1
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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2
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Han Y, Dong Q, Liu T, Chen X, Yu C, Zhang Y. The novel mechanism of Med12-mediated drug resistance in a TGFBR2-independent manner. Biochem Biophys Res Commun 2022; 610:1-7. [PMID: 35461070 DOI: 10.1016/j.bbrc.2022.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Inevitable emergence of drug resistance is the biggest hurdle to both chemotherapies and targeted therapies. Understanding the resistance mechanisms will contribute to identification of biomarkers for predicting response to therapy and design new therapeutic strategies to overcome drug resistance in human cancers. The type II transforming growth factor (TGF)-β receptor gene (TGFBR2) is frequently frameshift mutated in several cancer types, especially in colorectal, endometrium and gastric cancers cells. Here, we found that Med12, a component of the transcriptional mediator complex, plays a role in modulating chemosensitivity in TGFBR2 deficient cancer cells. Loss of Med12 leads to chemoresistance in multiple TGFBR2 deficient cancer cells. Interestingly, RNA sequencing data revealed that interferon IFN-related DNA damage resistance signature (IRDS) is upregulated in Med12 knockdown cancer cells. And the expression of IRDS pattern is negatively correlated with chemosensitivity. Therefore, our study identifies a novel mechanism of Med12-mediated drug resistance, which is a TGFBR-independent manner.
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Affiliation(s)
- Yumin Han
- The CAS_Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine & Chinese Academy of Sciences, Shanghai, 200031, China; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Qian Dong
- Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, 518000, China
| | - Tingting Liu
- The CAS_Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine & Chinese Academy of Sciences, Shanghai, 200031, China; Central Research Institute, Shanghai Pharmaceuticals Holding Co. Ltd, Shanghai, 201203, China
| | - Xiaomin Chen
- The CAS_Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine & Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chunhong Yu
- The CAS_Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine & Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yongfeng Zhang
- The CAS_Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Jiao Tong University School of Medicine & Chinese Academy of Sciences, Shanghai, 200031, China.
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3
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Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLife 2021; 10:75415. [PMID: 34898428 PMCID: PMC8747517 DOI: 10.7554/elife.75415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.
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Affiliation(s)
- Ganna Reint
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Zhuokun Li
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Kornel Labun
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Salla Keskitalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Inkeri Soppa
- Centre for Molecular Medicine, University of Oslo, Oslo, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eero Tolo
- Faculty of Social Sciences, University of Helsinki, Oslo, Finland
| | | | - Leonardo A Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Xian Hu
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Diana L Bordin
- Department of Clinical Molecular Biology, Akershus University Hospital, Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eivind Valen
- Center for Biotechnology, University of Bergen, Bergen, Norway
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markku Varjosalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emma Haapaniemi
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
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4
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Kumar D, Lak B, Suntio T, Vihinen H, Belevich I, Viita T, Xiaonan L, Vartiainen A, Vartiainen M, Varjosalo M, Jokitalo E. RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy. Mol Biol Cell 2021; 32:1158-1170. [PMID: 33826365 PMCID: PMC8351555 DOI: 10.1091/mbc.e20-06-0409] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1/Yop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes.
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Affiliation(s)
| | - Behnam Lak
- Cell and Tissue Dynamics Research Program
| | | | - Helena Vihinen
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
| | - Ilya Belevich
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
| | | | - Liu Xiaonan
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Markku Varjosalo
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Cell and Tissue Dynamics Research Program.,Electron Microscopy Unit, and
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5
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Targeting nuclear import and export in hematological malignancies. Leukemia 2020; 34:2875-2886. [PMID: 32624581 PMCID: PMC7584478 DOI: 10.1038/s41375-020-0958-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
The transport of proteins across the nuclear membrane is a highly regulated process, essential for the cell function. This transport is actively mediated by members of the karyopherin family, termed importins, or exportins, depending on the direction of transport. These proteins play an active part in tumorigenesis, through aberrant localization of their cargoes, which include oncogenes, tumor-suppressor genes and mediators of key signal transduction pathways. Overexpression of importins and exportins is reported in many malignancies, with implications in cell growth and viability, differentiation, drug resistance, and tumor microenvironment. Given their broad significance across tumors and pathways, much effort is being put to develop specific inhibitors as a novel anticancer therapeutics. Already, selinexor, a specific inhibitor of exportin-1 (XPO1), is approved for clinical use. This review will focus on the role of importins and exportins in hematological malignancies. We will discuss current preclinical and clinical data on importins and exportins, and demonstrate how our growing understanding of their functions has identified new therapeutic targets.
