain aminotransferases (BCAT) are enzymes that initiate the catabolism of branched-chain amino acids (BCAA), such as leucine, thereby providing macromolecule precursors; however, the function of BCATs in macrophages is unknown. Here we show that BCAT1 is the predominant BCAT isoform in human primary macrophages. We identify ERG240 as a leucine analogue that blocks BCAT1 activity. Selective inhibition of BCAT1 activity results in decreased oxygen consumption and glycolysis. This decrease is associated with reduced IRG1 levels and itaconate synthesis, suggesting involvement of BCAA catabolism through the IRG1/itaconate axis within the tricarboxylic acid cycle in activated macrophages. ERG240 suppresses production of IRG1 and itaconate in mice and contributes to a less proinflammatory transcriptome signature. Oral administration of ERG240 reduces the severity of collagen-induced arthritis in mice and crescentic glomerulonephritis in rats, in part by decreasing macrophage infiltration. These results establish a regulatory role for BCAT1 in macrophage function with therapeutic implications for inflammatory conditions.
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Affiliation(s)
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | - Martha Imprialou
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | - Marta Bagnati
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | | | - Hong A. Vu
- Ergon Pharmaceuticals, LLC, P.O. Box 1001, Silver Spring, Maryland 20910, USA
| | - Danilo Cucchi
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Institute Pasteur, Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Stephen P. McAdoo
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Elitsa A. Ananieva
- Biochemistry and Nutrition, Des Moines University, Des Moines, Iowa 50312, USA
| | - Claudio Mauro
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
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13
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Chen Y, Nielsen J. Flux control through protein phosphorylation in yeast. FEMS Yeast Res 2017; 16:fow096. [PMID: 27797916 DOI: 10.1093/femsyr/fow096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 01/26/2023] Open
Abstract
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
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14
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Hulley PA, Bishop T, Vernet A, Schneider JE, Edwards JR, Athanasou NA, Knowles HJ. Hypoxia-inducible factor 1-alpha does not regulate osteoclastogenesis but enhances bone resorption activity via prolyl-4-hydroxylase 2. J Pathol 2017; 242:322-333. [PMID: 28418093 PMCID: PMC5518186 DOI: 10.1002/path.4906] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 12/12/2022]
Abstract
Osteogenic-angiogenic coupling is promoted by the hypoxia-inducible factor 1-alpha (HIF-1α) transcription factor, provoking interest in HIF activation as a therapeutic strategy to improve osteoblast mineralization and treat pathological osteolysis. However, HIF also enhances the bone-resorbing activity of mature osteoclasts. It is therefore essential to determine the full effect(s) of HIF on both the formation and the bone-resorbing function of osteoclasts in order to understand how they might respond to such a strategy. Expression of HIF-1α mRNA and protein increased during osteoclast differentiation from CD14+ monocytic precursors, additionally inducing expression of the HIF-regulated glycolytic enzymes. However, HIF-1α siRNA only moderately affected osteoclast differentiation, accelerating fusion of precursor cells. HIF induction by inhibition of the regulatory prolyl-4-hydroxylase (PHD) enzymes reduced osteoclastogenesis, but was confirmed to enhance bone resorption by mature osteoclasts. Phd2+/- murine osteoclasts also exhibited enhanced bone resorption, associated with increased expression of resorption-associated Acp5, in comparison with wild-type cells from littermate controls. Phd3-/- bone marrow precursors displayed accelerated early fusion, mirroring results with HIF-1α siRNA. In vivo, Phd2+/- and Phd3-/- mice exhibited reduced trabecular bone mass, associated with reduced mineralization by Phd2+/- osteoblasts. These data indicate that HIF predominantly functions as a regulator of osteoclast-mediated bone resorption, with little effect on osteoclast differentiation. Inhibition of HIF might therefore represent an alternative strategy to treat diseases characterized by pathological levels of osteolysis. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Philippa A Hulley
- Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Tammie Bishop
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aude Vernet
- BHF Experimental MR Unit, University of Oxford, Oxford, UK
| | | | - James R Edwards
- Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Nick A Athanasou
- Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, Nuffield Orthopaedic Centre, University of Oxford, Oxford, UK
| | - Helen J Knowles
- Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
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15
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Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function. Genetics 2017; 206:1139-1151. [PMID: 28450461 PMCID: PMC5499168 DOI: 10.1534/genetics.116.197376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
Crescentic glomerulonephritis (Crgn) is a complex disorder where macrophage activity and infiltration are significant effector causes. In previous linkage studies using the uniquely susceptible Wistar Kyoto (WKY) rat strain, we have identified multiple crescentic glomerulonephritis QTL (Crgn) and positionally cloned genes underlying Crgn1 and Crgn2, which accounted for 40% of total variance in glomerular inflammation. Here, we have generated a backcross (BC) population (n = 166) where Crgn1 and Crgn2 were genetically fixed and found significant linkage to glomerular crescents on chromosome 2 (Crgn8, LOD = 3.8). Fine mapping analysis by integration with genome-wide expression QTLs (eQTLs) from the same BC population identified ceruloplasmin (Cp) as a positional eQTL in macrophages but not in serum. Liquid chromatography-tandem mass spectrometry confirmed Cp as a protein QTL in rat macrophages. WKY macrophages overexpress Cp and its downregulation by RNA interference decreases markers of glomerular proinflammatory macrophage activation. Similarly, short incubation with Cp results in a strain-dependent macrophage polarization in the rat. These results suggest that genetically determined Cp levels can alter susceptibility to Crgn through macrophage function and propose a new role for Cp in early macrophage activation.
