1
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Fedele G, Loh SHY, Celardo I, Leal NS, Lehmann S, Costa AC, Martins LM. Suppression of intestinal dysfunction in a Drosophila model of Parkinson's disease is neuroprotective. NATURE AGING 2022; 2:317-331. [PMID: 37117744 DOI: 10.1038/s43587-022-00194-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/16/2022] [Indexed: 04/30/2023]
Abstract
The innate immune response mounts a defense against foreign invaders and declines with age. An inappropriate induction of this response can cause diseases. Previous studies showed that mitochondria can be repurposed to promote inflammatory signaling. Damaged mitochondria can also trigger inflammation and promote diseases. Mutations in pink1, a gene required for mitochondrial health, cause Parkinson's disease, and Drosophila melanogaster pink1 mutants accumulate damaged mitochondria. Here, we show that defective mitochondria in pink1 mutants activate Relish targets and demonstrate that inflammatory signaling causes age-dependent intestinal dysfunction in pink1-mutant flies. These effects result in the death of intestinal cells, metabolic reprogramming and neurotoxicity. We found that Relish signaling is activated downstream of a pathway stimulated by cytosolic DNA. Suppression of Relish in the intestinal midgut of pink1-mutant flies restores mitochondrial function and is neuroprotective. We thus conclude that gut-brain communication modulates neurotoxicity in a fly model of Parkinson's disease through a mechanism involving mitochondrial dysfunction.
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Affiliation(s)
- Giorgio Fedele
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Ivana Celardo
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Susann Lehmann
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ana C Costa
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
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2
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Abstract
Neurodegenerative diseases, including Parkinson’s disease, are linked to the accumulation of defective mitochondria in the brain and to microbial dysbiosis in the gut. However, the interplay between these factors is incompletely understood. Fedele et al. reveal how gut mitochondrial dysfunction activates intestinal inflammation to drive neurodegeneration in a Parkinson’s disease model.
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Affiliation(s)
- Ricardo Aparicio
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Edward T Schmid
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - David W Walker
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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3
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Sensing microbial infections in the Drosophila melanogaster genetic model organism. Immunogenetics 2022; 74:35-62. [DOI: 10.1007/s00251-021-01239-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/20/2021] [Indexed: 12/17/2022]
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4
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The Eyes Absent proteins in development and in developmental disorders. Biochem Soc Trans 2021; 49:1397-1408. [PMID: 34196366 PMCID: PMC8286820 DOI: 10.1042/bst20201302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/23/2022]
Abstract
The Eyes Absent (EYA) transactivator-phosphatase proteins are important contributors to cell-fate determination processes and to the development of multiple organs. The transcriptional regulatory activity as well as the protein tyrosine phosphatase activities of the EYA proteins can independently contribute to proliferation, differentiation, morphogenesis and tissue homeostasis in different contexts. Aberrant EYA levels or activity are associated with numerous syndromic and non-syndromic developmental disorders, as well as cancers. Commensurate with the multiplicity of biochemical activities carried out by the EYA proteins, they impact upon a range of cellular signaling pathways. Here, we provide a broad overview of the roles played by EYA proteins in development, and highlight the molecular signaling pathways known to be linked with EYA-associated organ development and developmental disorders.
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5
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Roychoudhury K, Hegde RS. The Eyes Absent Proteins: Unusual HAD Family Tyrosine Phosphatases. Int J Mol Sci 2021; 22:ijms22083925. [PMID: 33920226 PMCID: PMC8069645 DOI: 10.3390/ijms22083925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/21/2023] Open
Abstract
Here, we review the haloacid dehalogenase (HAD) class of protein phosphatases, with a particular emphasis on an unusual group of enzymes, the eyes absent (EYA) family. EYA proteins have the unique distinction of being structurally and mechanistically classified as HAD enzymes, yet, unlike other HAD phosphatases, they are protein tyrosine phosphatases (PTPs). Further, the EYA proteins are unique among the 107 classical PTPs in the human genome because they do not use a Cysteine residue as a nucleophile in the dephosphorylation reaction. We will provide an overview of HAD phosphatase structure-function, describe unique features of the EYA family and their tyrosine phosphatase activity, provide a brief summary of the known substrates and cellular functions of the EYA proteins, and speculate about the evolutionary origins of the EYA family of proteins.