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6
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Hietamäki J, Gregory LC, Ayoub S, Iivonen AP, Vaaralahti K, Liu X, Brandstack N, Buckton AJ, Laine T, Känsäkoski J, Hero M, Miettinen PJ, Varjosalo M, Wakeling E, Dattani MT, Raivio T. Loss-of-Function Variants in TBC1D32 Underlie Syndromic Hypopituitarism. J Clin Endocrinol Metab 2020; 105:dgaa078. [PMID: 32060556 PMCID: PMC7138537 DOI: 10.1210/clinem/dgaa078] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
Abstract
CONTEXT Congenital pituitary hormone deficiencies with syndromic phenotypes and/or familial occurrence suggest genetic hypopituitarism; however, in many such patients the underlying molecular basis of the disease remains unknown. OBJECTIVE To describe patients with syndromic hypopituitarism due to biallelic loss-of-function variants in TBC1D32, a gene implicated in Sonic Hedgehog (Shh) signaling. SETTING Referral center. PATIENTS A Finnish family of 2 siblings with panhypopituitarism, absent anterior pituitary, and mild craniofacial dysmorphism, and a Pakistani family with a proband with growth hormone deficiency, anterior pituitary hypoplasia, and developmental delay. INTERVENTIONS The patients were investigated by whole genome sequencing. Expression profiling of TBC1D32 in human fetal brain was performed through in situ hybridization. Stable and dynamic protein-protein interaction partners of TBC1D32 were investigated in HEK cells followed by mass spectrometry analyses. MAIN OUTCOME MEASURES Genetic and phenotypic features of patients with biallelic loss-of-function mutations in TBC1D32. RESULTS The Finnish patients harboured compound heterozygous loss-of-function variants (c.1165_1166dup p.(Gln390Phefs*32) and c.2151del p.(Lys717Asnfs*29)) in TBC1D32; the Pakistani proband carried a known pathogenic homozygous TBC1D32 splice-site variant c.1372 + 1G > A p.(Arg411_Gly458del), as did a fetus with a cleft lip and partial intestinal malrotation from a terminated pregnancy within the same pedigree. TBC1D32 was expressed in the developing hypothalamus, Rathke's pouch, and areas of the hindbrain. TBC1D32 interacted with proteins implicated in cilium assembly, Shh signaling, and brain development. CONCLUSIONS Biallelic TBC1D32 variants underlie syndromic hypopituitarism, and the underlying mechanism may be via disrupted Shh signaling.
