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Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M. Structure and interactions of the endogenous human Commander complex. Nat Struct Mol Biol 2024; 31:925-938. [PMID: 38459129 PMCID: PMC11189303 DOI: 10.1038/s41594-024-01246-1] [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: 05/31/2023] [Accepted: 01/19/2024] [Indexed: 03/10/2024]
Abstract
The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.
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Affiliation(s)
- Saara Laulumaa
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
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2
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Leneva N, Kovtun O. The commander complex is the Swiss Army knife of endosomal trafficking. Nat Struct Mol Biol 2024; 31:856-858. [PMID: 38783077 DOI: 10.1038/s41594-024-01326-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Affiliation(s)
- Natalya Leneva
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Oleksiy Kovtun
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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3
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Selheim F, Aasebø E, Reikvam H, Bruserud Ø, Hernandez-Valladares M. Monocytic Differentiation of Human Acute Myeloid Leukemia Cells: A Proteomic and Phosphoproteomic Comparison of FAB-M4/M5 Patients with and without Nucleophosmin 1 Mutations. Int J Mol Sci 2024; 25:5080. [PMID: 38791118 PMCID: PMC11121526 DOI: 10.3390/ijms25105080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Even though morphological signs of differentiation have a minimal impact on survival after intensive cytotoxic therapy for acute myeloid leukemia (AML), monocytic AML cell differentiation (i.e., classified as French/American/British (FAB) subtypes M4/M5) is associated with a different responsiveness both to Bcl-2 inhibition (decreased responsiveness) and possibly also bromodomain inhibition (increased responsiveness). FAB-M4/M5 patients are heterogeneous with regard to genetic abnormalities, even though monocytic differentiation is common for patients with Nucleophosmin 1 (NPM1) insertions/mutations; to further study the heterogeneity of FAB-M4/M5 patients we did a proteomic and phosphoproteomic comparison of FAB-M4/M5 patients with (n = 13) and without (n = 12) NPM1 mutations. The proteomic profile of NPM1-mutated FAB-M4/M5 patients was characterized by increased levels of proteins involved in the regulation of endocytosis/vesicle trafficking/organellar communication. In contrast, AML cells without NPM1 mutations were characterized by increased levels of several proteins involved in the regulation of cytoplasmic translation, including a large number of ribosomal proteins. The phosphoproteomic differences between the two groups were less extensive but reflected similar differences. To conclude, even though FAB classification/monocytic differentiation are associated with differences in responsiveness to new targeted therapies (e.g., Bcl-2 inhibition), our results shows that FAB-M4/M5 patients are heterogeneous with regard to important biological characteristics of the leukemic cells.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
| | - Håkon Reikvam
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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Hicks C, Gardner J, Eiger DS, Camarda ND, Pham U, Dhar S, Rodriguez H, Chundi A, Rajagopal S. ACKR3 Proximity Labeling Identifies Novel G protein- and β-arrestin-independent GPCR Interacting Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577545. [PMID: 38410489 PMCID: PMC10896341 DOI: 10.1101/2024.01.27.577545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The canonical paradigm of GPCR signaling recognizes G proteins and β-arrestins as the two primary transducers that promote GPCR signaling. Recent evidence suggests the atypical chemokine receptor 3 (ACKR3) does not couple to G proteins, and β-arrestins are dispensable for some of its functions. Here, we employed proximity labeling to identify proteins that interact with ACKR3 in cells devoid of β-arrestin. We identified proteins involved in the endocytic machinery and evaluated a subset of proteins conserved across several GPCR-based proximity labeling experiments. We discovered that the bone morphogenic protein 2-inducible kinase (BMP2K) interacts with many different GPCRs with varying dependency on β-arrestin. Together, our work highlights the existence of modulators that can act independently of G proteins and β-arrestins to regulate GPCR signaling and provides important evidence for other targets that may regulate GPCR signaling.
