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Ramprasad S, Nyarko A. Ensembles of interconverting protein complexes with multiple interaction domains. Curr Opin Struct Biol 2024; 88:102874. [PMID: 38981144 DOI: 10.1016/j.sbi.2024.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Many critical biological processes depend on protein complexes that exist as ensembles of subcomplexes rather than a discrete complex. The subcomplexes dynamically interconvert with one another, and the ability to accurately resolve the composition of the diverse molecular species in the ensemble is crucial for understanding the contribution of each subcomplex to the overall function of the protein complex. Advances in computational programs have made it possible to predict the various molecular species in these ensembles, but experimental approaches to identify the pool of subcomplexes and associated stoichiometries are often challenging. This review highlights some experimental approaches that can be used to resolve the diverse molecular species in protein complexes that exist as ensembles of sub complexes.
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Affiliation(s)
- Sanjay Ramprasad
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Afua Nyarko
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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2
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Rovsing AB, Thomsen EA, Nielsen I, Skov TW, Luo Y, Dybkaer K, Mikkelsen JG. Resistance to vincristine in DLBCL by disruption of p53-induced cell cycle arrest and apoptosis mediated by KIF18B and USP28. Br J Haematol 2023; 202:825-839. [PMID: 37190875 DOI: 10.1111/bjh.18872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
The frontline therapy R-CHOP for patients with diffuse large B-cell lymphoma (DLBCL) has remained unchanged for two decades despite numerous Phase III clinical trials investigating new alternatives. Multiple large studies have uncovered genetic subtypes of DLBCL enabling a targeted approach. To further pave the way for precision oncology, we perform genome-wide CRISPR screening to uncover the cellular response to one of the components of R-CHOP, vincristine, in the DLBCL cell line SU-DHL-5. We discover important pathways and subnetworks using gene-set enrichment analysis and protein-protein interaction networks and identify genes related to mitotic spindle organization that are essential during vincristine treatment. The inhibition of KIF18A, a mediator of chromosome alignment, using the small molecule inhibitor BTB-1 causes complete cell death in a synergistic manner when administered together with vincristine. We also identify the genes KIF18B and USP28 of which CRISPR/Cas9-directed knockout induces vincristine resistance across two DLBCL cell lines. Mechanistic studies show that lack of KIF18B or USP28 counteracts a vincristine-induced p53 response suggesting that resistance to vincristine has origin in the mitotic surveillance pathway (USP28-53BP1-p53). Collectively, our CRISPR screening data uncover potential drug targets and mechanisms behind vincristine resistance, which may support the development of future drug regimens.
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Affiliation(s)
| | | | - Ian Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Shenzhen, China
| | - Karen Dybkaer
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
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Walker DR, Jara KA, Rolland AD, Brooks C, Hare W, Swansiger AK, Reardon PN, Prell JS, Barbar EJ. Linker Length Drives Heterogeneity of Multivalent Complexes of Hub Protein LC8 and Transcription Factor ASCIZ. Biomolecules 2023; 13:404. [PMID: 36979339 PMCID: PMC10046861 DOI: 10.3390/biom13030404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
LC8, a ubiquitous and highly conserved hub protein, binds over 100 proteins involved in numerous cellular functions, including cell death, signaling, tumor suppression, and viral infection. LC8 binds intrinsically disordered proteins (IDPs), and although several of these contain multiple LC8 binding motifs, the effects of multivalency on complex formation are unclear. Drosophila ASCIZ has seven motifs that vary in sequence and inter-motif linker lengths, especially within subdomain QT2-4 containing the second, third, and fourth LC8 motifs. Using isothermal-titration calorimetry, analytical-ultracentrifugation, and native mass-spectrometry of QT2-4 variants, with methodically deactivated motifs, we show that inter-motif spacing and specific motif sequences combine to control binding affinity and compositional heterogeneity of multivalent duplexes. A short linker separating strong and weak motifs results in stable duplexes but forms off-register structures at high LC8 concentrations. Contrastingly, long linkers engender lower cooperativity and heterogeneous complexation at low LC8 concentrations. Accordingly, two-mers, rather than the expected three-mers, dominate negative-stain electron-microscopy images of QT2-4. Comparing variants containing weak-strong and strong-strong motif combinations demonstrates sequence also regulates IDP/LC8 assembly. The observed trends persist for trivalent ASCIZ subdomains: QT2-4, with long and short linkers, forms heterogeneous complexes, whereas QT4-6, with similar mid-length linkers, forms homogeneous complexes. Implications of linker length variations for function are discussed.
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Affiliation(s)
- Douglas R. Walker
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Kayla A. Jara
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Amber D. Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Wendy Hare
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew K. Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Patrick N. Reardon
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- NMR Facility, Oregon State University, Corvallis, OR 97331, USA
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
- Materials Science Institute, University of Oregon, Eugene, OR 97403, USA
| | - Elisar J. Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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Miao YR, Thakkar K, Cenik C, Jiang D, Mizuno K, Jia C, Li CG, Zhao H, Diep A, Xu Y, Zhang XE, Yang TTC, Liedtke M, Abidi P, Leung WS, Koong AC, Giaccia AJ. Developing high-affinity decoy receptors to treat multiple myeloma and diffuse large B cell lymphoma. J Exp Med 2022; 219:213366. [PMID: 35881112 PMCID: PMC9428257 DOI: 10.1084/jem.20220214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/05/2022] [Accepted: 06/17/2022] [Indexed: 11/12/2022] Open
Abstract
Disease relapse and treatment-induced immunotoxicity pose significant clinical challenges for patients with hematological cancers. Here, we reveal distinctive requirements for neutralizing TNF receptor ligands APRIL and BAFF and their receptor activity in MM and DLBCL, impacting protein translation and production in MM cells and modulating the translation efficiency of the ATM interactor (ATMIN/ACSIZ). Therapeutically, we investigated the use of BCMA decoy receptor (sBCMA-Fc) as an inhibitor of APRIL and BAFF. While wild-type sBCMA-Fc effectively blocked APRIL signaling in MM, it lacked activity in DLBCL due to its weak BAFF binding. To expand the therapeutic utility of sBCMA-Fc, we engineered an affinity-enhanced mutant sBCMA-Fc fusion molecule (sBCMA-Fc V3) 4- and 500-fold stronger in binding to APRIL and BAFF, respectively. The mutant sBCMA-Fc V3 clone significantly enhanced antitumor activity against both MM and DLBCL. Importantly, we also demonstrated an adequate toxicity profile and on-target mechanism of action in nonhuman primate studies.
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Affiliation(s)
- Yu Rebecca Miao
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Kaushik Thakkar
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX
| | - Dadi Jiang
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX
| | - Kazue Mizuno
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | | | - Caiyun Grace Li
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Hongjuan Zhao
- Department of Urology, Stanford University, Stanford, CA
| | - Anh Diep
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Yu Xu
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Xin Eric Zhang
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Michaela Liedtke
- Department of Medicine (Hematology), Stanford University, Stanford, CA
| | - Parveen Abidi
- Department of Medicine (Hematology), Stanford University, Stanford, CA
| | - Wing-Sze Leung
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - Albert C Koong
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University, Stanford, CA.,Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
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Li YJ, Yang CN, Kuo MYP, Lai WT, Wu TS, Lin BR. ATMIN enhances invasion by altering PARP1 in MSS colorectal cancer. Am J Cancer Res 2022; 12:3799-3810. [PMID: 36119811 PMCID: PMC9441994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023] Open
Abstract
Genomic instability is a key cancer indicator. It results from defects in the DNA damage response (DDR) and increased replication stress. Herein, we examined how ataxia-telangiectasia mutated interactor (ATMIN), a DDR pathway involved in mismatch repair-proficient (microsatellite stability [MSS]), acts in colorectal carcinoma (CRC). Firstly, ATMIN mRNA expression was detected in CRC specimens with MSS characteristics, and the effects of ectopic ATMIN expression and ATMIN knockdown on invasion abilities were gauged in MSS cell lines. To understand the molecular mechanism, co-immunoprecipitation analyses in vitro were employed. Interestingly, ATMIN expression was positively correlated with advanced stages (P < .001), lymph node metastases (P = .002), and deeper invasion (P = .037) in MSS tumors; and significantly changed the cell motility in vitro. In the high-throughput analysis, ATMIN was found to act on the Wnt signaling pathway via PARP1. PAPR1 inhibition, in turn, significantly decreased invasion abilities resulting from ATMIN overexpression in cancer cell. Taken together, ATMIN, which alters the Wnt signaling pathway regulating CRC progression, plays as a crucial prognostic factor in MSS tumors.
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Affiliation(s)
- Yue-Ju Li
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan UniversityTaipei, Taiwan
- Department of Surgery, National Taiwan University Hospital and College of MedicineTaipei, Taiwan
| | - Cheng-Ning Yang
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan UniversityTaipei, Taiwan
| | - Mark Yen-Ping Kuo
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan UniversityTaipei, Taiwan
| | - Wei-Ting Lai
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan UniversityTaipei, Taiwan
| | - Tai-Sheng Wu
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan UniversityTaipei, Taiwan
| | - Been-Ren Lin
- Department of Surgery, National Taiwan University Hospital and College of MedicineTaipei, Taiwan
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Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM. J Mol Biol 2022; 434:167520. [PMID: 35245498 PMCID: PMC9050902 DOI: 10.1016/j.jmb.2022.167520] [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: 07/02/2021] [Revised: 01/17/2022] [Accepted: 02/27/2022] [Indexed: 12/29/2022]
Abstract
Multivalent intrinsically disordered protein (IDP) complexes are prevalent in biology and act in regulation of diverse processes, including transcription, signaling events, and the assembly and disassembly of complex macromolecular architectures. These systems pose significant challenges to structural investigation, due to continuum dynamics imparted by the IDP and compositional heterogeneity resulting from characteristic low-affinity interactions. Here, we developed a modular pipeline for automated single-particle electron microscopy (EM) distribution analysis of common but relatively understudied semi-ordered systems: 'beads-on-a-string' assemblies, composed of IDPs bound at multivalent sites to the ubiquitous ∼20 kDa cross-linking hub protein LC8. This approach quantifies conformational geometries and compositional heterogeneity on a single-particle basis, and statistically corrects spurious observations arising from random proximity of bound and unbound LC8. The statistical correction is generically applicable to oligomer characterization and not specific to our pipeline. Following validation, the approach was applied to the nuclear pore IDP Nup159 and the transcription factor ASCIZ. This analysis unveiled significant compositional and conformational diversity in both systems that could not be obtained from ensemble single particle EM class-averaging strategies, and new insights for exploring how these architectural properties might contribute to their physiological roles in supramolecular assembly and transcriptional regulation. We expect that this approach may be adopted to many other intrinsically disordered systems that have evaded traditional methods of structural characterization.