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6
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Merk DJ, Zhou P, Cohen SM, Pazyra-Murphy MF, Hwang GH, Rehm KJ, Alfaro J, Reid CM, Zhao X, Park E, Xu PX, Chan JA, Eck MJ, Nazemi KJ, Harwell CC, Segal RA. The Eya1 Phosphatase Mediates Shh-Driven Symmetric Cell Division of Cerebellar Granule Cell Precursors. Dev Neurosci 2021; 42:170-186. [PMID: 33472197 DOI: 10.1159/000512976] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022] Open
Abstract
During neural development, stem and precursor cells can divide either symmetrically or asymmetrically. The transition between symmetric and asymmetric cell divisions is a major determinant of precursor cell expansion and neural differentiation, but the underlying mechanisms that regulate this transition are not well understood. Here, we identify the Sonic hedgehog (Shh) pathway as a critical determinant regulating the mode of division of cerebellar granule cell precursors (GCPs). Using partial gain and loss of function mutations within the Shh pathway, we show that pathway activation determines spindle orientation of GCPs, and that mitotic spindle orientation correlates with the mode of division. Mechanistically, we show that the phosphatase Eya1 is essential for implementing Shh-dependent GCP spindle orientation. We identify atypical protein kinase C (aPKC) as a direct target of Eya1 activity and show that Eya1 dephosphorylates a critical threonine (T410) in the activation loop. Thus, Eya1 inactivates aPKC, resulting in reduced phosphorylation of Numb and other components that regulate the mode of division. This Eya1-dependent cascade is critical in linking spindle orientation, cell cycle exit and terminal differentiation. Together these findings demonstrate that a Shh-Eya1 regulatory axis selectively promotes symmetric cell divisions during cerebellar development by coordinating spindle orientation and cell fate determinants.
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Affiliation(s)
- Daniel J Merk
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology & Interdisciplinary Neuro-Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Pengcheng Zhou
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel M Cohen
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria F Pazyra-Murphy
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Grace H Hwang
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kristina J Rehm
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jose Alfaro
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher M Reid
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Xuesong Zhao
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eunyoung Park
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, USA
| | - Jennifer A Chan
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael J Eck
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kellie J Nazemi
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, USA
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA,
| | - Rosalind A Segal
- Department of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
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7
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Non-del(5q) myelodysplastic syndromes-associated loci detected by SNP-array genome-wide association meta-analysis. Blood Adv 2020; 3:3579-3589. [PMID: 31738830 DOI: 10.1182/bloodadvances.2019000922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are hematopoietic stem cell malignancies. Known predisposing factors to adult MDS include rare germline mutations, cytotoxic therapy, age-related clonal hematopoiesis, and autoimmune or chronic inflammatory disorders. To date, no published studies characterizing MDS-associated germline susceptibility polymorphisms exist. We performed a genome-wide association study of 2 sample sets (555 MDS cases vs 2964 control subjects; 352 MDS cases vs 2640 control subjects) in non-del(5q) MDS cases of European genomic ancestry. Meta-analysis identified 8 MDS-associated loci at 1q31.1 (PLA2G4A), 3p14.1 (FAM19A4), 5q21.3 (EFNA5), 6p21.33, 10q23.1 (GRID1), 12q24.32, 15q26.1, and 20q13.12 (EYA2) that approached genome-wide significance. Gene expression for 5 loci that mapped within or near genes was significantly upregulated in MDS bone marrow cells compared with those of control subjects (P < .01). Higher PLA2G4A expression and lower EYA2 expression were associated with poorer overall survival (P = .039 and P = .037, respectively). Higher PLA2G4A expression is associated with mutations in NRAS (P < .001), RUNX1 (P = .012), ASXL1 (P = .007), and EZH2 (P = .038), all of which are known to contribute to MDS development. EYA2 expression was an independently favorable risk factor irrespective of age, sex, and Revised International Scoring System score (relative risk, 0.67; P = .048). Notably, these genes have regulatory roles in innate immunity, a critical driver of MDS pathogenesis. EYA2 overexpression induced innate immune activation, whereas EYA2 inhibition restored colony-forming potential in primary MDS cells indicative of hematopoietic restoration and possible clinical relevance. In conclusion, among 8 suggestive MDS-associated loci, 5 map to genes upregulated in MDS with functional roles in innate immunity and potential biological relevance to MDS.
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8
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Hegde RS, Roychoudhury K, Pandey RN. The multi-functional eyes absent proteins. Crit Rev Biochem Mol Biol 2020; 55:372-385. [PMID: 32727223 PMCID: PMC7727457 DOI: 10.1080/10409238.2020.1796922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 07/14/2020] [Indexed: 12/13/2022]
Abstract
The Eyes Absent (EYA) proteins are the only known instance of a single polypeptide housing the following three separable biochemical activities: tyrosine phosphatase, threonine phosphatase, and transactivation. This uniquely positions the EYAs to participate in both transcriptional regulation and signal transduction pathways. But it also complicates the assignment of biological roles to individual biochemical activities through standard loss-of-function experiments. Nevertheless, there is an emerging literature linking developmental and pathological functions with the various EYA activities, and a growing list of disease states that might benefit from EYA-targeted therapeutics. There also remain multiple unresolved issues with significant implications for our understanding of how the EYAs might impact such ubiquitous signaling cascades as the MYC and Notch pathways. This review will describe the unique juxtaposition of biochemical activities in the EYAs, their interaction with signaling pathways and cellular processes, emerging evidence of roles in disease states, and the feasibility of therapeutic targeting of individual EYA activities. We will focus on the phosphatase activities of the vertebrate EYA proteins and will examine the current state of knowledge regarding: • substrates and signaling pathways affected by the EYA tyrosine phosphatase activity; • modes of regulation of the EYA tyrosine phosphatase activity; • signaling pathways that implicate the threonine phosphatase activity of the EYAs including a potential interaction with PP2A-B55α; • the interplay between the two phosphatase activities and the transactivation function of the EYAs; • disease states associated with the EYAs and the current state of development of EYA-targeted therapeutics.