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Affiliation(s)
- Johanna Hietamäki
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Louise C Gregory
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sandy Ayoub
- North West Thames Regional Genetic Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Anna-Pauliina Iivonen
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi Vaaralahti
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology & HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Brandstack
- Department of Radiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Andrew J Buckton
- London North Genomic Laboratory Hub, Great Ormond Street Hospital NHS Trust, London, UK
| | - Tiina Laine
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Johanna Känsäkoski
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Hero
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Päivi J Miettinen
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology & HiLIFE, University of Helsinki, Helsinki, Finland
| | - Emma Wakeling
- North West Thames Regional Genetic Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Mehul T Dattani
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular Basis of Rare Diseases Section, Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Endocrinology, Great Ormond Street Hospital for Children, London, UK
| | - Taneli Raivio
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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7
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Zhang S, O'Regan R, Xu W. The emerging role of mediator complex subunit 12 in tumorigenesis and response to chemotherapeutics. Cancer 2019; 126:939-948. [PMID: 31869450 DOI: 10.1002/cncr.32672] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022]
Abstract
Transcriptional dysregulation induced by disease-defining genetic alterations of proteins in transcriptional machinery is a key feature of cancers. Mediator complex subunit 12 (MED12) is the central architectural subunit in the kinase module of Mediator, a large transcriptional regulatory complex that controls essential steps of transcription. Emerging evidence links deregulated MED12 to human cancers. MED12 is frequently mutated in benign tumors and cancers. Although the missense mutations of MED12 in benign tumors disrupt the kinase activity of Mediator, MED12 mutations in cancers could eliminate the interaction between Mediator complex and RNA polymerase II, leading to severe transcriptional misregulation. Aberrant expression of MED12 is associated with the prognosis of various types of human cancers. Loss of MED12 function has been associated with the development of resistance to chemotherapeutics. Moreover, MED12 is modified by posttranscriptional regulations. Arginine methylation of MED12 has been shown to regulate MED12-mediated transcriptional regulation and response to chemotherapeutics in human cancer cell lines. In this mini-review, the authors provide an overview of the roles of MED12 in the development of benign and malignant tumors as well as its roles in chemoresistance. The studies of MED12 exemplify that aberrant transcriptional programming is a therapeutic vulnerability for certain types of cancer.
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Affiliation(s)
- Shengjie Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin.,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Ruth O'Regan
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
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8
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Keskitalo S, Haapaniemi E, Einarsdottir E, Rajamäki K, Heikkilä H, Ilander M, Pöyhönen M, Morgunova E, Hokynar K, Lagström S, Kivirikko S, Mustjoki S, Eklund K, Saarela J, Kere J, Seppänen MRJ, Ranki A, Hannula-Jouppi K, Varjosalo M. Novel TMEM173 Mutation and the Role of Disease Modifying Alleles. Front Immunol 2019; 10:2770. [PMID: 31866997 PMCID: PMC6907089 DOI: 10.3389/fimmu.2019.02770] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 02/02/2023] Open
Abstract
Upon binding to pathogen or self-derived cytosolic nucleic acids cyclic GMP-AMP synthase (cGAS) triggers the production of cGAMP that further activates transmembrane protein STING. Upon activation STING translocates from ER via Golgi to vesicles. Monogenic STING gain-of-function mutations cause early-onset type I interferonopathy, with disease presentation ranging from fatal vasculopathy to mild chilblain lupus. Molecular mechanisms underlying the variable phenotype-genotype correlation are presently unclear. Here, we report a novel gain-of-function G207E STING mutation causing a distinct phenotype with alopecia, photosensitivity, thyroid dysfunction, and features of STING-associated vasculopathy with onset in infancy (SAVI), such as livedo reticularis, skin vasculitis, nasal septum perforation, facial erythema, and bacterial infections. Polymorphism in TMEM173 and IFIH1 showed variable penetrance in the affected family, implying contribution to varying phenotype spectrum. The G207E mutation constitutively activates inflammation-related pathways in vitro, and causes aberrant interferon signature and inflammasome activation in patient PBMCs. Treatment with Janus kinase 1 and 2 (JAK1/2) inhibitor baricitinib was beneficiary for a vasculitic ulcer, induced hair regrowth and improved overall well-being in one patient. Protein-protein interactions propose impaired cellular trafficking of G207E mutant. These findings reveal the molecular landscape of STING and propose common polymorphisms in TMEM173 and IFIH1 as likely modifiers of the phenotype.