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Goggolidou P, Richards T. The genetics of Autosomal Recessive Polycystic Kidney Disease (ARPKD). Biochim Biophys Acta Mol Basis Dis 2022; 1868:166348. [PMID: 35032595 DOI: 10.1016/j.bbadis.2022.166348] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/27/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022]
Abstract
ARPKD is a genetically inherited kidney disease that manifests by bilateral enlargement of cystic kidneys and liver fibrosis. It shows a range of severity, with 30% of individuals dying early on and the majority having good prognosis if they survive the first year of life. The reasons for this variability remain unclear. Two genes have been shown to cause ARPKD when mutated, PKHD1, mutations in which lead to most of ARPKD cases and DZIP1L, which is associated with moderate ARPKD. This mini review will explore the genetics of ARPKD and discuss potential genetic modifiers and phenocopies that could affect diagnosis.
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Affiliation(s)
- Paraskevi Goggolidou
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK.
| | - Taylor Richards
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
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8
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Liu R, King A, Tarlinton D, Heierhorst J. The ASCIZ-DYNLL1 Axis Is Essential for TLR4-Mediated Antibody Responses and NF-κB Pathway Activation. Mol Cell Biol 2021; 41:e0025121. [PMID: 34543116 PMCID: PMC8608018 DOI: 10.1128/mcb.00251-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Toll-like receptors (TLRs) and interleukin-1 (IL-1) receptors regulate immune and inflammatory responses by activating the NF-κB pathway. Here, we report that B-cell-specific loss of dynein light chain 1 (DYNLL1, LC8) or its designated transcription factor ASCIZ (ATMIN) leads to severely reduced in vivo antibody responses to TLR4-dependent but not T-cell-dependent antigens in mice. This defect was independent of DYNLL1's established roles in modulating BIM-dependent apoptosis and 53BP1-dependent antibody class-switch recombination. In B cells and fibroblasts, the ASCIZ-DYNLL1 axis was required for TLR4-, IL-1-, and CD40-mediated NF-κB pathway activation but dispensable for antigen receptor and tumor necrosis factor α (TNF-α) signaling. In contrast to previous reports that overexpressed DYNLL1 directly inhibits the phosphorylation and degradation of the NF-κB inhibitor IκBα, we found here that under physiological conditions, DYNLL1 is required for signal-specific activation of the NF-κB pathway upstream of IκBα. Our data identify DYNLL1 as a signal-specific regulator of the NF-κB pathway and indicate that it may act as a universal modulator of TLR4 (and IL-1) signaling with wide-ranging roles in inflammation and immunity.
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Affiliation(s)
- Rui Liu
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Ashleigh King
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - David Tarlinton
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Jörg Heierhorst
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine at St. Vincent’s Hospital, University of Melbourne Medical School, Fitzroy, Victoria, Australia
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9
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The role of dancing duplexes in biology and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021. [PMID: 34656330 DOI: 10.1016/bs.pmbts.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Across species, a common protein assembly arises: proteins containing structured domains separated by long intrinsically disordered regions, and dimerized through a self-association domain or through strong protein interactions. These systems are termed "IDP duplexes." These flexible dimers have roles in diverse pathologies including development of cancer, viral infections, and neurodegenerative disease. Here we discuss the role of disorder in IDP duplexes with similar domain architectures that bind hub protein, LC8. LC8-binding IDP duplexes are categorized into three groups: IDP duplexes that contain a self-association domain that is extended by LC8 binding, IDP duplexes that have no self-association domain and are dimerized through binding several copies of LC8, and multivalent LC8-binders that also have a self-association domain. Additionally, we discuss non-LC8-binding IDP duplexes with similar domain organizations, including the Nucleocapsid protein of SARS-CoV-2. We propose that IDP duplexes have structural features that are essential in many biological processes and that improved understanding of their structure function relationship will provide new therapeutic opportunities.
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Berkel C, Cacan E. Involvement of ATMIN-DYNLL1-MRN axis in the progression and aggressiveness of serous ovarian cancer. Biochem Biophys Res Commun 2021; 570:74-81. [PMID: 34273621 DOI: 10.1016/j.bbrc.2021.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/02/2021] [Indexed: 12/24/2022]
Abstract
The loss of DYNLL1 contributes to chemoresistance in ovarian cancer. DYNLL1 binds to MRE11, a component of MRN complex (MRE11-RAD50-NBS1), and limits its function in homologous recombination (HR) repair in BRCA1-mutant cells. Decreased activity of MRE11 results in less HR-repair events and thus leads to higher sensitivity against DNA-damaging agents such as cisplatin. Therefore, a better understanding of the cellular changes in DYNLL1-MRN axis in ovarian cancer is needed. Here, we showed that DYNLL1 overexpression leads to decreased chemoresistance even in BRCA-proficient ovarian cancer cells. ATMIN, a transcriptional activator of DYNLL1, showed decreased expression; however, two components of MRN complex, MRE11 and NBS1 (NBN), showed increased expression in high grade compared to low grade serous ovarian cancer. We found that the components of MRN complex (MRE11-RAD50-NBS1) have higher protein levels in sites of omental metastasis and serous tubal intraepithelial carcinoma (STIC) compared to surrounding non-malignant stromal cells in patients with high grade serous ovarian cancer. We showed that the percentage of copy number variation (CNV) events in genes encoding ATMIN, DYNLL1, MRE11 and NBN are the highest in ovarian cancer among other cancer types. ATMIN and DYNLL1 genes are mostly characterized by copy number losses; however, CNV events in MRN complex components are mostly copy number gains. This study highlights the importance of ATMIN-DYNLL1-MRN axis in the development, progression and therapy response of ovarian cancer. MRN levels in ovarian cancer that differ from adjacent, non-malignant tissues may represent actionable therapeutic vulnerabilities.
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Affiliation(s)
- Caglar Berkel
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, 60250, Turkey.
| | - Ercan Cacan
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, 60250, Turkey.
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11
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White KA, McEntire KD, Buan NR, Robinson L, Barbar E. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems. Integr Comp Biol 2021; 61:2255-2266. [PMID: 34283225 DOI: 10.1093/icb/icab165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Nicole R Buan
- University of Nebraska-Lincoln, Department of Biochemistry
| | | | - Elisar Barbar
- Oregon State University, Department of Biochemistry and Biophysics
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12
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Li YJ, Yang CN, Kuo MYP, Lai WT, Wu TS, Lin BR. ATMIN Suppresses Metastasis by Altering the WNT-Signaling Pathway via PARP1 in MSI-High Colorectal Cancer. Ann Surg Oncol 2021; 28:8544-8554. [PMID: 34148137 DOI: 10.1245/s10434-021-10322-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Constant DNA damage occurs in cells, and the cells are programmed to respond constitutively. This study explored the roles of ataxia-telangiectasia mutated interactor (ATMIN), one of the impaired pathways involving the DNA damage response (DDR) in mismatch repair-deficient [microsatellite instability (MSI)-high] colorectal carcinoma (CRC). METHODS Expression of ATMIN messenger RNA (mRNA) was detected in CRC specimens with microsatellite instability (MSI) characteristics. The effects of ectopic ATMIN expression and ATMIN knockdown on invasion abilities were evaluated in MSI-high cell lines, and liver metastasis ability was investigated in vivo. Protein-protein interactions were assessed by coimmunoprecipitation analyses in vitro. RESULTS Decreased ATMIN expression was positively correlated with advanced stage of disease (P < 0.05), lymph node metastases (P < 0.05), and deeper invasion (P < 0.05) in MSI-high tumors. Transient or stable ATMIN knockdown significantly increased cell motility. Moreover, in the high-throughput microarray and gene set enrichment analysis, ATMIN was shown to act on the Wnt-signaling pathway via PARP1. This cascade influences β-catenin/transcription factor 4 (TCF4) binding affinity in MSI-high tumors, and PARP1 inhibition significantly decreased the number of metastases from ATMIN knockdown cancer cells. CONCLUSIONS The results not only indicated the critical role of ATMIN, but also shed new light on PARP1 inhibitors, providing a basis for further clinical trials of MSI-high CRC.
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Affiliation(s)
- Yue-Ju Li
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan.,Division of Colorectal Surgery, Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei City, Taiwan
| | - Cheng-Ning Yang
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Mark Yen-Ping Kuo
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Wei-Ting Lai
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Tai-Sheng Wu
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Been-Ren Lin
- Division of Colorectal Surgery, Department of Surgery, National Taiwan University Hospital and College of Medicine, Taipei City, Taiwan.
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Primary cilia and the DNA damage response: linking a cellular antenna and nuclear signals. Biochem Soc Trans 2021; 49:829-841. [PMID: 33843966 DOI: 10.1042/bst20200751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/17/2022]
Abstract
The maintenance of genome stability involves integrated biochemical activities that detect DNA damage or incomplete replication, delay the cell cycle, and direct DNA repair activities on the affected chromatin. These processes, collectively termed the DNA damage response (DDR), are crucial for cell survival and to avoid disease, particularly cancer. Recent work has highlighted links between the DDR and the primary cilium, an antenna-like, microtubule-based signalling structure that extends from a centriole docked at the cell surface. Ciliary dysfunction gives rise to a range of complex human developmental disorders termed the ciliopathies. Mutations in ciliopathy genes have been shown to impact on several functions that relate to centrosome integrity, DNA damage signalling, responses to problems in DNA replication and the control of gene expression. This review covers recent findings that link cilia and the DDR and explores the various roles played by key genes in these two contexts. It outlines how proteins encoded by ciliary genes impact checkpoint signalling, DNA replication and repair, gene expression and chromatin remodelling. It discusses how these diverse activities may integrate nuclear responses with those that affect a structure of the cell periphery. Additional directions for exploration of the interplay between these pathways are highlighted, with a focus on new ciliary gene candidates that alter genome stability.