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Affiliation(s)
- Rashmi S. Hegde
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
| | - Kaushik Roychoudhury
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
| | - Ram Naresh Pandey
- Division of Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Department of Pediatrics, University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati OH 45229
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9
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Vartuli RL, Zhou H, Zhang L, Powers RK, Klarquist J, Rudra P, Vincent MY, Ghosh D, Costello JC, Kedl RM, Slansky JE, Zhao R, Ford HL. Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation. J Clin Invest 2018; 128:2535-2550. [PMID: 29757193 DOI: 10.1172/jci96784] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/22/2018] [Indexed: 12/12/2022] Open
Abstract
Eya proteins are critical developmental regulators that are highly expressed in embryogenesis but downregulated after development. Amplification and/or re-expression of Eyas occurs in many tumor types. In breast cancer, Eyas regulate tumor progression by acting as transcriptional cofactors and tyrosine phosphatases. Intriguingly, Eyas harbor a separate threonine (Thr) phosphatase activity, which was previously implicated in innate immunity. Here we describe what we believe to be a novel role for Eya3 in mediating triple-negative breast cancer-associated immune suppression. Eya3 loss decreases tumor growth in immune-competent mice and is associated with increased numbers of infiltrated CD8+ T cells, which, when depleted, reverse the effects of Eya3 knockdown. Mechanistically, Eya3 utilizes its Thr phosphatase activity to dephosphorylate Myc at pT58, resulting in a stabilized form. We show that Myc is required for Eya3-mediated increases in PD-L1, and that rescue of PD-L1 in Eya3-knockdown cells restores tumor progression. Finally, we demonstrate that Eya3 significantly correlates with PD-L1 in human breast tumors, and that tumors expressing high levels of Eya3 have a decreased CD8+ T cell signature. Our data uncover a role for Eya3 in mediating tumor-associated immune suppression, and suggest that its inhibition may enhance checkpoint therapies.
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Affiliation(s)
- Rebecca L Vartuli
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA.,Molecular Biology Program
| | - Hengbo Zhou
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA.,Cancer Biology Program
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics
| | - Rani K Powers
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA.,Computational Bioscience Graduate Program
| | | | - Pratyaydipta Rudra
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Melanie Y Vincent
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA.,Cancer Biology Program.,Computational Bioscience Graduate Program
| | - Ross M Kedl
- Department of Immunology and Microbiology, and
| | - Jill E Slansky
- Cancer Biology Program.,Department of Immunology and Microbiology, and
| | - Rui Zhao
- Molecular Biology Program.,Department of Biochemistry and Molecular Genetics
| | - Heide L Ford
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado, USA.,Molecular Biology Program.,Cancer Biology Program.,Department of Biochemistry and Molecular Genetics
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10
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Zhang L, Zhou H, Li X, Vartuli RL, Rowse M, Xing Y, Rudra P, Ghosh D, Zhao R, Ford HL. Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nat Commun 2018; 9:1047. [PMID: 29535359 PMCID: PMC5849647 DOI: 10.1038/s41467-018-03327-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
Eya genes encode a unique family of multifunctional proteins that serve as transcriptional co-activators and as haloacid dehalogenase-family Tyr phosphatases. Intriguingly, the N-terminal domain of Eyas, which does not share sequence similarity to any known phosphatases, contains a separable Ser/Thr phosphatase activity. Here, we demonstrate that the Ser/Thr phosphatase activity of Eya is not intrinsic, but arises from its direct interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme. Importantly, Eya3 alters the regulation of c-Myc by PP2A, increasing c-Myc stability by enabling PP2A-B55α to dephosphorylate pT58, in direct contrast to the previously described PP2A-B56α-mediated dephosphorylation of pS62 and c-Myc destabilization. Furthermore, Eya3 and PP2A-B55α promote metastasis in a xenograft model of breast cancer, opposing the canonical tumor suppressive function of PP2A-B56α. Our study identifies Eya3 as a regulator of PP2A, a major cellular Ser/Thr phosphatase, and uncovers a mechanism of controlling the stability of a critical oncogene, c-Myc.
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Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Hengbo Zhou
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
- Cancer Biology Program, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Rebecca L Vartuli
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Michael Rowse
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Pratyaydipta Rudra
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, 80045, CO, USA.
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA.
| | - Heide L Ford
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, 80045, CO, USA.
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA.
- Cancer Biology Program, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA.
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, 80045, CO, USA.