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Affiliation(s)
- Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Emma Haapaniemi
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, Helsinki, Finland.,Department of Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kristiina Rajamäki
- Faculty of Medicine, University of Helsinki, Clinicum, Helsinki, Finland
| | - Hannele Heikkilä
- Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Mette Ilander
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Minna Pöyhönen
- Department of Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Ekaterina Morgunova
- Department of Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Kati Hokynar
- Clinical Research Institute HUCH Ltd., Helsinki, Finland
| | - Sonja Lagström
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sirpa Kivirikko
- Department of Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Kari Eklund
- Faculty of Medicine, University of Helsinki, Clinicum, Helsinki, Finland.,Department of Rheumatology, Helsinki University Hospital, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Mikko R J Seppänen
- Rare Disease Center, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Immunodeficiency Unit, Inflammation Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Annamari Ranki
- Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Katariina Hannula-Jouppi
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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9
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Dominant TOM1 mutation associated with combined immunodeficiency and autoimmune disease. NPJ Genom Med 2019; 4:14. [PMID: 31263572 PMCID: PMC6597545 DOI: 10.1038/s41525-019-0088-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/04/2019] [Indexed: 01/19/2023] Open
Abstract
Mutations in several proteins functioning as endolysosomal components cause monogenic autoimmune diseases, of which pathogenesis is linked to increased endoplasmic reticulum stress, inefficient autophagy, and defective recycling of immune receptors. We report here a heterozygous TOM1 p.G307D missense mutation, detected by whole-exome sequencing, in two related patients presenting with early-onset autoimmunity, antibody deficiency, and features of combined immunodeficiency. The index patient suffered from recurrent respiratory tract infections and oligoarthritis since early teens, and later developed persistent low-copy EBV-viremia, as well as an antibody deficiency. Her infant son developed hypogammaglobulinemia, autoimmune enteropathy, interstitial lung disease, profound growth failure, and treatment-resistant psoriasis vulgaris. Consistent with previous knowledge on TOM1 protein function, we detected impaired autophagy and enhanced susceptibility to apoptosis in patient-derived cells. In addition, we noted diminished STAT and ERK1/2 signaling in patient fibroblasts, as well as poor IFN-γ and IL-17 secretion in T cells. The mutant TOM1 failed to interact with TOLLIP, a protein required for IL-1 recycling, PAMP signaling and autophagosome maturation, further strengthening the link between the candidate mutation and patient pathophysiology. In sum, we report here an identification of a novel gene, TOM1, associating with early-onset autoimmunity, antibody deficiency, and features of combined immunodeficiency. Other patient cases from unrelated families are needed to firmly establish a causal relationship between the genotype and the phenotype.
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10
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Li X, Liu M, Ji JY. Understanding Obesity as a Risk Factor for Uterine Tumors Using Drosophila. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1167:129-155. [PMID: 31520353 DOI: 10.1007/978-3-030-23629-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple large-scale epidemiological studies have identified obesity as an important risk factor for a variety of human cancers, particularly cancers of the uterus, gallbladder, kidney, liver, colon, and ovary, but there is much uncertainty regarding how obesity increases the cancer risks. Given that obesity has been consistently identified as a major risk factor for uterine tumors, the most common malignancies of the female reproductive system, we use uterine tumors as a pathological context to survey the relevant literature and propose a novel hypothesis: chronic downregulation of the cyclin-dependent kinase 8 (CDK8) module, composed of CDK8 (or its paralog CDK19), Cyclin C, MED12 (or MED12L), and MED13 (or MED13L), by elevated insulin or insulin-like growth factor signaling in obese women may increase the chances to dysregulate the activities of transcription factors regulated by the CDK8 module, thereby increasing the risk of uterine tumors. Although we focus on endometrial cancer and uterine leiomyomas (or fibroids), two major forms of uterine tumors, our model may offer additional insights into how obesity increases the risk of other types of cancers and diseases. To illustrate the power of model organisms for studying human diseases, here we place more emphasis on the findings obtained from Drosophila melanogaster.
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Affiliation(s)
- Xiao Li
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Mengmeng Liu
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, TX, USA.