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14
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Eastwood EL, Jara KA, Bornelöv S, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B, Hannon GJ. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila. eLife 2021; 10:e65557. [PMID: 33538693 PMCID: PMC7861614 DOI: 10.7554/elife.65557] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
In animal gonads, the PIWI-interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.
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Affiliation(s)
- Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Vasileios Frantzis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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15
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Adivitiya, Kaushik MS, Chakraborty S, Veleri S, Kateriya S. Mucociliary Respiratory Epithelium Integrity in Molecular Defense and Susceptibility to Pulmonary Viral Infections. BIOLOGY 2021; 10:95. [PMID: 33572760 PMCID: PMC7911113 DOI: 10.3390/biology10020095] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Mucociliary defense, mediated by the ciliated and goblet cells, is fundamental to respiratory fitness. The concerted action of ciliary movement on the respiratory epithelial surface and the pathogen entrapment function of mucus help to maintain healthy airways. Consequently, genetic or acquired defects in lung defense elicit respiratory diseases and secondary microbial infections that inflict damage on pulmonary function and may even be fatal. Individuals living with chronic and acute respiratory diseases are more susceptible to develop severe coronavirus disease-19 (COVID-19) illness and hence should be proficiently managed. In light of the prevailing pandemic, we review the current understanding of the respiratory system and its molecular components with a major focus on the pathophysiology arising due to collapsed respiratory epithelium integrity such as abnormal ciliary movement, cilia loss and dysfunction, ciliated cell destruction, and changes in mucus rheology. The review includes protein interaction networks of coronavirus infection-manifested implications on the molecular machinery that regulates mucociliary clearance. We also provide an insight into the alteration of the transcriptional networks of genes in the nasopharynx associated with the mucociliary clearance apparatus in humans upon infection by severe acute respiratory syndrome coronavirus-2.
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Affiliation(s)
- Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Manish Singh Kaushik
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad 500007, India;
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; (A.); (M.S.K.); (S.C.)
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16
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Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Melé M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell 2020; 183:1383-1401.e19. [PMID: 33159858 PMCID: PMC7707107 DOI: 10.1016/j.cell.2020.10.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/10/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.
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Affiliation(s)
- Dylan Kotliar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA.
| | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Travis K Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nadine M Khoury
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siddharth S Raju
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jonathan R Kurtz
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Bonnie Dighero-Kemp
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Zach B Bjornson
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Matthew R Bauer
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ricky Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - John L Rinn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - David R McIlwain
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
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17
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Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020; 45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
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18
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Reardon PN, Jara KA, Rolland AD, Smith DA, Hoang HTM, Prell JS, Barbar EJ. The dynein light chain 8 (LC8) binds predominantly "in-register" to a multivalent intrinsically disordered partner. J Biol Chem 2020; 295:4912-4922. [PMID: 32139510 PMCID: PMC7152752 DOI: 10.1074/jbc.ra119.011653] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 03/03/2020] [Indexed: 01/18/2023] Open
Abstract
Dynein light chain 8 (LC8) interacts with intrinsically disordered proteins (IDPs) and influences a wide range of biological processes. It is becoming apparent that among the numerous IDPs that interact with LC8, many contain multiple LC8-binding sites. Although it is established that LC8 forms parallel IDP duplexes with some partners, such as nucleoporin Nup159 and dynein intermediate chain, the molecular details of these interactions and LC8's interactions with other diverse partners remain largely uncharacterized. LC8 dimers could bind in either a paired "in-register" or a heterogeneous off-register manner to any of the available sites on a multivalent partner. Here, using NMR chemical shift perturbation, analytical ultracentrifugation, and native electrospray ionization MS, we show that LC8 forms a predominantly in-register complex when bound to an IDP domain of the multivalent regulatory protein ASCIZ. Using saturation transfer difference NMR, we demonstrate that at substoichiometric LC8 concentrations, the IDP domain preferentially binds to one of the three LC8 recognition motifs. Further, the differential dynamic behavior for the three sites and the size of the fully bound complex confirmed an in-register complex. Dynamics measurements also revealed that coupling between sites depends on the linker length separating these sites. These results identify linker length and motif specificity as drivers of in-register binding in the multivalent LC8-IDP complex assembly and the degree of compositional and conformational heterogeneity as a promising emerging mechanism for tuning of binding and regulation.
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Affiliation(s)
- Patrick N Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon 97331
| | - Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Delaney A Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Hanh T M Hoang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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19
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Jespersen NE, Leyrat C, Gérard FC, Bourhis JM, Blondel D, Jamin M, Barbar E. The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality. J Mol Biol 2019; 431:4959-4977. [PMID: 31634467 PMCID: PMC7060403 DOI: 10.1016/j.jmb.2019.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
The rabies and Ebola viruses recruit the highly conserved host protein LC8 for their own reproductive success. In vivo knockouts of the LC8 recognition motif within the rabies virus phosphoprotein (RavP) result in completely nonlethal viral infections. In this work, we examine the molecular role LC8 plays in viral lethality. We show that RavP and LC8 colocalize in rabies infected cells, and that LC8 interactions are essential for efficient viral polymerase functionality. NMR, SAXS, and molecular modeling demonstrate that LC8 binding to a disordered linker adjacent to an endogenous dimerization domain results in restrictions in RavP domain orientations. The resulting ensemble structure of RavP-LC8 tetrameric complex is similar to that of a related virus phosphoprotein that does not bind LC8, suggesting that with RavP, LC8 binding acts as a switch to induce a more active conformation. The high conservation of the LC8 motif in Lyssavirus phosphoproteins and its presence in other analogous proteins such as the Ebola virus VP35 evinces a broader purpose for LC8 in regulating downstream phosphoprotein functions vital for viral replication.
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Affiliation(s)
- Nathan E Jespersen
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Cedric Leyrat
- Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, Montpellier, France
| | - Francine C Gérard
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Jean-Marie Bourhis
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Danielle Blondel
- Institut de Biologie Intégrative de La Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Marc Jamin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000, Grenoble, France
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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20
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Zalmas LP, Lu WT, Kanu N. An emerging regulatory network of NHEJ via DYNLL1-mediated 53BP1 redistribution. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S93. [PMID: 31576301 DOI: 10.21037/atm.2019.04.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- Cancer Evolution and Genome Instability Laboratory, UCL Cancer Institute, London, UK
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21
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Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub protein LC8. Life Sci Alliance 2019; 2:2/4/e201900366. [PMID: 31266884 PMCID: PMC6607443 DOI: 10.26508/lsa.201900366] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 01/17/2023] Open
Abstract
LC8 is a eukaryotic hub protein that interacts with multifarious partners; analysis of more than 100 binding/nonbinding sequences led to an algorithm that predicts LC8 partners with 78% accuracy. Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the “LC8Pred” algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with ∼78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome.
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Affiliation(s)
- Nathan Jespersen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Aidan Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Nathan Waugh
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Cecilia Blikstad
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | | | - Anna Akhmanova
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Ylva Ivarsson
- Department of Chemistry - Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.,School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
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22
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Sharma NM, Liu X, Llewellyn TL, Katsurada K, Patel KP. Exercise training augments neuronal nitric oxide synthase dimerization in the paraventricular nucleus of rats with chronic heart failure. Nitric Oxide 2019; 87:73-82. [PMID: 30878404 PMCID: PMC6527363 DOI: 10.1016/j.niox.2019.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/06/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
Exercise training (ExT) is an established non-pharmacological therapy that improves the health and quality of life in patients with chronic heart failure (CHF). Exaggerated sympathetic drive characterizes CHF due to an imbalance of the autonomic nervous system. Neuronal nitric oxide synthase (nNOS) in the paraventricular nucleus (PVN) produce nitric oxide (NO•), which is known to regulate the sympathetic tone. Previously we have shown that during CHF, the catalytically active dimeric form of nNOS is significantly decreased with a concurrent increase in protein inhibitor of nNOS (PIN) expression, a protein that dissociates dimeric nNOS to monomers and facilitates its degradation. Dimerization of nNOS also requires (6R)-5,6,7,8-tetrahydrobiopterin (BH4) for stability and activity. Previously, we have shown that ExT improves NO-mediated sympathetic inhibition in the PVN; however, the molecular mechanism remains elusive. We hypothesized; ExT restores the sympathetic drive by increasing the levels and catalytically active form of nNOS by abrogating changes in the PIN in the PVN of CHF rats. CHF was induced in adult male Sprague-Dawley rats by coronary artery ligation, which reliably mimics CHF in patients with myocardial infarction. After 4 weeks of surgery, Sham and CHF rats were subjected to 3 weeks of progressive treadmill exercise. ExT significantly (p < 0.05) decreased PIN expression and increased dimer/monomer ratio of nNOS in the PVN of rats with CHF. Moreover, we found decreased GTP cyclohydrolase 1(GCH1) expression: a rate-limiting enzyme for BH4 biosynthesis in the PVN of CHF rats suggesting that perhaps reduced BH4 availability may also contribute to decreased nNOS dimers. Interestingly, CHF induced decrease in GCH1 expression was increased with ExT. Our findings revealed that ExT rectified decreased PIN and GCH1 expression and increased dimer/monomer ratio of nNOS in the PVN, which may lead to increase NO• bioavailability resulting in amelioration of activated sympathetic drive during CHF.