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16
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Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLoS Comput Biol 2017; 13:e1005432. [PMID: 28306714 PMCID: PMC5376343 DOI: 10.1371/journal.pcbi.1005432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/31/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk) protein, a well-characterized key player in immune cell signaling, was surprisingly first shown by our group to exhibit an onco-suppressive function in mammary epithelial cells and corroborated by many other studies, but the molecular mechanisms of this function remain largely unsolved. Based on existing proteomic data, we report here the generation of an interaction-based network of signaling pathways controlled by Syk in breast cancer cells. Pathway enrichment of the Syk targets previously identified by quantitative phospho-proteomics indicated that Syk is engaged in cell adhesion, motility, growth and death. Using the components and interactions of these pathways, we bootstrapped the reconstruction of a comprehensive network covering Syk signaling in breast cancer cells. To generate in silico hypotheses on Syk signaling propagation, we developed a method allowing to rank paths between Syk and its targets. We first annotated the network according to experimental datasets. We then combined shortest path computation with random walk processes to estimate the importance of individual interactions and selected biologically relevant pathways in the network. Molecular and cell biology experiments allowed to distinguish candidate mechanisms that underlie the impact of Syk on the regulation of cortactin and ezrin, both involved in actin-mediated cell adhesion and motility. The Syk network was further completed with the results of our biological validation experiments. The resulting Syk signaling sub-networks can be explored via an online visualization platform.
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17
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A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation. Genetics 2017; 205:1443-1458. [PMID: 28213474 PMCID: PMC5378105 DOI: 10.1534/genetics.116.195008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/03/2017] [Indexed: 12/13/2022] Open
Abstract
Whole-genome bisulphite sequencing (WGBS) can identify important methylation differences between diseased and healthy samples. However, results from... DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome while taking into account the distance between CpG sites as a covariate. Our simulation study shows that ABBA has greater power to detect DMRs than existing methods, providing an accurate identification of DMRs in the large majority of simulated cases. To empirically demonstrate the method’s efficacy in generating biological hypotheses, we performed WGBS of primary macrophages derived from an experimental rat system of glomerulonephritis and used ABBA to identify >1000 disease-associated DMRs. Investigation of these DMRs revealed differential DNA methylation localized to a 600 bp region in the promoter of the Ifitm3 gene. This was confirmed by ChIP-seq and RNA-seq analyses, showing differential transcription factor binding at the Ifitm3 promoter by JunD (an established determinant of glomerulonephritis), and a consistent change in Ifitm3 expression. Our ABBA analysis allowed us to propose a new role for Ifitm3 in the pathogenesis of glomerulonephritis via a mechanism involving promoter hypermethylation that is associated with Ifitm3 repression in the rat strain susceptible to glomerulonephritis.
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18
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Moreno-Moral A, Pesce F, Behmoaras J, Petretto E. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease. Methods Mol Biol 2017; 1488:337-362. [PMID: 27933533 DOI: 10.1007/978-1-4939-6427-7_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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19
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Segeletz S, Hoflack B. Proteomic approaches to study osteoclast biology. Proteomics 2016; 16:2545-2556. [PMID: 27350065 DOI: 10.1002/pmic.201500519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/13/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Abstract
Bone is a dynamic tissue whose remodeling throughout life is orchestrated by repeated cycles of destruction mediated by osteoclasts and rebuilding by osteoblasts. Current understanding of osteoclast biology has largely relied on the generation of knockout mice exhibiting an abnormal bone phenotype. This has provided a better understanding of osteoclast biology and the key proteins that support osteoclast function. However, mouse models alone do not provide an integrated view on protein networks and post-translational modifications that might be important for osteoclast function. During the past years, a number of MS-based quantitative methods have been developed to investigate the complexity of biological systems. This review will summarize how such approaches have contributed to the understanding of osteoclast differentiation and function.