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11
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Davis TL, Rebay I. Pleiotropy in Drosophila organogenesis: Mechanistic insights from Combgap and the retinal determination gene network. Fly (Austin) 2018; 12:62-70. [PMID: 29125381 DOI: 10.1080/19336934.2017.1402994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Master regulatory transcription factors cooperate in networks to shepherd cells through organogenesis. In the Drosophila eye, a collection of master control proteins known as the retinal determination gene network (RDGN) switches the direction and targets of its output to choreograph developmental transitions, but the molecular partners that enable such regulatory flexibility are not known. We recently showed that two RDGN members, Eyes absent (Eya) and Sine oculis (So), promote exit from the terminal cell cycle known as the second mitotic wave (SMW) to permit differentiation. A search for co-factors identified the ubiquitously expressed Combgap (Cg) as a novel transcriptional partner that impedes cell cycle exit and interferes with Eya-So activity specifically in this context. Here, we argue that Cg acts as a flexible transcriptional platform that contributes to numerous gene expression outcomes by a variety of mechanisms. For example, Cg provides repressive activities that dampen Eya-So output, but not by recruiting Polycomb chromatin-remodeling complexes as it does in other contexts. We propose that master regulators depend on both specifically expressed co-factors that assemble the combinatorial code and broadly expressed partners like Cg that recruit the diverse molecular activities needed to appropriately regulate their target enhancers.
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Affiliation(s)
- Trevor L Davis
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA
| | - Ilaria Rebay
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA.,b Ben May Department for Cancer Research , University of Chicago , Chicago , IL , USA
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12
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Mutations that impair Eyes absent tyrosine phosphatase activity in vitro reduce robustness of retinal determination gene network output in Drosophila. PLoS One 2017; 12:e0187546. [PMID: 29108015 PMCID: PMC5673202 DOI: 10.1371/journal.pone.0187546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/20/2017] [Indexed: 12/01/2022] Open
Abstract
A limited collection of signaling networks and transcriptional effectors directs the full spectrum of cellular behaviors that comprise development. One mechanism to diversify regulatory potential is to combine multiple biochemical activities into the same protein. Exemplifying this principle of modularity, Eyes absent (Eya), originally identified as a transcriptional co-activator within the retinal determination gene network (RDGN), also harbors tyrosine and threonine phosphatase activities. Although mounting evidence argues for the importance of Eya’s phosphatase activities to mammalian biology, genetic rescue experiments in Drosophila have shown that the tyrosine phosphatase function is dispensable for normal development. In this study, we repeated these rescue experiments in genetically sensitized backgrounds in which the dose of one or more RDGN factor was reduced. Heterozygosity for sine oculis or dachshund, both core RDGN members, compromised the ability of phosphatase-dead eya, but not of the control wild type eya transgene, to rescue the retinal defects and reduced viability associated with eya loss. We speculate that Eya’s tyrosine phosphatase activity, although non-essential, confers robustness to RDGN output.
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13
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The Eya phosphatase: Its unique role in cancer. Int J Biochem Cell Biol 2017; 96:165-170. [PMID: 28887153 DOI: 10.1016/j.biocel.2017.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/11/2017] [Accepted: 09/04/2017] [Indexed: 12/12/2022]
Abstract
The Eya proteins were originally identified as essential transcriptional co-activators of the Six family of homeoproteins. Subsequently, the highly conserved C-terminal domains of the Eya proteins were discovered to act as a Mg2+-dependent Tyr phosphatases, making Eyas the first transcriptional activators to harbor intrinsic phosphatase activity. Only two direct targets of the Eya Tyr phosphatase have been identified: H2AX, whose dephosphorylation directs cells to the DNA repair instead of the apoptotic pathway upon DNA damage, and ERβ, whose dephosphorylation inhibits its anti-tumor transcriptional activity. The Eya Tyr phosphatase mediates breast cancer cell transformation, migration, invasion, as well as metastasis, through targets not yet identified. Intriguingly, the N-terminal domain of Eya contains a separate Ser/Thr phosphatase activity implicated in innate immunity and in regulating c-Myc stability. Thus, Eya proteins are highly complex, containing two separable phosphatase domains and a transcriptional activation domain, thereby influencing tumor progression through multiple mechanisms.
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14
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Mussabekova A, Daeffler L, Imler JL. Innate and intrinsic antiviral immunity in Drosophila. Cell Mol Life Sci 2017; 74:2039-2054. [PMID: 28102430 PMCID: PMC5419870 DOI: 10.1007/s00018-017-2453-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/11/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Abstract
The fruit fly Drosophila melanogaster has been a valuable model to investigate the genetic mechanisms of innate immunity. Initially focused on the resistance to bacteria and fungi, these studies have been extended to include antiviral immunity over the last decade. Like all living organisms, insects are continually exposed to viruses and have developed efficient defense mechanisms. We review here our current understanding on antiviral host defense in fruit flies. A major antiviral defense in Drosophila is RNA interference, in particular the small interfering (si) RNA pathway. In addition, complex inducible responses and restriction factors contribute to the control of infections. Some of the genes involved in these pathways have been conserved through evolution, highlighting loci that may account for susceptibility to viral infections in humans. Other genes are not conserved and represent species-specific innovations.