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Affiliation(s)
- Chloe Hicks
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia Gardner
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dylan Scott Eiger
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02215, USA
| | - Nicholas D. Camarda
- Genetics, Molecular, and Cellular Biology Program, Tufts Graduate School of Biomedical Sciences, Boston, MA, 02111, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Saisha Dhar
- Trinity College, Duke University, Durham, NC, 27710, USA
| | | | - Anand Chundi
- Pratt School of Engineering, Duke University, Durham, NC, 27710, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
- Department of Medicine, Duke University, Durham, NC, 27710, USA
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Hancock JL, Kalimutho M, Straube J, Lim M, Gresshoff I, Saunus JM, Lee JS, Lakhani SR, Simpson KJ, Bush AI, Anderson RL, Khanna KK. COMMD3 loss drives invasive breast cancer growth by modulating copper homeostasis. J Exp Clin Cancer Res 2023; 42:90. [PMID: 37072858 PMCID: PMC10111822 DOI: 10.1186/s13046-023-02663-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Despite overall improvement in breast cancer patient outcomes from earlier diagnosis and personalised treatment approaches, some patients continue to experience recurrence and incurable metastases. It is therefore imperative to understand the molecular changes that allow transition from a non-aggressive state to a more aggressive phenotype. This transition is governed by a number of factors. METHODS As crosstalk with extracellular matrix (ECM) is critical for tumour cell growth and survival, we applied high throughput shRNA screening on a validated '3D on-top cellular assay' to identify novel growth suppressive mechanisms. RESULTS A number of novel candidate genes were identified. We focused on COMMD3, a previously poorly characterised gene that suppressed invasive growth of ER + breast cancer cells in the cellular assay. Analysis of published expression data suggested that COMMD3 is normally expressed in the mammary ducts and lobules, that expression is lost in some tumours and that loss is associated with lower survival probability. We performed immunohistochemical analysis of an independent tumour cohort to investigate relationships between COMMD3 protein expression, phenotypic markers and disease-specific survival. This revealed an association between COMMD3 loss and shorter survival in hormone-dependent breast cancers and in particularly luminal-A-like tumours (ER+/Ki67-low; 10-year survival probability 0.83 vs. 0.73 for COMMD3-positive and -negative cases, respectively). Expression of COMMD3 in luminal-A-like tumours was directly associated with markers of luminal differentiation: c-KIT, ELF5, androgen receptor and tubule formation (the extent of normal glandular architecture; p < 0.05). Consistent with this, depletion of COMMD3 induced invasive spheroid growth in ER + breast cancer cell lines in vitro, while Commd3 depletion in the relatively indolent 4T07 TNBC mouse cell line promoted tumour expansion in syngeneic Balb/c hosts. Notably, RNA sequencing revealed a role for COMMD3 in copper signalling, via regulation of the Na+/K+-ATPase subunit, ATP1B1. Treatment of COMMD3-depleted cells with the copper chelator, tetrathiomolybdate, significantly reduced invasive spheroid growth via induction of apoptosis. CONCLUSION Overall, we found that COMMD3 loss promoted aggressive behaviour in breast cancer cells.
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Affiliation(s)
- Janelle L Hancock
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Jasmin Straube
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Malcolm Lim
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Irma Gresshoff
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Jodi M Saunus
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Jason S Lee
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Sunil R Lakhani
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology and the Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashley I Bush
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
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Essletzbichler P, Sedlyarov V, Frommelt F, Soulat D, Heinz LX, Stefanovic A, Neumayer B, Superti-Furga G. A genome-wide CRISPR functional survey of the human phagocytosis molecular machinery. Life Sci Alliance 2023; 6:e202201715. [PMID: 36725334 PMCID: PMC9892931 DOI: 10.26508/lsa.202201715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Phagocytosis, the process by which cells engulf large particles, plays a vital role in driving tissue clearance and host defense. Its dysregulation is connected to autoimmunity, toxic accumulation of proteins, and increased risks for infections. Despite its importance, we lack full understanding of all molecular components involved in the process. To create a functional map in human cells, we performed a genome-wide CRISPRko FACS screen that identified 716 genes. Mapping those hits to a comprehensive protein-protein interaction network annotated for functional cellular processes allowed retrieval of protein complexes identified multiple times and detection of missing phagocytosis regulators. In addition to known components, such as the Arp2/3 complex, the vacuolar-ATPase-Rag machinery, and the Wave-2 complex, we identified and validated new phagocytosis-relevant functions, including the oligosaccharyltransferase complex (MAGT1/SLC58A1, DDOST, STT3B, and RPN2) and the hypusine pathway (eIF5A, DHPS, and DOHH). Overall, our phagocytosis network comprises elements of cargo uptake, shuffling, and biotransformation through the cell, providing a resource for the identification of potential novel drivers for diseases of the endo-lysosomal system. Our approach of integrating protein-protein interaction offers a broadly applicable way to functionally interpret genome-wide screens.