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Affiliation(s)
- Neeru M Sharma
- Department of Cellular and Integrative Physiology, UNMC, Omaha, NE 68198-5850, USA.
| | - Xuefei Liu
- Department of Cellular and Integrative Physiology, UNMC, Omaha, NE 68198-5850, USA
| | - Tamra L Llewellyn
- Department of Cellular and Integrative Physiology, UNMC, Omaha, NE 68198-5850, USA
| | - Kenichi Katsurada
- Department of Cellular and Integrative Physiology, UNMC, Omaha, NE 68198-5850, USA
| | - Kaushik P Patel
- Department of Cellular and Integrative Physiology, UNMC, Omaha, NE 68198-5850, USA
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23
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King A, Hoch NC, McGregor NE, Sims NA, Smyth IM, Heierhorst J. Dynll1 is essential for development and promotes endochondral bone formation by regulating intraflagellar dynein function in primary cilia. Hum Mol Genet 2019; 28:2573-2588. [DOI: 10.1093/hmg/ddz083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/15/2023] Open
Abstract
AbstractMutations in subunits of the cilia-specific cytoplasmic dynein-2 (CD2) complex cause short-rib thoracic dystrophy syndromes (SRTDs), characterized by impaired bone growth and life-threatening perinatal respiratory complications. Different SRTD mutations result in varying disease severities. It remains unresolved whether this reflects the extent of retained hypomorphic protein functions or relative importance of the affected subunits for the activity of the CD2 holoenzyme. To define the contribution of the LC8-type dynein light chain subunit to the CD2 complex, we have generated Dynll1-deficient mouse strains, including the first-ever conditional knockout (KO) mutant for any CD2 subunit. Germline Dynll1 KO mice exhibit a severe ciliopathy-like phenotype similar to mice lacking another CD2 subunit, Dync2li1. Limb mesoderm-specific loss of Dynll1 results in severe bone shortening similar to human SRTD patients. Mechanistically, loss of Dynll1 leads to a partial depletion of other SRTD-related CD2 subunits, severely impaired retrograde intra-flagellar transport, significant thickening of primary cilia and cilia signaling defects. Interestingly, phenotypes of Dynll1-deficient mice are very similar to entirely cilia-deficient Kif3a/Ift88-null mice, except that they never present with polydactyly and retain relatively higher signaling outputs in parts of the hedgehog pathway. Compared to complete loss of Dynll1, maintaining very low DYNLL1 levels in mice lacking the Dynll1-transcription factor ASCIZ (ATMIN) results in significantly attenuated phenotypes and improved CD2 protein levels. The results suggest that primary cilia can maintain some functionality in the absence of intact CD2 complexes and provide a viable animal model for the analysis of the underlying bone development defects of SRTDs.
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Affiliation(s)
- Ashleigh King
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
| | | | | | - Natalie A Sims
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jörg Heierhorst
- St. Vincent’s Institute of Medical Research
- Department of Medicine at St. Vincent’s Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, Victoria, Australia
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24
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Richards T, Modarage K, Dean C, McCarthy-Boxer A, Hilton H, Esapa C, Norman J, Wilson P, Goggolidou P. Atmin modulates Pkhd1 expression and may mediate Autosomal Recessive Polycystic Kidney Disease (ARPKD) through altered non-canonical Wnt/Planar Cell Polarity (PCP) signalling. Biochim Biophys Acta Mol Basis Dis 2019; 1865:378-390. [PMID: 30414501 PMCID: PMC6335440 DOI: 10.1016/j.bbadis.2018.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/10/2018] [Accepted: 11/05/2018] [Indexed: 12/25/2022]
Abstract
Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a genetic disorder with an incidence of ~1:20,000 that manifests in a wide range of renal and liver disease severity in human patients and can lead to perinatal mortality. ARPKD is caused by mutations in PKHD1, which encodes the large membrane protein, Fibrocystin, required for normal branching morphogenesis of the ureteric bud during embryonic renal development. The variation in ARPKD phenotype suggests that in addition to PKHD1 mutations, other genes may play a role, acting as modifiers of disease severity. One such pathway involves non-canonical Wnt/Planar Cell Polarity (PCP) signalling that has been associated with other cystic kidney diseases, but has not been investigated in ARPKD. Analysis of the AtminGpg6 mouse showed kidney, liver and lung abnormalities, suggesting it as a novel mouse tool for the study of ARPKD. Further, modulation of Atmin affected Pkhd1 mRNA levels, altered non-canonical Wnt/PCP signalling and impacted cellular proliferation and adhesion, although Atmin does not bind directly to the C-terminus of Fibrocystin. Differences in ATMIN and VANGL2 expression were observed between normal human paediatric kidneys and age-matched ARPKD kidneys. Significant increases in ATMIN, WNT5A, VANGL2 and SCRIBBLE were seen in human ARPKD versus normal kidneys; no substantial differences were seen in DAAM2 or NPHP2. A striking increase in E-cadherin was also detected in ARPKD kidneys. This work indicates a novel role for non-canonical Wnt/PCP signalling in ARPKD and suggests ATMIN as a modulator of PKHD1.
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MESH Headings
- Adolescent
- Apoptosis
- Cadherins/metabolism
- Cell Adhesion
- Cell Line
- Cell Polarity
- Cell Proliferation
- Child
- Child, Preschool
- Cytoskeleton/metabolism
- Embryo, Mammalian/metabolism
- Humans
- Infant
- Infant, Newborn
- Kidney Tubules, Collecting
- Phenotype
- Polycystic Kidney, Autosomal Recessive/genetics
- Polycystic Kidney, Autosomal Recessive/pathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Transcription Factors/metabolism
- Wnt Signaling Pathway
- beta Catenin/metabolism
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Affiliation(s)
- Taylor Richards
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Kavindiya Modarage
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Charlotte Dean
- National Heart and Lung Institute, Imperial College, South Kensington Campus, London SW7 2AZ, UK; MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Aidan McCarthy-Boxer
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Helen Hilton
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Chris Esapa
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Jill Norman
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Patricia Wilson
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Paraskevi Goggolidou
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK; MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK; Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK.
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25
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Becker JR, Cuella-Martin R, Barazas M, Liu R, Oliveira C, Oliver AW, Bilham K, Holt AB, Blackford AN, Heierhorst J, Jonkers J, Rottenberg S, Chapman JR. The ASCIZ-DYNLL1 axis promotes 53BP1-dependent non-homologous end joining and PARP inhibitor sensitivity. Nat Commun 2018; 9:5406. [PMID: 30559443 PMCID: PMC6297349 DOI: 10.1038/s41467-018-07855-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
53BP1 controls a specialized non-homologous end joining (NHEJ) pathway that is essential for adaptive immunity, yet oncogenic in BRCA1 mutant cancers. Intra-chromosomal DNA double-strand break (DSB) joining events during immunoglobulin class switch recombination (CSR) require 53BP1. However, in BRCA1 mutant cells, 53BP1 blocks homologous recombination (HR) and promotes toxic NHEJ, resulting in genomic instability. Here, we identify the protein dimerization hub-DYNLL1-as an organizer of multimeric 53BP1 complexes. DYNLL1 binding stimulates 53BP1 oligomerization, and promotes 53BP1's recruitment to, and interaction with, DSB-associated chromatin. Consequently, DYNLL1 regulates 53BP1-dependent NHEJ: CSR is compromised upon deletion of Dynll1 or its transcriptional regulator Asciz, or by mutation of DYNLL1 binding motifs in 53BP1; furthermore, Brca1 mutant cells and tumours are rendered resistant to poly-ADP ribose polymerase (PARP) inhibitor treatments upon deletion of Dynll1 or Asciz. Thus, our results reveal a mechanism that regulates 53BP1-dependent NHEJ and the therapeutic response of BRCA1-deficient cancers.
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Affiliation(s)
- Jordan R Becker
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Raquel Cuella-Martin
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Marco Barazas
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Rui Liu
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Catarina Oliveira
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Kirstin Bilham
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Abbey B Holt
- MRC Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, OX1 3TH, UK
| | - Andrew N Blackford
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jörg Heierhorst
- St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine at St. Vincent's Hospital, Melbourne Medical School, The University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3012, Switzerland
| | - J Ross Chapman
- Genome Integrity Laboratory, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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26
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Avolio R, Järvelin AI, Mohammed S, Agliarulo I, Condelli V, Zoppoli P, Calice G, Sarnataro D, Bechara E, Tartaglia GG, Landriscina M, Castello A, Esposito F, Matassa DS. Protein Syndesmos is a novel RNA-binding protein that regulates primary cilia formation. Nucleic Acids Res 2018; 46:12067-12086. [PMID: 30260431 PMCID: PMC6294507 DOI: 10.1093/nar/gky873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 12/24/2022] Open
Abstract
Syndesmos (SDOS) is a functionally poorly characterized protein that directly interacts with p53 binding protein 1 (53BP1) and regulates its recruitment to chromatin. We show here that SDOS interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS directly binds RNA in living cells. Combining individual gene expression profiling, nucleotide crosslinking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS. Among them, we identify a small subset of mRNAs responsible for the biogenesis of primary cilium that have been linked to developmental and degenerative diseases, known as ciliopathies, and cancer. We discover that SDOS binds and regulates the translation of several of these mRNAs, controlling cilia development.
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Affiliation(s)
- Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Napoli, Italy
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Proteomics Technology Development and Application, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ilenia Agliarulo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Napoli, Italy
| | - Valentina Condelli
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy
| | - Pietro Zoppoli
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy
| | - Giovanni Calice
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Napoli, Italy
- Ceinge-Biotecnologie avanzate, s.c.a r.l., Via G. Salvatore 486, 80145, Napoli, Italy
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), Dr. Aiguader St. 88, 08003 Barcelona, Spain
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), Dr. Aiguader St. 88, 08003 Barcelona, Spain
| | - Matteo Landriscina
- Laboratory of Pre-clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy
- Medical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 7100 Foggia, Italy
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Napoli, Italy
| | - Danilo S Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Napoli, Italy
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27
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DYNLL1 binds to MRE11 to limit DNA end resection in BRCA1-deficient cells. Nature 2018; 563:522-526. [PMID: 30464262 DOI: 10.1038/s41586-018-0670-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
Abstract
Limited DNA end resection is the key to impaired homologous recombination in BRCA1-mutant cancer cells. Here, using a loss-of-function CRISPR screen, we identify DYNLL1 as an inhibitor of DNA end resection. The loss of DYNLL1 enables DNA end resection and restores homologous recombination in BRCA1-mutant cells, thereby inducing resistance to platinum drugs and inhibitors of poly(ADP-ribose) polymerase. Low BRCA1 expression correlates with increased chromosomal aberrations in primary ovarian carcinomas, and the junction sequences of somatic structural variants indicate diminished homologous recombination. Concurrent decreases in DYNLL1 expression in carcinomas with low BRCA1 expression reduced genomic alterations and increased homology at lesions. In cells, DYNLL1 limits nucleolytic degradation of DNA ends by associating with the DNA end-resection machinery (MRN complex, BLM helicase and DNA2 endonuclease). In vitro, DYNLL1 binds directly to MRE11 to limit its end-resection activity. Therefore, we infer that DYNLL1 is an important anti-resection factor that influences genomic stability and responses to DNA-damaging chemotherapy.