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Affiliation(s)
- Assel Mussabekova
- Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9022, Université de Strasbourg, 15 rue René Descartes, 67000, Strasbourg, France.
| | - Laurent Daeffler
- Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9022, Université de Strasbourg, 15 rue René Descartes, 67000, Strasbourg, France
| | - Jean-Luc Imler
- Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9022, Université de Strasbourg, 15 rue René Descartes, 67000, Strasbourg, France
- Faculté des Sciences de la Vie, Université de Strasbourg, 28 rue Goethe, 67000, Strasbourg, France
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15
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Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila. Genetics 2016; 203:1283-95. [PMID: 27194748 DOI: 10.1534/genetics.115.185918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
The transcriptional coactivator and phosphatase eyes absent (Eya) is dynamically compartmentalized between the nucleus and cytoplasm. Although the nuclear transcriptional circuits within which Eya operates have been extensively characterized, understanding of its cytoplasmic functions and interactions remains limited. Our previous work showed that phosphorylation of Drosophila Eya by the Abelson tyrosine kinase can recruit Eya to the cytoplasm and that eya-abelson interactions are required for photoreceptor axons to project to correct layers in the brain. Based on these observations, we postulated that photoreceptor axon targeting might provide a suitable context for identifying the cytoplasmic signaling cascades with which Eya interacts. Using a dose-sensitive eya misexpression background, we performed an RNA interference-based genetic screen to identify suppressors. Included among the top 10 hits were nonreceptor tyrosine kinases and multiple members of the Jak/Stat signaling network (hop, Stat92E, Socs36E, and Socs44A), a pathway not previously implicated in axon targeting. Individual loss-of-function phenotypes combined with analysis of axonal projections in Stat92E null clones confirmed the importance of photoreceptor autonomous Jak/Stat signaling. Experiments in cultured cells detected cytoplasmic complexes between Eya and Hop, Socs36E and Socs44A; the latter interaction required both the Src homology 2 motif in Socs44A and tyrosine phosphorylated Eya, suggesting direct binding and validating the premise of the screen. Taken together, our data provide new insight into the cytoplasmic phosphotyrosine signaling networks that operate during photoreceptor axon guidance and suggest specific points of interaction with Eya.
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Distinct Biochemical Activities of Eyes absent During Drosophila Eye Development. Sci Rep 2016; 6:23228. [PMID: 26980695 PMCID: PMC4793267 DOI: 10.1038/srep23228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/02/2016] [Indexed: 12/13/2022] Open
Abstract
Eyes absent (Eya) is a highly conserved transcriptional coactivator and protein phosphatase that plays vital roles in multiple developmental processes from Drosophila to humans. Eya proteins contain a PST (Proline-Serine-Threonine)-rich transactivation domain, a threonine phosphatase motif (TPM), and a tyrosine protein phosphatase domain. Using a genomic rescue system, we find that the PST domain is essential for Eya activity and Dac expression, and the TPM is required for full Eya function. We also find that the threonine phosphatase activity plays only a minor role during Drosophila eye development and the primary function of the PST and TPM domains is transactivation that can be largely substituted by the heterologous activation domain VP16. Along with our previous results that the tyrosine phosphatase activity of Eya is dispensable for normal Eya function in eye formation, we demonstrate that a primary function of Eya during Drosophila eye development is as a transcriptional coactivator. Moreover, the PST/TPM and the threonine phosphatase activity are not required for in vitro interaction between retinal determination factors. Finally, this work is the first report of an Eya-Ey physical interaction. These findings are particularly important because they highlight the need for an in vivo approach that accurately dissects protein function.
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Abstract
Eyes absent (Eya), a protein conserved from plants to humans and best characterized as a transcriptional coactivator, is also the prototype for a novel class of eukaryotic aspartyl protein tyrosine phosphatases. This minireview discusses recent breakthroughs in elucidating the substrates and cellular events regulated by Eya's tyrosine phosphatase function and highlights some of the complexities, new questions, and surprises that have emerged from efforts to understand how Eya's unusual multifunctionality influences developmental regulation and signaling.
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Frykholm C, Klar J, Arnesson H, Rehnman AC, Lodahl M, Wedén U, Dahl N, Tranebjærg L, Rendtorff ND. Phenotypic variability in a seven-generation Swedish family segregating autosomal dominant hearing impairment due to a novel EYA4 frameshift mutation. Gene 2015; 563:10-6. [DOI: 10.1016/j.gene.2015.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/04/2015] [Indexed: 11/26/2022]
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Sterile inflammation in Drosophila. Mediators Inflamm 2015; 2015:369286. [PMID: 25948885 PMCID: PMC4408615 DOI: 10.1155/2015/369286] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/27/2015] [Accepted: 03/27/2015] [Indexed: 12/18/2022] Open
Abstract
The study of immune responses in Drosophila has already yielded significant results with impacts on our understanding of vertebrate immunity, such as the characterization of the Toll receptor. Several recent papers have focused on the humoral response to damage signals rather than pathogens, particularly damage signals from tumour-like tissues generated by loss of cell polarity or chromosomal instability. Both the triggers that generate this sterile inflammation and the systemic and local effects of it are only just beginning to be characterized in Drosophila. Here we review the molecular mechanisms that are known that give rise to the recruitment of Drosophila phagocytes, called hemocytes, as well as the signals, such as TNFα, that stimulated hemocytes emit at sites of perceived damage. The signalling consequences of inflammation, such as the activation of JNK, and the potential for modifying this response are also discussed.