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Affiliation(s)
- Sandra Segeletz
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Bernard Hoflack
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany.
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20
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Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC. Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol Cell Proteomics 2015; 15:692-702. [PMID: 26635363 DOI: 10.1074/mcp.o115.052266] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 12/24/2022] Open
Abstract
A robust method was developed and optimized for enrichment and quantitative analysis of posttranslational modifications (PTMs) in serum/plasma samples by combining immunoaffinity purification and LC-MS/MS without depletion of abundant proteins. The method was used to survey serum samples of patients with acute myeloid leukemia (AML), breast cancer (BC), and nonsmall cell lung cancer (NSCLC). Peptides were identified from serum samples containing phosphorylation, acetylation, lysine methylation, and arginine methylation. Of the PTMs identified, lysine acetylation (AcK) and arginine mono-methylation (Rme) were more prevalent than other PTMs. Label-free quantitative analysis of AcK and Rme peptides was performed for sera from AML, BC, and NSCLC patients. Several AcK and Rme sites showed distinct abundance distribution patterns across the three cancer types. The identification and quantification of posttranslationally modified peptides in serum samples reported here can be used for patient profiling and biomarker discovery research.
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Affiliation(s)
- Hongbo Gu
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jian Min Ren
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Xiaoying Jia
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Tyler Levy
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Klarisa Rikova
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Vicky Yang
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Kimberly A Lee
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Matthew P Stokes
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
| | - Jeffrey C Silva
- From the § Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923
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21
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Behmoaras J, Diaz AG, Venda L, Ko JH, Srivastava P, Montoya A, Faull P, Webster Z, Moyon B, Pusey CD, Abraham DJ, Petretto E, Cook TH, Aitman TJ. Macrophage epoxygenase determines a profibrotic transcriptome signature. THE JOURNAL OF IMMUNOLOGY 2015; 194:4705-4716. [PMID: 25840911 DOI: 10.4049/jimmunol.1402979] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/03/2015] [Indexed: 12/20/2022]
Abstract
Epoxygenases belong to the cytochrome P450 family. They generate epoxyeicosatrienoic acids, which are known to have anti-inflammatory effects, but little is known about their role in macrophage function. By high-throughput sequencing of RNA in primary macrophages derived from rodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major rat macrophage epoxygenase Cyp2j4 (ortholog of human CYP2J2) resulted in reduced epoxyeicosatrienoic acid synthesis. Cyp2j4(-/-) macrophages have relatively increased peroxisome proliferator-activated receptor-γ levels and show a profibrotic transcriptome, displaying overexpression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript. Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the in vitro findings, Cyp2j4(-/-) rats show upregulation of type I collagen following unilateral ureter obstruction of the kidney, and quantitative proteomics analysis (liquid chromatography-tandem mass spectrometry) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a profibrotic macrophage transcriptome that could have implications in various inflammatory conditions, depending on macrophage function.
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Affiliation(s)
- Jacques Behmoaras
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, W12 0NN, London, UK
| | - Ana Garcia Diaz
- Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Lara Venda
- Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, W12 0NN, London, UK
| | - Prashant Srivastava
- Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK and Duke-NUS Graduate Medical School Singapore. 8 College Road, 169857 Singapore, Republic of Singapore
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Peter Faull
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Zoe Webster
- ES Cell and Transgenics Facility, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Ben Moyon
- ES Cell and Transgenics Facility, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK
| | - Charles D Pusey
- Renal Section, Department of Medicine, Imperial College London, Hammersmith Campus, London, UK
| | - David J Abraham
- Centre for Rheumatology & Connective Tissue Diseases, University College London Medical School, London, UK
| | - Enrico Petretto
- Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK and Duke-NUS Graduate Medical School Singapore. 8 College Road, 169857 Singapore, Republic of Singapore
| | - Terence H Cook
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, W12 0NN, London, UK
| | - Timothy J Aitman
- Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, W12 0NN, UK.,Institute of Genetics & Molecular Medicine, University of Edinburgh, EH4 2XU, UK
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