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28
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Singh PK, Weber A, Häcker G. The established and the predicted roles of dynein light chain in the regulation of mitochondrial apoptosis. Cell Cycle 2018; 17:1037-1047. [PMID: 30019621 DOI: 10.1080/15384101.2018.1464851] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The mitochondrial pathway of apoptosis is regulated by the interplay between the members of Bcl-2 family. Within this family, BH3-only proteins are the sensors of apoptotic stimuli and can trigger apoptosis either by inhibiting the anti-apoptotic Bcl-2-family proteins or by directly activating the effectors Bax and Bak. An expanding body of research suggests that a number of non-Bcl-2 proteins can also interact with Bcl-2 proteins and contribute to the decision of cell fate. Dynein light chain (LC8, DYNLL or DLC), a hub protein and a dimerizing engine has been proposed to regulate the pro-apoptotic activity of two BH3-only proteins, Bim and Bmf. Our recent work has provided insight into the mechanisms through which DLC1 (DYNLL1) modulates Bim activity. Here we discuss the present day understanding of Bim-DLC interaction and endeavor to evaluate this interaction in the light of information from studies of DLC with other binding partners.
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Affiliation(s)
- Prafull Kumar Singh
- a Institute of Medical Microbiology and Hygiene, Faculty of Medicine , Medical Center-University of Freiburg , Freiburg , Germany
| | - Arnim Weber
- a Institute of Medical Microbiology and Hygiene, Faculty of Medicine , Medical Center-University of Freiburg , Freiburg , Germany
| | - Georg Häcker
- a Institute of Medical Microbiology and Hygiene, Faculty of Medicine , Medical Center-University of Freiburg , Freiburg , Germany.,b BIOSS Centre for Biological Signalling Studies , University of Freiburg , Freiburg , Germany
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29
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Clark S, Myers JB, King A, Fiala R, Novacek J, Pearce G, Heierhorst J, Reichow SL, Barbar EJ. Multivalency regulates activity in an intrinsically disordered transcription factor. eLife 2018; 7:36258. [PMID: 29714690 PMCID: PMC5963919 DOI: 10.7554/elife.36258] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference for low occupancy complexes at saturating LC8 concentrations with both human and Drosophila ASCIZ indicates that negative cooperativity is an important feature of ASCIZ-LC8 interactions. The prevalence of intrinsic disorder and multivalency among transcription factors suggests that formation of heterogeneous, dynamic complexes is a widespread mechanism for tuning transcriptional regulation.
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Affiliation(s)
- Sarah Clark
- Department of Biochemistry and Biophysics, Oregon State University, Oregon, United States
| | - Janette B Myers
- Department of Chemistry, Portland State University, Oregon, United States
| | - Ashleigh King
- St. Vincent's Institute of Medical Research, The University of Melbourne, Victoria, Australia.,Department of Medicine, St. Vincent's Health, The University of Melbourne, Victoria, Australia
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiri Novacek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Grant Pearce
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jörg Heierhorst
- St. Vincent's Institute of Medical Research, The University of Melbourne, Victoria, Australia.,Department of Medicine, St. Vincent's Health, The University of Melbourne, Victoria, Australia
| | - Steve L Reichow
- Department of Chemistry, Portland State University, Oregon, United States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Oregon, United States
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30
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King A, Li L, Wong DM, Liu R, Bamford R, Strasser A, Tarlinton DM, Heierhorst J. Dynein light chain regulates adaptive and innate B cell development by distinctive genetic mechanisms. PLoS Genet 2017; 13:e1007010. [PMID: 28922373 PMCID: PMC5619840 DOI: 10.1371/journal.pgen.1007010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 09/28/2017] [Accepted: 09/07/2017] [Indexed: 11/29/2022] Open
Abstract
Mechanistic differences in the development and function of adaptive, high-affinity antibody-producing B-2 cells and innate-like, “natural” antibody-producing B-1a cells remain poorly understood. Here we show that the multi-functional dynein light chain (DYNLL1/LC8) plays important roles in the establishment of B-1a cells in the peritoneal cavity and in the ongoing development of B-2 lymphoid cells in the bone marrow of mice. Epistasis analyses indicate that Dynll1 regulates B-1a and early B-2 cell development in a single, linear pathway with its direct transcriptional activator ASCIZ (ATMIN/ZNF822), and that the two genes also have complementary functions during late B-2 cell development. The B-2 cell defects caused by loss of DYNLL1 were associated with lower levels of the anti-apoptotic protein BCL-2, and could be supressed by deletion of pro-apoptotic BIM which is negatively regulated by both DYNLL1 and BCL-2. Defects in B cell development caused by loss of DYNLL1 could also be partially suppressed by a pre-arranged SWHELIgm-B cell receptor transgene. In contrast to the rescue of B-2 cell numbers, the B-1a cell deficiency in Dynll1-deleted mice could not be suppressed by the loss of Bim, and was further compounded by the SWHEL transgene. Conversely, oncogenic MYC expression, which is synthetic lethal with Dynll1 deletion in B-2 cells, did not further reduce B-1a cell numbers in Dynll1-defcient mice. Finally, we found that the ASCIZ-DYNLL1 axis was also required for the early-juvenile development of aggressive MYC-driven and p53-deficient B cell lymphomas. These results identify ASCIZ and DYNLL1 as the core of a transcriptional circuit that differentially regulates the development of the B-1a and B-2 B lymphoid cell lineages and plays a critical role in lymphomagenesis. Antibody-producing B cells can be segregated into two major populations: The better known conventional B-2 cells typically produce high-affinity and mono-specific antibodies, but only after they encounter a particular pathogen or in response to vaccines. In contrast, the B-1a cells constitutively produce lower-affinity broad-specificity “natural” antibodies that serve as a preemptive defense against a wide range of microbes. Here we reveal that the transcription factor ASCIZ and its target DYNLL1 are essential for mice to have a normally sized pool of B-1a cells in place shortly after birth. We show that these two factors function in a single linear pathway during the development of B-1a cells. This interaction represents a rare example where the activity of a transcription factor, in this case ASCIZ, can be explained by the effects of a single target gene, in this case Dynll1. While ASCIZ and DYNLL1 are also required for producing normal numbers of B-2 cells, we discovered that they regulate B-1a cells and B-2 cells by distinct genetic mechanisms. Finally, we found that ASCIZ also contributes to the early onset of B-1a B cell-derived lymphoid cancers in juvenile mice. The results provide insight into the development of an important cell population of the immune system.
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Affiliation(s)
- Ashleigh King
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), University of Melbourne, Fitzroy, Victoria, Australia
| | - Lingli Li
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), University of Melbourne, Fitzroy, Victoria, Australia
| | - David M. Wong
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Rui Liu
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Rebecca Bamford
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Andreas Strasser
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David M. Tarlinton
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Jörg Heierhorst
- Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), University of Melbourne, Fitzroy, Victoria, Australia
- * E-mail:
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31
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Novel biomarkers in kidney disease: roles for cilia, Wnt signalling and ATMIN in polycystic kidney disease. Biochem Soc Trans 2017; 44:1745-1751. [PMID: 27913685 DOI: 10.1042/bst20160124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 01/24/2023]
Abstract
Biomarkers, the measurable indicators of biological conditions, are fast becoming a popular approach in providing information to track disease processes that could lead to novel therapeutic interventions for chronic conditions. Inherited, chronic kidney disease affects millions of people worldwide and although pharmacological treatments exist for some conditions, there are still patients whose only option is kidney dialysis and kidney transplantation. In the past 10 years, certain chronic kidney diseases have been reclassified as ciliopathies. Cilia in the kidney are antenna-like, sensory organelles that are required for signal transduction. One of the signalling pathways that requires the primary cilium in the kidney is Wnt signalling and it has three components such as canonical Wnt, non-canonical Wnt/planar cell olarity (PCP) and non-canonical Wnt/Ca2+ signalling. Identification of the novel role of ATM INteractor (ATMIN) as an effector molecule in the non-canonical Wnt/PCP pathway has intrigued us to investigate its potential role in chronic kidney disease. ATMIN could thus be an important biomarker in disease prognosis and treatment that might lighten the burden of chronic kidney disease and also affect on its progression.
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32
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Abstract
ASCIZ/ATMIN is not required for ATM activation by replication stress in MEFs. ATM activation is normal in human ASCIZ/ATMIN KO cells. ASCIZ/ATMIN is dispensable for aphidicolin-induced 53BP1 focus formation.
The ATM kinase plays critical roles in the response to DNA double-strand breaks, and can also be activated by prolonged DNA replication blocks. It has recently been proposed that replication stress-dependent ATM activation is mediated by ASCIZ (also known as ATMIN, ZNF822), an essential developmental transcription factor. In contrast, we show here that ATM activation, and phosphorylation of its substrates KAP1, p53 and H2AX in response to the replication blocking agent aphidicolin was unaffected in both immortalized and primary ASCIZ/ATMIN-deficient murine embryonic fibroblasts compared to control cells. Similar results were also obtained in human ASCIZ/ATMIN-deleted lymphoma cells. The results demonstrate that ASCIZ/ATMIN is dispensable for ATM activation, and contradict the previously reported dependence of ATM on ASCIZ/ATMIN.
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33
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Wright DJ, Day FR, Kerrison ND, Zink F, Cardona A, Sulem P, Thompson DJ, Sigurjonsdottir S, Gudbjartsson DF, Helgason A, Chapman JR, Jackson SP, Langenberg C, Wareham NJ, Scott RA, Thorsteindottir U, Ong KK, Stefansson K, Perry JR. Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility. Nat Genet 2017; 49:674-679. [PMID: 28346444 PMCID: PMC5973269 DOI: 10.1038/ng.3821] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/26/2017] [Indexed: 12/14/2022]
Abstract
The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10-8) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10-6). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY. The genes identified converge on aspects of cell proliferation and cell cycle regulation, including DNA synthesis (NPAT), DNA damage response (ATM), mitosis (PMF1, CENPN and MAD1L1) and apoptosis (TP53). We highlight the shared genetic architecture between mLOY and cancer susceptibility, in addition to inferring a causal effect of smoking on mLOY. Collectively, our results demonstrate that genotype-array-intensity data enables a measure of cell cycle efficiency at population scale and identifies genes implicated in aneuploidy, genome instability and cancer susceptibility.