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20
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Katzenberger RJ, Chtarbanova S, Rimkus SA, Fischer JA, Kaur G, Seppala JM, Swanson LC, Zajac JE, Ganetzky B, Wassarman DA. Death following traumatic brain injury in Drosophila is associated with intestinal barrier dysfunction. eLife 2015; 4. [PMID: 25742603 PMCID: PMC4377547 DOI: 10.7554/elife.04790] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/05/2015] [Indexed: 12/15/2022] Open
Abstract
Traumatic brain injury (TBI) is a major cause of death and disability worldwide. Unfavorable TBI outcomes result from primary mechanical injuries to the brain and ensuing secondary non-mechanical injuries that are not limited to the brain. Our genome-wide association study of Drosophila melanogaster revealed that the probability of death following TBI is associated with single nucleotide polymorphisms in genes involved in tissue barrier function and glucose homeostasis. We found that TBI causes intestinal and blood–brain barrier dysfunction and that intestinal barrier dysfunction is highly correlated with the probability of death. Furthermore, we found that ingestion of glucose after a primary injury increases the probability of death through a secondary injury mechanism that exacerbates intestinal barrier dysfunction. Our results indicate that natural variation in the probability of death following TBI is due in part to genetic differences that affect intestinal barrier dysfunction. DOI:http://dx.doi.org/10.7554/eLife.04790.001 Traumatic brain injury (TBI) caused by a violent blow to the head or body and the resultant collision of the brain against the skull is a major cause of disability and death in humans. Primary injury to the brain triggers secondary injuries that further damage the brain and other organs, generating many of the detrimental consequences of TBI. However, despite decades of study, the exact nature of these secondary injuries and their origin are poorly understood. A better understanding of secondary injuries should help to develop novel therapies to improve TBI outcomes in affected individuals. To obtain this information, in 2013 researchers devised a method to inflict TBI in the common fruit fly, Drosophila melanogaster, an organism that is readily amenable to detailed genetic and molecular studies. This investigation demonstrated that flies subjected to TBI display many of the same symptoms observed in humans after a brain injury, including temporary loss of mobility and damage to the brain that becomes worse over time. In addition, many of the flies die within 24 hr after brain injury. Now Katzenberger et al. use this experimental system to investigate the secondary injuries responsible for these deaths. First, genetic variants were identified that confer increased or decreased susceptibility to death after brain injury. Several of the identified genes affect the structural integrity of the intestinal barrier that isolates the contents of the gut—including nutrients and bacteria—from the circulatory system. Katzenberger et al. subsequently found that the breakdown of this barrier after brain injury permits bacteria and glucose to leak out of the intestine. Treating flies with antibiotics did not increase survival, whereas reducing glucose levels in the circulatory system after brain injury did. Thus, Katzenberger et al. conclude that high levels of glucose in the circulatory system, a condition known as hyperglycemia, is a key culprit in death following TBI. Notably, these results parallel findings in humans, where hyperglycemia is highly predictive of death following TBI. Similarly, individuals with diabetes have a significantly increased risk of death after TBI. These results suggest that the secondary injuries leading to death are the same in flies and humans and that further studies in flies are likely to provide additional new information that will help us understand the complex consequences of TBI. Important challenges remain, including understanding precisely how the brain and intestine communicate, how injury to the brain leads to disruption of the intestinal barrier, and why elevated glucose levels increase mortality after brain injury. Answers to these questions could help pave the way to new therapies for TBI. DOI:http://dx.doi.org/10.7554/eLife.04790.002
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Affiliation(s)
- Rebeccah J Katzenberger
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | | | - Stacey A Rimkus
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Julie A Fischer
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Gulpreet Kaur
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Jocelyn M Seppala
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Laura C Swanson
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Jocelyn E Zajac
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
| | - Barry Ganetzky
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - David A Wassarman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
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Goto A, Fukuyama H, Imler JL, Hoffmann JA. The chromatin regulator DMAP1 modulates activity of the nuclear factor B (NF-B) transcription factor Relish in the Drosophila innate immune response. J Biol Chem 2015; 289:20470-6. [PMID: 24947515 DOI: 10.1074/jbc.c114.553719] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The host defense of the model organism Drosophila is under the control of two major signaling cascades controlling transcription factors of the NF-B family, the Toll and the immune deficiency (IMD) pathways. The latter shares extensive similarities with the mammalian TNF-R pathway and was initially discovered for its role in anti-Gram-negative bacterial reactions. A previous interactome study from this laboratory reported that an unexpectedly large number of proteins are binding to the canonical components of the IMD pathway. Here, we focus on DNA methyltransferase-associated protein 1 (DMAP1), which this study identified as an interactant of Relish, a Drosophila transcription factor reminiscent of the mammalian p105 NF-B protein. We show that silencing of DMAP1 expression both in S2 cells and in flies results in a significant reduction of Escherichia coli-induced expression of antimicrobial peptides. Epistatic analysis indicates that DMAP1 acts in parallel or downstream of Relish. Co-immunoprecipitation experiments further reveal that, in addition to Relish, DMAP1 also interacts with Akirin and the Brahma-associated protein 55 kDa (BAP55). Taken together, these results reveal that DMAP1 is a novel nuclear modulator of the IMD pathway, possibly acting at the level of chromatin remodeling.