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Affiliation(s)
- Patrick Essletzbichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Didier Soulat
- Institute of Clinical Microbiology, Immunology and Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrijana Stefanovic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Benedikt Neumayer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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7
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Wang S, Liu Y, Li S, Chen Y, Liu Y, Yan J, Wu J, Li J, Wang L, Xiang R, Shi Y, Qin X, Yang S. COMMD3-Mediated Endosomal Trafficking of HER2 Inhibits the Progression of Ovarian Carcinoma. Mol Cancer Res 2023; 21:199-213. [PMID: 36445330 DOI: 10.1158/1541-7786.mcr-22-0333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
The dysregulated endocytic traffic of oncogenic receptors, such as the EGFR family especially HER2, contributes to the uncontrolled activation of the downstream oncogenic signaling and progression of various carcinomas, including 90% of ovarian carcinoma. However, the key regulators in the intracellular trafficking of HER2 and their impacts for cancer progression remain largely unknown. In this study, through a genome-wide CRISPR/Cas9 screening for key genes affecting the peritoneal disseminated metastasis of ovarian carcinoma, we identified a member of COMMD family, that is, COMMD3, as a key regulator in the endosomal trafficking of HER2. In the patients with high-grade serous ovarian carcinoma (HGSOC), the expression of COMMD3 is dramatically decreased in the peritoneal disseminated ovarian carcinoma cells comparing with that in the primary ovarian carcinoma cells. COMMD3 greatly inhibits the proliferation, migration, and epithelial-mesenchymal transition (EMT) of HGSOC cells, and dramatically suppresses the tumor growth, the formation of malignant ascites, and the peritoneal dissemination of cancer cells in the orthotopic murine model of HGSOC. Further transcriptome analysis reveals that silencing COMMD3 boosts the activation of HER2 downstream signaling. As a component in the Retriever-associated COMMD/CCDC22/CCDC93 complex responsible for the recognition and recycling of membrane receptors, COMMD3 physically interacts with HER2 for directing it to the slow recycling pathway, leading to the attenuated downstream tumor-promoting signaling. IMPLICATIONS Collectively, this study reveals a novel HER2 inactivation mechanism with a high value for the clinic diagnosis of new ovarian carcinoma types and the design of new therapeutic strategy.
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Affiliation(s)
- Shiqing Wang
- The School of Medicine, Nankai University, Tianjin, China
- Department of Oncology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuxin Liu
- The School of Medicine, Nankai University, Tianjin, China
| | - Siyu Li
- The School of Medicine, Nankai University, Tianjin, China
| | - Yanan Chen
- The School of Medicine, Nankai University, Tianjin, China
| | - Yanhua Liu
- The School of Medicine, Nankai University, Tianjin, China
| | - Jie Yan
- The School of Medicine, Nankai University, Tianjin, China
| | - Jiayi Wu
- The School of Medicine, Nankai University, Tianjin, China
| | - Jia Li
- The School of Medicine, Nankai University, Tianjin, China
| | - Longlong Wang
- The School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- The School of Medicine, Nankai University, Tianjin, China
| | - Yi Shi
- The School of Medicine, Nankai University, Tianjin, China
| | - Xuan Qin
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Shuang Yang
- The School of Medicine, Nankai University, Tianjin, China
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