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Affiliation(s)
- Daniel J. Wright
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Felix R. Day
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Nicola D. Kerrison
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Florian Zink
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
| | - Deborah J. Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | | | - J. Ross Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Steve P. Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Robert A. Scott
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Unnur Thorsteindottir
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ken K. Ong
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - John R.B. Perry
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
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34
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Sengupta S, Rath U, Yao C, Zavortink M, Wang C, Girton J, Johansen KM, Johansen J. Digitor/dASCIZ Has Multiple Roles in Drosophila Development. PLoS One 2016; 11:e0166829. [PMID: 27861562 PMCID: PMC5115829 DOI: 10.1371/journal.pone.0166829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/05/2016] [Indexed: 12/02/2022] Open
Abstract
In this study we provide evidence that the spindle matrix protein Skeletor in Drosophila interacts with the human ASCIZ (also known as ATMIN and ZNF822) ortholog, Digitor/dASCIZ. This interaction was first detected in a yeast two-hybrid screen and subsequently confirmed by pull-down assays. We also confirm a previously documented function of Digitor/dASCIZ as a regulator of Dynein light chain/Cut up expression. Using transgenic expression of a mCitrine-labeled Digitor construct, we show that Digitor/dASCIZ is a nuclear protein that is localized to interband and developmental puff chromosomal regions during interphase but redistributes to the spindle region during mitosis. Its mitotic localization and physical interaction with Skeletor suggest the possibility that Digitor/dASCIZ plays a direct role in mitotic progression as a member of the spindle matrix complex. Furthermore, we have characterized a P-element insertion that is likely to be a true null Digitor/dASCIZ allele resulting in complete pupal lethality when homozygous, indicating that Digitor/dASCIZ is an essential gene. Phenotypic analysis of the mutant provided evidence that Digitor/dASCIZ plays critical roles in regulation of metamorphosis and organogenesis as well as in the DNA damage response. In the Digitor/dASCIZ null mutant larvae there was greatly elevated levels of γH2Av, indicating accumulation of DNA double-strand breaks. Furthermore, reduced levels of Digitor/dASCIZ decreased the resistance to paraquat-induced oxidative stress resulting in increased mortality in a stress test paradigm. We show that an early developmental consequence of the absence of Digitor/dASCIZ is reduced third instar larval brain size although overall larval development appeared otherwise normal at this stage. While Digitor/dASCIZ mutant larvae initiate pupation, all mutant pupae failed to eclose and exhibited various defects in metamorphosis such as impaired differentiation, incomplete disc eversion, and faulty apoptosis. Altogether we provide evidence that Digitor/dASCIZ is a nuclear protein that performs multiple roles in Drosophila larval and pupal development.
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Affiliation(s)
- Saheli Sengupta
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Uttama Rath
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Changfu Yao
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Michael Zavortink
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Chao Wang
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Jack Girton
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Kristen M. Johansen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (JJ); (KMJ)
| | - Jørgen Johansen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (JJ); (KMJ)
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Anjos-Afonso F, Loizou JI, Bradburn A, Kanu N, Purewal S, Da Costa C, Bonnet D, Behrens A. Perturbed hematopoiesis in mice lacking ATMIN. Blood 2016; 128:2017-2021. [PMID: 27581360 PMCID: PMC5147016 DOI: 10.1182/blood-2015-09-672980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/25/2016] [Indexed: 01/20/2023] Open
Abstract
The ataxia telangiectasia mutated (ATM)-interacting protein ATMIN mediates noncanonical ATM signaling in response to oxidative and replicative stress conditions. Like ATM, ATMIN can function as a tumor suppressor in the hematopoietic system: deletion of Atmin under the control of CD19-Cre results in B-cell lymphomas in aging mice. ATM signaling is essential for lymphopoiesis and hematopoietic stem cell (HSC) function; however, little is known about the role of ATMIN in hematopoiesis. We thus sought to investigate whether the absence of ATMIN would affect primitive hematopoietic cells in an ATM-dependent or -independent manner. Apart from its role in B-cell development, we show that ATMIN has an ATM-independent function in the common myeloid progenitors (CMPs) by deletion of Atmin in the entire hematopoietic system using Vav-Cre. Despite the lack of lymphoma formation, ATMIN-deficient mice developed chronic leukopenia as a result of high levels of apoptosis in B cells and CMPs and induced a compensatory mechanism in which HSCs displayed enhanced cycling. Consequently, ATMIN-deficient HSCs showed impaired regeneration ability with the induction of the DNA oxidative stress response, especially when aged. ATMIN, therefore, has multiple roles in different cell types, and its absence results in perturbed hematopoiesis, especially during stress conditions and aging.
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Affiliation(s)
- Fernando Anjos-Afonso
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
- Haematopoietic Signalling Group, European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Joanna I Loizou
- Mammalian Genetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amy Bradburn
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
| | - Nnennaya Kanu
- Mammalian Genetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
- Translational Cancer Therapeutics Laboratory, UCL Cancer Institute, University College London, London, United Kingdom
| | - Sukhveer Purewal
- Flow Cytometry Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom; and
| | - Clive Da Costa
- Mammalian Genetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
| | - Axel Behrens
- Mammalian Genetics Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom
- Diabetes & Nutritional Sciences Division, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
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36
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Blake SM, Stricker SH, Halavach H, Poetsch AR, Cresswell G, Kelly G, Kanu N, Marino S, Luscombe NM, Pollard SM, Behrens A. Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation. eLife 2016; 5:e08711. [PMID: 26984279 PMCID: PMC4811777 DOI: 10.7554/elife.08711] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 02/18/2016] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive human primary brain cancer. Using a Trp53-deficient mouse model of GBM, we show that genetic inactivation of the Atm cofactor Atmin, which is dispensable for embryonic and adult neural development, strongly suppresses GBM formation. Mechanistically, expression of several GBM-associated genes, including Pdgfra, was normalized by Atmin deletion in the Trp53-null background. Pharmacological ATM inhibition also reduced Pdgfra expression, and reduced the proliferation of Trp53-deficient primary glioma cells from murine and human tumors, while normal neural stem cells were unaffected. Analysis of GBM datasets showed that PDGFRA expression is also significantly increased in human TP53-mutant compared with TP53-wild-type tumors. Moreover, combined treatment with ATM and PDGFRA inhibitors efficiently killed TP53-mutant primary human GBM cells, but not untransformed neural stem cells. These results reveal a new requirement for ATMIN-dependent ATM signaling in TP53-deficient GBM, indicating a pro-tumorigenic role for ATM in the context of these tumors.
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Affiliation(s)
- Sophia M Blake
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stefan H Stricker
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Hanna Halavach
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anna R Poetsch
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - George Cresswell
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gavin Kelly
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Nnennaya Kanu
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Silvia Marino
- Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Nicholas M Luscombe
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Steven M Pollard
- Samantha Dickson Brain Cancer Unit and Department of Cancer Biology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London, United Kingdom
- Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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Leszczynska KB, Göttgens EL, Biasoli D, Olcina MM, Ient J, Anbalagan S, Bernhardt S, Giaccia AJ, Hammond EM. Mechanisms and consequences of ATMIN repression in hypoxic conditions: roles for p53 and HIF-1. Sci Rep 2016; 6:21698. [PMID: 26875667 PMCID: PMC4753685 DOI: 10.1038/srep21698] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/29/2016] [Indexed: 12/30/2022] Open
Abstract
Hypoxia-induced replication stress is one of the most physiologically relevant signals known to activate ATM in tumors. Recently, the ATM interactor (ATMIN) was identified as critical for replication stress-induced activation of ATM in response to aphidicolin and hydroxyurea. This suggests an essential role for ATMIN in ATM regulation during hypoxia, which induces replication stress. However, ATMIN also has a role in base excision repair, a process that has been demonstrated to be repressed and less efficient in hypoxic conditions. Here, we demonstrate that ATMIN is dispensable for ATM activation in hypoxia and in contrast to ATM, does not affect cell survival and radiosensitivity in hypoxia. Instead, we show that in hypoxic conditions ATMIN expression is repressed. Repression of ATMIN in hypoxia is mediated by both p53 and HIF-1α in an oxygen dependent manner. The biological consequence of ATMIN repression in hypoxia is decreased expression of the target gene, DYNLL1. An expression signature associated with p53 activity was negatively correlated with DYNLL1 expression in patient samples further supporting the p53 dependent repression of DYNLL1. Together, these data demonstrate multiple mechanisms of ATMIN repression in hypoxia with consequences including impaired BER and down regulation of the ATMIN transcriptional target, DYNLL1.
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Affiliation(s)
- Katarzyna B. Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Eva-Leonne Göttgens
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Deborah Biasoli
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Monica M. Olcina
- Division of Cancer and Radiation Oncology, Department of Radiation Oncology, Stanford University, Stanford, California 94305, USA
| | - Jonathan Ient
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Selvakumar Anbalagan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephan Bernhardt
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Amato J. Giaccia
- Division of Cancer and Radiation Oncology, Department of Radiation Oncology, Stanford University, Stanford, California 94305, USA
| | - Ester M. Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
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Wong D, Li L, Jurado S, King A, Bamford R, Wall M, Walia M, Kelly G, Walkley C, Tarlinton D, Strasser A, Heierhorst J. The Transcription Factor ASCIZ and Its Target DYNLL1 Are Essential for the Development and Expansion of MYC-Driven B Cell Lymphoma. Cell Rep 2016; 14:1488-1499. [DOI: 10.1016/j.celrep.2016.01.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022] Open
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The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development. Sci Rep 2016; 6:19050. [PMID: 26743489 PMCID: PMC4705472 DOI: 10.1038/srep19050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
ATM and ATR are cellular kinases with a well-characterized role in the DNA-damage response. Although the complete set of ATM/ATR targets is unknown, they often contain clusters of S/TQ motifs that constitute an SCD domain. In this study, we identified putative ATM/ATR targets that have a conserved SCD domain across vertebrates. Using this approach, we have identified novel putative ATM/ATR targets in pathways known to be under direct control of these kinases. Our analysis has also unveiled significant enrichment of SCD-containing proteins in cellular pathways, such as vesicle trafficking and actin cytoskeleton, where a regulating role for ATM/ATR is either unknown or poorly understood, hinting at a much broader and overarching role for these kinases in the cell. Of particular note is the overrepresentation of conserved SCD-containing proteins involved in pathways related to neural development. This finding suggests that ATM/ATR could be directly involved in controlling this process, which may be linked to the adverse neurological effects observed in patients with mutations in ATM.