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22
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Kim SJ, Tae CH, Hong SN, Min BH, Chang DK, Rhee PL, Kim JJ, Kim HC, Kim DH, Kim YH. EYA4 Acts as a New Tumor Suppressor Gene in Colorectal Cancer. Mol Carcinog 2015; 54:1748-57. [PMID: 25620232 DOI: 10.1002/mc.22247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/05/2014] [Accepted: 10/10/2014] [Indexed: 12/19/2022]
Abstract
A previous genome-wide methylation array for colorectal cancer (CRC) identified aberrant promoter methylation of eyes absent 4 (EYA4). However, the correlations between EYA4 methylation and gene expression, the role played by EYA4 protein in colorectal carcinogenesis, and results of the gene-enrichment and functional annotation analysis have not yet been established. We analyzed the EYA4 methylation status and found EYA4 promoter methylation in CRC cell lines (100%), CRC tissues (93.5%) and advanced adenoma tissues (50.7%), compared with normal mucosa (32.6%). There was a significant inverse correlation between EYA4 methylation and expression. EYA4 transfection led to inhibition of cell proliferation in colony assays and xenograft studies. On performing the gene-enrichment and functional annotation analysis, we observed that the differentially expressed genes have been associated with the Wnt and MAPK signaling pathways. Our results demonstrate that EYA4 is under epigenetic regulation in CRC. It is a candidate tumor suppressor gene that acts by inducing up-regulation of DKK1 and inhibiting the Wnt signaling pathway. In addition, EYA4 methylation may be identified in stool samples and it serves as a potential stool biomarker for detection of advanced adenoma and CRC.
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Affiliation(s)
- Sung-Jin Kim
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Chung Hyun Tae
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung-Hoon Min
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong Kyung Chang
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Poong-Lyul Rhee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae J Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk-Hwan Kim
- Center for Genome Research, Samsung Biomedical Research Institute, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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23
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Seong CS, Varela-Ramirez A, Tang X, Anchondo B, Magallanes D, Aguilera RJ. Cloning and characterization of a novel Drosophila stress induced DNase. PLoS One 2014; 9:e103564. [PMID: 25083901 PMCID: PMC4118900 DOI: 10.1371/journal.pone.0103564] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 07/04/2014] [Indexed: 01/04/2023] Open
Abstract
Drosophila melanogaster flies mount an impressive immune response to a variety of pathogens with an efficient system comprised of both humoral and cellular responses. The fat body is the main producer of the anti-microbial peptides (AMPs) with anti-pathogen activity. During bacterial infection, an array of secreted peptidases, proteases and other enzymes are involved in the dissolution of debris generated by pathogen clearance. Although pathogen destruction should result in the release a large amount of nucleic acids, the mechanisms for its removal are still not known. In this report, we present the characterization of a nuclease gene that is induced not only by bacterial infection but also by oxidative stress. Expression of the identified protein has revealed that it encodes a potent nuclease that has been named Stress Induced DNase (SID). SID belongs to a family of evolutionarily conserved cation-dependent nucleases that degrade both single and double-stranded nucleic acids. Down-regulation of sid expression via RNA interference leads to significant reduction of fly viability after bacterial infection and oxidative stress. Our results indicate that SID protects flies from the toxic effects of excess DNA/RNA released by pathogen destruction and from oxidative damage.
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Affiliation(s)
- Chang-Soo Seong
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Armando Varela-Ramirez
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Xiaolei Tang
- Department of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Brenda Anchondo
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Diego Magallanes
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Renato J. Aguilera
- Border Biomedical Research Center and Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
- * E-mail:
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24
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Wilson IM, Vucic EA, Enfield KSS, Thu KL, Zhang YA, Chari R, Lockwood WW, Radulovich N, Starczynowski DT, Banáth JP, Zhang M, Pusic A, Fuller M, Lonergan KM, Rowbotham D, Yee J, English JC, Buys TPH, Selamat SA, Laird-Offringa IA, Liu P, Anderson M, You M, Tsao MS, Brown CJ, Bennewith KL, MacAulay CE, Karsan A, Gazdar AF, Lam S, Lam WL. EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk. Oncogene 2013; 33:4464-73. [PMID: 24096489 PMCID: PMC4527534 DOI: 10.1038/onc.2013.396] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/30/2013] [Accepted: 08/06/2013] [Indexed: 02/07/2023]
Abstract
In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.