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11
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Rajamäki K, Keskitalo S, Seppänen M, Kuismin O, Vähäsalo P, Trotta L, Väänänen A, Glumoff V, Keskitalo P, Kaarteenaho R, Jartti A, Hautala N, Jackson P, Nordström DC, Saarela J, Hautala T, Eklund KK, Varjosalo M. Haploinsufficiency of A20 impairs protein-protein interactome and leads into caspase-8-dependent enhancement of NLRP3 inflammasome activation. RMD Open 2018. [PMID: 30402268 DOI: 10.1136/rmdopen-2018-000740)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVES TNFAIP3 encodes A20 that negatively regulates nuclear factor kappa light chain enhancer of activated B cells (NF-κB), the major transcription factor coordinating inflammatory gene expression. TNFAIP3 polymorphisms have been linked with a spectrum of inflammatory and autoimmune diseases and, recently, loss-of-function mutations in A20 were found to cause a novel inflammatory disease 'haploinsufficiency of A20' (HA20). Here we describe a family with HA20 caused by a novel TNFAIP3 loss-of-function mutation and elucidate the upstream molecular mechanisms linking HA20 to dysregulation of NF-κB and the related inflammasome pathway. METHODS NF-κB activation was studied in a mutation-expressing cell line using luciferase reporter assay. Physical and close-proximity protein-protein interactions of wild-type and TNFAIP3 p.(Lys91*) mutant A20 were analysed using mass spectrometry. NF-κB -dependent transcription, cytokine secretion and inflammasome activation were compared in immune cells of the HA20 patients and control subjects. RESULTS The protein-protein interactome of p.(Lys91*) mutant A20 was severely impaired, including interactions with proteins regulating NF-κB activation, DNA repair responses and the NLR family pyrin domain containing 3 (NLRP3) inflammasome. The p.(Lys91*) mutant A20 failed to suppress NF-κB signalling, which led to increased NF-κB -dependent proinflammatory cytokine transcription. Functional experiments in the HA20 patients' immune cells uncovered a novel caspase-8-dependent mechanism of NLRP3 inflammasome hyperresponsiveness that mediated the excessive secretion of interleukin-1β and interleukin-18. CONCLUSIONS The current findings significantly deepen our understanding of the molecular mechanisms underlying HA20 and other diseases associated with reduced A20 expression or function, paving the way for future therapeutic targeting of the pathway.
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Affiliation(s)
- Kristiina Rajamäki
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mikko Seppänen
- Immunodeficiency Unit, Inflammation Center and Rare Diseases Center, Children's Hospital, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Paula Vähäsalo
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Luca Trotta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Väänänen
- Department of Infection Control, Lapland Central Hospital, Rovaniemi, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Paula Keskitalo
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Riitta Kaarteenaho
- Respiratory Diseases, Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Airi Jartti
- Department of Radiology, Oulu University Hospital, Oulu, Finland
| | - Nina Hautala
- Department of Ophthalmology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Päivi Jackson
- Department of Ophthalmology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Dan C Nordström
- Department of Medicine and Rehabilitation, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Timo Hautala
- Research Unit of Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Kari K Eklund
- Department of Rheumatology, Inflammation Center, Helsinki University and Helsinki University Hospital, Helsinki, Finland.,Research Institute, Invalid Foundation, Helsinki, Finland.,Orton Orthopaedic Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Rajamäki K, Keskitalo S, Seppänen M, Kuismin O, Vähäsalo P, Trotta L, Väänänen A, Glumoff V, Keskitalo P, Kaarteenaho R, Jartti A, Hautala N, Jackson P, Nordström DC, Saarela J, Hautala T, Eklund KK, Varjosalo M. Haploinsufficiency of A20 impairs protein-protein interactome and leads into caspase-8-dependent enhancement of NLRP3 inflammasome activation. RMD Open 2018; 4:e000740. [PMID: 30402268 PMCID: PMC6203104 DOI: 10.1136/rmdopen-2018-000740] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/03/2018] [Accepted: 09/07/2018] [Indexed: 01/11/2023] Open
Abstract
Objectives TNFAIP3 encodes A20 that negatively regulates nuclear factor kappa light chain enhancer of activated B cells (NF-κB), the major transcription factor coordinating inflammatory gene expression. TNFAIP3 polymorphisms have been linked with a spectrum of inflammatory and autoimmune diseases and, recently, loss-of-function mutations in A20 were found to cause a novel inflammatory disease ‘haploinsufficiency of A20’ (HA20). Here we describe a family with HA20 caused by a novel TNFAIP3 loss-of-function mutation and elucidate the upstream molecular mechanisms linking HA20 to dysregulation of NF-κB and the related inflammasome pathway. Methods NF-κB activation was studied in a mutation-expressing cell line using luciferase reporter assay. Physical and close-proximity protein–protein interactions of wild-type and TNFAIP3 p.(Lys91*) mutant A20 were analysed using mass spectrometry. NF-κB -dependent transcription, cytokine secretion and inflammasome activation were compared in immune cells of the HA20 patients and control subjects. Results The protein–protein interactome of p.(Lys91*) mutant A20 was severely impaired, including interactions with proteins regulating NF-κB activation, DNA repair responses and the NLR family pyrin domain containing 3 (NLRP3) inflammasome. The p.(Lys91*) mutant A20 failed to suppress NF-κB signalling, which led to increased NF-κB -dependent proinflammatory cytokine transcription. Functional experiments in the HA20 patients’ immune cells uncovered a novel caspase-8-dependent mechanism of NLRP3 inflammasome hyperresponsiveness that mediated the excessive secretion of interleukin-1β and interleukin-18. Conclusions The current findings significantly deepen our understanding of the molecular mechanisms underlying HA20 and other diseases associated with reduced A20 expression or function, paving the way for future therapeutic targeting of the pathway.