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40
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Clark S, Nyarko A, Löhr F, Karplus PA, Barbar E. The Anchored Flexibility Model in LC8 Motif Recognition: Insights from the Chica Complex. Biochemistry 2015; 55:199-209. [PMID: 26652654 DOI: 10.1021/acs.biochem.5b01099] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
LC8 is a dimeric hub protein involved in a large number of interactions central to cell function. It binds short linear motifs--usually containing a Thr-Gln-Thr (TQT) triplet--in intrinsically disordered regions of its binding partners, some of which have several LC8 recognition motifs in tandem. Hallmarks of the 7-10 amino acid motif are a high variability of LC8 binding affinity and extensive sequence permutation outside the TQT triplet. To elucidate the molecular basis of motif recognition, we use a 69-residue segment of the human Chica spindle adaptor protein that contains four putative TQT recognition motifs in tandem. NMR-derived secondary chemical shifts and relaxation properties show that the Chica LC8 binding domain is essentially disordered with a dynamically restricted segment in one linker between motifs. Calorimetry of LC8 binding to synthetic motif-mimicking peptides shows that the first motif dominates LC8 recruitment. Crystal structures of the complexes of LC8 bound to each of two motif peptides show highly ordered and invariant TQT-LC8 interactions and more flexible and conformationally variable non-TQT-LC8 interactions. These data highlight rigidity in both LC8 residues that bind TQT and in the TQT portion of the motif as an important new characteristic of LC8 recognition. On the basis of these data and others in the literature, we propose that LC8 recognition is based on rigidly fixed interactions between LC8 and TQT residues that act as an anchor, coupled with inherently flexible interactions between LC8 and non-TQT residues. The "anchored flexibility" model explains the requirement for the TQT triplet and the ability of LC8 to accommodate a large variety of motif sequences and affinities.
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Affiliation(s)
- Sarah Clark
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Afua Nyarko
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe-University , D-60438 Frankfurt, Germany
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 97331, United States
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Vertii A, Bright A, Delaval B, Hehnly H, Doxsey S. New frontiers: discovering cilia-independent functions of cilia proteins. EMBO Rep 2015; 16:1275-87. [PMID: 26358956 DOI: 10.15252/embr.201540632] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/17/2015] [Indexed: 12/11/2022] Open
Abstract
In most vertebrates, mitotic spindles and primary cilia arise from a common origin, the centrosome. In non-cycling cells, the centrosome is the template for primary cilia assembly and, thus, is crucial for their associated sensory and signaling functions. During mitosis, the duplicated centrosomes mature into spindle poles, which orchestrate mitotic spindle assembly, chromosome segregation, and orientation of the cell division axis. Intriguingly, both cilia and spindle poles are centrosome-based, functionally distinct structures that require the action of microtubule-mediated, motor-driven transport for their assembly. Cilia proteins have been found at non-cilia sites, where they have distinct functions, illustrating a diverse and growing list of cellular processes and structures that utilize cilia proteins for crucial functions. In this review, we discuss cilia-independent functions of cilia proteins and re-evaluate their potential contributions to "cilia" disorders.
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Affiliation(s)
- Anastassiia Vertii
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Alison Bright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Heidi Hehnly
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephen Doxsey
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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42
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Clark SA, Jespersen N, Woodward C, Barbar E. Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds. FEBS Lett 2015; 589:2543-51. [PMID: 26226419 DOI: 10.1016/j.febslet.2015.07.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/17/2023]
Abstract
A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.
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Affiliation(s)
- Sarah A Clark
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Nathan Jespersen
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Clare Woodward
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, St. Paul, MN 55108, United States
| | - Elisar Barbar
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, United States.
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43
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A Dynein Light Chain 1 Binding Motif in Rabies Virus Polymerase L Protein Plays a Role in Microtubule Reorganization and Viral Primary Transcription. J Virol 2015; 89:9591-600. [PMID: 26157129 DOI: 10.1128/jvi.01298-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/04/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Rabies virus (RABV) polymerase L together with phosphoprotein P forms the PL polymerase complex that is essential for replication and transcription. However, its exact mechanism of action, interactions with cellular factors, and intracellular distribution are yet to be understood. Here by imaging a fluorescently tagged polymerase (mCherry-RABV-L), we show that L accumulates at acetylated and reorganized microtubules (MT). In silico analysis revealed a dynein light chain 1 (DLC1) binding motif in L that could mediate MT binding through dynein motors. As DLC1 binding by polymerase cofactor P is known, we compared the impact of the DLC1-binding motifs in P and L. Viruses with mutations in the respective motifs revealed that both motifs are required for efficient primary transcription, indicating that DLC1 acts as a transcription enhancer by binding to both P and L. Notably, also the levels of cellular DLC1 protein were regulated by both motifs, suggesting regulation of the DLC1 gene expression by both P and L. Finally, disruption of the motif in L resulted in a cell-type-specific loss of MT localization, demonstrating that DLC1 is involved in L-mediated cytoskeleton reorganization. Overall, we conclude that DLC1 acts as a transcription factor that stimulates primary RABV transcription by binding to both P and L. We further conclude that L influences MT organization and posttranslational modification, suggesting a model in which MT manipulation by L contributes to efficient intracellular transport of virus components and thus may serve as an important step in virus replication. IMPORTANCE Regulation of rabies virus polymerase complex by viral and cellular factors thus far has not been fully understood. Although cellular dynein light chain 1 (DLC1) has been reported to increase primary transcription by binding to polymerase cofactor phosphoprotein P, the detailed mechanism is unknown, and it is also not known whether the large enzymatic polymerase subunit L is involved. By fluorescence microscopy analysis of fluorescence-tagged rabies virus L, in silico identification of a potential DLC1 binding site in L, and characterization of recombinant rabies virus mutants, we show that a DLC1 binding motif in L is involved in cytoskeleton localization and reorganization, primary transcription regulation by DLC1, and regulation of cellular DLC1 gene expression. By providing evidence for a direct contribution of a DLC1 binding motif in L, our data significantly increase the understanding of rabies virus polymerase regulation and host manipulation by the virus as well.
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44
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BET inhibitors induce apoptosis through a MYC independent mechanism and synergise with CDK inhibitors to kill osteosarcoma cells. Sci Rep 2015; 5:10120. [PMID: 25944566 PMCID: PMC4421868 DOI: 10.1038/srep10120] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/27/2015] [Indexed: 12/11/2022] Open
Abstract
Osteosarcoma (OS) survival rates have plateaued in part due to a lack of new therapeutic options. Here we demonstrate that bromodomain inhibitors (BETi), JQ1, I-BET151, I-BET762, exert potent anti-tumour activity against primary and established OS cell lines, mediated by inhibition of BRD4. Strikingly, unlike previous observations in long-term established human OS cell lines, the antiproliferative activity of JQ1 in primary OS cells was driven by the induction of apoptosis, not cell cycle arrest. In further contrast, JQ1 activity in OS was mediated independently of MYC downregulation. We identified that JQ1 suppresses the transcription factor FOSL1 by displacement of BRD4 from its locus. Loss of FOSL1 phenocopied the antiproliferative effects of JQ1, identifying FOSL1 suppression as a potential novel therapeutic approach for OS. As a monotherapy JQ1 demonstrated significant anti-tumour activity in vivo in an OS graft model. Further, combinatorial treatment approaches showed that JQ1 increased the sensitivity of OS cells to doxorubicin and induced potent synergistic activity when rationally combined with CDK inhibitors. The greater level of activity achieved with the combination of BETi with CDK inhibitors demonstrates the efficacy of this combination therapy. Taken together, our studies show that BET inhibitors are a promising new therapeutic for OS.
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Baker EK, Taylor S, Gupte A, Chalk AM, Bhattacharya S, Green AC, Martin TJ, Strbenac D, Robinson MD, Purton LE, Walkley CR. Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma. Bone 2015; 73:223-32. [PMID: 25571841 DOI: 10.1016/j.bone.2014.12.063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/03/2014] [Accepted: 12/28/2014] [Indexed: 12/29/2022]
Abstract
Wnt pathway targeting is of high clinical interest for treating bone loss disorders such as osteoporosis. These therapies inhibit the action of negative regulators of osteoblastic Wnt signaling. The report that Wnt inhibitory factor 1 (WIF1) was epigenetically silenced via promoter DNA methylation in osteosarcoma (OS) raised potential concerns for such treatment approaches. Here we confirm that Wif1 expression is frequently reduced in OS. However, we demonstrate that silencing is not driven by DNA methylation. Treatment of mouse and human OS cells showed that Wif1 expression was robustly induced by HDAC inhibition but not by methylation inhibition. Consistent with HDAC dependent silencing, the Wif1 locus in OS was characterized by low acetylation levels and a bivalent H3K4/H3K27-trimethylation state. Wif1 expression marked late stages of normal osteoblast maturation and stratified OS tumors based on differentiation stage across species. Culture of OS cells under differentiation inductive conditions increased expression of Wif1. Together these results demonstrate that Wif1 is not targeted for silencing by DNA methylation in OS. Instead, the reduced expression of Wif1 in OS cells is in context with their stage in differentiation.
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Affiliation(s)
- Emma K Baker
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia.
| | - Scott Taylor
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Ankita Gupte
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Alistair M Chalk
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia
| | - Shreya Bhattacharya
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia
| | - Alanna C Green
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia
| | - T John Martin
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia; Bone Cell Biology and Disease Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Dario Strbenac
- Cancer Epigenetics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Louise E Purton
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia
| | - Carl R Walkley
- Stem Cell Regulation Unit, St. Vincent's Institute of Medical Research, Fitzroy, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Australia.