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Affiliation(s)
- I M Wilson
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - E A Vucic
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K S S Enfield
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K L Thu
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Y A Zhang
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R Chari
- 1] Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada [2] Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - W W Lockwood
- 1] Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada [2] National Human Genome Research Institute, Cancer Genetics Branch, Bethesda, MD, USA
| | - N Radulovich
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON, Canada
| | - D T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - J P Banáth
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - M Zhang
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A Pusic
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - M Fuller
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - K M Lonergan
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - D Rowbotham
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - J Yee
- Department of Surgery, Vancouver General Hospital, Vancouver, BC, Canada
| | - J C English
- Department of Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - T P H Buys
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - S A Selamat
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - I A Laird-Offringa
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - P Liu
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M Anderson
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M You
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA
| | - M S Tsao
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON, Canada
| | - C J Brown
- Department of Medical Genetics, University of British Columbia, Life Sciences Centre, Vancouver, BC, Canada
| | - K L Bennewith
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - C E MacAulay
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A Karsan
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - A F Gazdar
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - S Lam
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - W L Lam
- Integrative Oncology Genetics Unit, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proc Natl Acad Sci U S A 2013; 110:10717-22. [PMID: 23749869 DOI: 10.1073/pnas.1304380110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Drosophila defense against pathogens largely relies on the activation of two signaling pathways: immune deficiency (IMD) and Toll. The IMD pathway is triggered mainly by Gram-negative bacteria, whereas the Toll pathway responds predominantly to Gram-positive bacteria and fungi. The activation of these pathways leads to the rapid induction of numerous NF-κB-induced immune response genes, including antimicrobial peptide genes. The IMD pathway shows significant similarities with the TNF receptor pathway. Recent evidence indicates that the IMD pathway is also activated in response to various noninfectious stimuli (i.e., inflammatory-like reactions). To gain a better understanding of the molecular machinery underlying the pleiotropic functions of this pathway, we first performed a comprehensive proteomics analysis to identify the proteins interacting with the 11 canonical members of the pathway initially identified by genetic studies. We identified 369 interacting proteins (corresponding to 291 genes) in heat-killed Escherichia coli-stimulated Drosophila S2 cells, 92% of which have human orthologs. A comparative analysis of gene ontology from fly or human gene annotation databases points to four significant common categories: (i) the NuA4, nucleosome acetyltransferase of H4, histone acetyltransferase complex, (ii) the switching defective/sucrose nonfermenting-type chromatin remodeling complex, (iii) transcription coactivator activity, and (iv) translation factor activity. Here we demonstrate that sumoylation of the IκB kinase homolog immune response-deficient 5 plays an important role in the induction of antimicrobial peptide genes through a highly conserved sumoylation consensus site during bacterial challenge. Taken together, the proteomics data presented here provide a unique avenue for a comparative functional analysis of proteins involved in innate immune reactions in flies and mammals.
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Jin M, Jusiak B, Bai Z, Mardon G. Eyes absent tyrosine phosphatase activity is not required for Drosophila development or survival. PLoS One 2013; 8:e58818. [PMID: 23554934 PMCID: PMC3595212 DOI: 10.1371/journal.pone.0058818] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 12/15/2022] Open
Abstract
Eyes absent (Eya) is an evolutionarily conserved transcriptional coactivator and protein phosphatase that regulates multiple developmental processes throughout the metazoans. Drosophila eya is necessary for survival as well as for the formation of the adult eye. Eya contains a tyrosine phosphatase domain, and mutations altering presumptive active-site residues lead to strongly reduced activities in ectopic eye induction, in vivo genetic rescue using the Gal4-UAS system, and in vitro phosphatase assays. However, these mutations have not been analyzed during normal development with the correct levels, timing, and patterns of endogenous eya expression. To investigate whether the tyrosine phosphatase activity of Eya plays a role in Drosophila survival or normal eye formation, we generated three eya genomic rescue (eyaGR) constructs that alter key active-site residues and tested them in vivo. In striking contrast to previous studies, all eyaGR constructs fully restore eye formation as well as viability in an eya null mutant background. We conclude that the tyrosine phosphatase activity of Eya is not required for normal eye development or survival in Drosophila. Our study suggests the need for a re-evaluation of the mechanism of Eya action and underscores the importance of studying genes in their native context.
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Affiliation(s)
- Meng Jin
- Laboratory of Developmental Immunology, School of Life Science, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Barbara Jusiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zengliang Bai
- Laboratory of Developmental Immunology, School of Life Science, Shandong University, Jinan, Shandong, People’s Republic of China
- * E-mail: (GM); (ZB)
| | - Graeme Mardon
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (GM); (ZB)
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Atypical protein phosphatases: emerging players in cellular signaling. Int J Mol Sci 2013; 14:4596-612. [PMID: 23443160 PMCID: PMC3634448 DOI: 10.3390/ijms14034596] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 12/23/2022] Open
Abstract
It has generally been considered that protein phosphatases have more diverse catalytic domain structures and mechanisms than protein kinases; however, gene annotation efforts following the human genome project appeared to have completed the whole array of protein phosphatases. Ser/Thr phosphatases are divided into three subfamilies that have different structures from each other, whereas Tyr phosphatases and dual-specificity phosphatases targeting Tyr, Ser and Thr belong to a single large family based on their common structural features. Several years of research have revealed, however, the existence of unexpected proteins, designated here as “atypical protein phosphatases”, that have structural and enzymatic features different from those of the known protein phosphatases and are involved in important biological processes. In this review, we focus on the identification and functional characterization of atypical protein phosphatases, represented by eyes absent (EYA), suppressor of T-cell receptor signaling (Sts) and phosphoglycerate mutase family member 5 (PGAM5) and discuss their biological significance in cellular signaling.
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