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Affiliation(s)
- Kristiina Rajamäki
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mikko Seppänen
- Immunodeficiency Unit, Inflammation Center and Rare Diseases Center, Children's Hospital, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Paula Vähäsalo
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Luca Trotta
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Väänänen
- Department of Infection Control, Lapland Central Hospital, Rovaniemi, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Paula Keskitalo
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Riitta Kaarteenaho
- Respiratory Diseases, Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Airi Jartti
- Department of Radiology, Oulu University Hospital, Oulu, Finland
| | - Nina Hautala
- Department of Ophthalmology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Päivi Jackson
- Department of Ophthalmology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Dan C Nordström
- Department of Medicine and Rehabilitation, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Timo Hautala
- Research Unit of Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Kari K Eklund
- Department of Rheumatology, Inflammation Center, Helsinki University and Helsinki University Hospital, Helsinki, Finland.,Research Institute, Invalid Foundation, Helsinki, Finland.,Orton Orthopaedic Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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13
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Konovalova S, Liu X, Manjunath P, Baral S, Neupane N, Hilander T, Yang Y, Balboa D, Terzioglu M, Euro L, Varjosalo M, Tyynismaa H. Redox regulation of GRPEL2 nucleotide exchange factor for mitochondrial HSP70 chaperone. Redox Biol 2018; 19:37-45. [PMID: 30098457 PMCID: PMC6089081 DOI: 10.1016/j.redox.2018.07.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are central organelles to cellular metabolism. Their function relies largely on nuclear-encoded proteins that must be imported from the cytosol, and thus the protein import pathways are important for the maintenance of mitochondrial proteostasis. Mitochondrial HSP70 (mtHsp70) is a key component in facilitating the translocation of proteins through the inner membrane into the mitochondrial matrix. Its protein folding cycle is regulated by the nucleotide-exchange factor GrpE, which triggers the release of folded proteins by ATP rebinding. Vertebrates have two mitochondrial GrpE paralogs, GRPEL1 and 2, but without clearly defined roles. Using BioID proximity labeling to identify potential binding partners of the GRPELs in the mitochondrial matrix, we obtained results supporting a model where both GRPELs regulate mtHsp70 as homodimers. We show that GRPEL2 is not essential in human cultured cells, and its absence does not prevent mitochondrial protein import. Instead we find that GRPEL2 is redox regulated in oxidative stress. In the presence of hydrogen peroxide, GRPEL2 forms dimers through intermolecular disulfide bonds in which Cys87 is the thiol switch. We propose that the dimerization of GRPEL2 may activate the folding machinery responsible for protein import into mitochondrial matrix or enhance the chaperone activity of mtHSP70, thus protecting mitochondrial proteostasis in oxidative stress.
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Affiliation(s)
- Svetlana Konovalova
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pooja Manjunath
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Sundar Baral
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Nirajan Neupane
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Taru Hilander
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Yang Yang
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Mügen Terzioglu
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Liliya Euro
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland; Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.
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