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46
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Goggolidou P, Stevens JL, Agueci F, Keynton J, Wheway G, Grimes DT, Patel SH, Hilton H, Morthorst SK, DiPaolo A, Williams DJ, Sanderson J, Khoronenkova SV, Powles-Glover N, Ermakov A, Esapa CT, Romero R, Dianov GL, Briscoe J, Johnson CA, Pedersen LB, Norris DP. ATMIN is a transcriptional regulator of both lung morphogenesis and ciliogenesis. Development 2014; 141:3966-77. [PMID: 25294941 PMCID: PMC4197704 DOI: 10.1242/dev.107755] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Initially identified in DNA damage repair, ATM-interactor (ATMIN) further functions as a transcriptional regulator of lung morphogenesis. Here we analyse three mouse mutants, Atmingpg6/gpg6, AtminH210Q/H210Q and Dynll1GT/GT, revealing how ATMIN and its transcriptional target dynein light chain LC8-type 1 (DYNLL1) are required for normal lung morphogenesis and ciliogenesis. Expression screening of ciliogenic genes confirmed Dynll1 to be controlled by ATMIN and further revealed moderately altered expression of known intraflagellar transport (IFT) protein-encoding loci in Atmin mutant embryos. Significantly, Dynll1GT/GT embryonic cilia exhibited shortening and bulging, highly similar to the characterised retrograde IFT phenotype of Dync2h1. Depletion of ATMIN or DYNLL1 in cultured cells recapitulated the in vivo ciliogenesis phenotypes and expression of DYNLL1 or the related DYNLL2 rescued the effects of loss of ATMIN, demonstrating that ATMIN primarily promotes ciliogenesis by regulating Dynll1 expression. Furthermore, DYNLL1 as well as DYNLL2 localised to cilia in puncta, consistent with IFT particles, and physically interacted with WDR34, a mammalian homologue of the Chlamydomonas cytoplasmic dynein 2 intermediate chain that also localised to the cilium. This study extends the established Atmin-Dynll1 relationship into a developmental and a ciliary context, uncovering a novel series of interactions between DYNLL1, WDR34 and ATMIN. This identifies potential novel components of cytoplasmic dynein 2 and furthermore provides fresh insights into the molecular pathogenesis of human skeletal ciliopathies.
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Affiliation(s)
- Paraskevi Goggolidou
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jonathan L Stevens
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Francesco Agueci
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jennifer Keynton
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Gabrielle Wheway
- Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Daniel T Grimes
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Saloni H Patel
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Stine K Morthorst
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, OE DK-2100, Denmark
| | - Antonella DiPaolo
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Debbie J Williams
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Jeremy Sanderson
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Svetlana V Khoronenkova
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-11, Moscow 119991, Russia
| | - Nicola Powles-Glover
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Alexander Ermakov
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Chris T Esapa
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Rosario Romero
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Grigory L Dianov
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - James Briscoe
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Colin A Johnson
- Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen, OE DK-2100, Denmark
| | - Dominic P Norris
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
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Goggolidou P, Hadjirin NF, Bak A, Papakrivopoulou E, Hilton H, Norris DP, Dean CH. Atmin mediates kidney morphogenesis by modulating Wnt signaling. Hum Mol Genet 2014; 23:5303-16. [PMID: 24852369 PMCID: PMC4168818 DOI: 10.1093/hmg/ddu246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The DNA damage protein and transcription factor Atmin (Asciz) is required for both lung tubulogenesis and ciliogenesis. Like the lungs, kidneys contain a tubular network that is critical for their function and in addition, renal ciliary dysfunction has been implicated in the pathogenesis of cystic kidney disease. Using the Atmin mouse mutant Gasping6 (Gpg6), we investigated kidney development and found it severely disrupted with reduced branching morphogenesis, resulting in fewer epithelial structures being formed. Unexpectedly, transcriptional levels of key cilia associated genes were not altered in AtminGpg6/Gpg6 kidneys. Instead, Gpg6 homozygous kidneys exhibited altered cytoskeletal organization and modulation of Wnt signaling pathway molecules, including β-catenin and non-canonical Wnt/planar cell polarity (PCP) pathway factors, such as Daam2 and Vangl2. Wnt signaling is important for kidney development and perturbation of Wnt signaling pathways can result in cystic, and other, renal abnormalities. In common with other PCP pathway mutants, AtminGpg6/Gpg6 mice displayed a shortened rostral-caudal axis and mis-oriented cell division. Moreover, intercrosses between AtminGpg6/+ and Vangl2Lp/+ mice revealed a genetic interaction between Atmin and Vangl2. Thus we show for the first time that Atmin is critical for normal kidney development and we present evidence that mechanistically, Atmin modifies Wnt signaling pathways, specifically placing it as a novel effector molecule in the non-canonical Wnt/PCP pathway. The identification of a novel modulator of Wnt signaling has important implications for understanding the pathobiology of renal disease.
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Affiliation(s)
- Paraskevi Goggolidou
- Leukocyte Biology, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Aggie Bak
- College of Nursing, Midwifery & Healthcare, University of West London, Middlesex TW8 9GB, UK
| | | | - Helen Hilton
- Mammalian Genetics Unit, Medical Research Council, Harwell, UK
| | | | - Charlotte H Dean
- Leukocyte Biology, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK Mammalian Genetics Unit, Medical Research Council, Harwell, UK
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Barbar E, Nyarko A. NMR Characterization of Self-Association Domains Promoted by Interactions with LC8 Hub Protein. Comput Struct Biotechnol J 2014; 9:e201402003. [PMID: 24757501 PMCID: PMC3995210 DOI: 10.5936/csbj.201402003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/04/2014] [Accepted: 02/08/2014] [Indexed: 01/04/2023] Open
Abstract
Most proteins in interaction networks have a small number of partners, while a few, called hubs, participate in a large number of interactions and play a central role in cell homeostasis. One highly conserved hub is a protein called LC8 that was originally identified as an essential component of the multi-subunit complex dynein but later shown to be also critical in multiple protein complexes in diverse systems. What is intriguing about this hub protein is that it does not passively bind its various partners but emerging evidence suggests that LC8 acts as a dimerization engine that promotes self-association and/or higher order organization of its primarily disordered monomeric partners. This structural organization process does not require ATP but is triggered by long-range allosteric regulation initiated by LC8 binding a pair of disordered chains forming a bivalent or polybivalent scaffold. This review focuses on the role of LC8 in promoting self-association of two of its binding partners, a dynein intermediate chain and a non dynein protein called Swallow.
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Affiliation(s)
- Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Afua Nyarko
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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49
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The novel zinc finger protein dASCIZ regulates mitosis in Drosophila via an essential role in dynein light-chain expression. Genetics 2013; 196:443-53. [PMID: 24336747 DOI: 10.1534/genetics.113.159541] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The essential zinc finger protein ASCIZ (also known as ATMIN, ZNF822) plays critical roles during lung organogenesis and B cell development in mice, where it regulates the expression of dynein light chain (DYNLL1/LC8), but its functions in other species including invertebrates are largely unknown. Here we report the identification of the Drosophila ortholog of ASCIZ (dASCIZ) and show that loss of dASCIZ function leads to pronounced mitotic delays with centrosome and spindle positioning defects during development, reminiscent of impaired dynein motor functions. Interestingly, similar mitotic and developmental defects were observed upon knockdown of the DYNLL/LC8-type dynein light chain Cutup (Ctp), and dASCIZ loss-of-function phenotypes could be suppressed by ectopic Ctp expression. Consistent with a genetic function of dASCIZ upstream of Ctp, we show that loss of dASCIZ led to reduced endogenous Ctp mRNA and protein levels and dramatically reduced Ctp-LacZ reporter gene activity in vivo, indicating that dASCIZ regulates development and mitosis as a Ctp transcription factor. We speculate that the more severe mitotic defects in the absence of ASCIZ in flies compared to mice may be due to redundancy with a second, ASCIZ-independent, Dynll2 gene in mammals in contrast to a single Ctp gene in Drosophila. Altogether, our data demonstrate that ASCIZ is an evolutionary highly conserved transcriptional regulator of dynein light-chain levels and a novel regulator of mitosis in flies.
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50
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Jurado S, Gleeson K, O'Donnell K, Izon DJ, Walkley CR, Strasser A, Tarlinton DM, Heierhorst J. The Zinc-finger protein ASCIZ regulates B cell development via DYNLL1 and Bim. ACTA ACUST UNITED AC 2012; 209:1629-39. [PMID: 22891272 PMCID: PMC3428950 DOI: 10.1084/jem.20120785] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Developing B lymphocytes expressing defective or autoreactive pre-B or B cell receptors (BCRs) are eliminated by programmed cell death, but how the balance between death and survival signals is regulated to prevent immunodeficiency and autoimmunity remains incompletely understood. In this study, we show that absence of the essential ATM (ataxia telangiectasia mutated) substrate Chk2-interacting Zn(2+)-finger protein (ASCIZ; also known as ATMIN/ZNF822), a protein with dual functions in the DNA damage response and as a transcription factor, leads to progressive cell loss from the pre-B stage onwards and severely diminished splenic B cell numbers in mice. This lymphopenia cannot be suppressed by deletion of p53 or complementation with a prearranged BCR, indicating that it is not caused by impaired DNA damage responses or defective V(D)J recombination. Instead, ASCIZ-deficient B cell precursors contain highly reduced levels of DYNLL1 (dynein light chain 1; LC8), a recently identified transcriptional target of ASCIZ, and normal B cell development can be restored by ectopic Dynll1 expression. Remarkably, the B cell lymphopenia in the absence of ASCIZ can also be fully suppressed by deletion of the proapoptotic DYNLL1 target Bim. Our findings demonstrate a key role for ASCIZ in regulating the survival of developing B cells by activating DYNLL1 expression, which may then modulate Bim-dependent apoptosis.
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Affiliation(s)
- Sabine Jurado
- St. Vincent's Institute of Medical Research, The University of Melbourne, Melbourne, Victoria 3052, Australia
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