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Wimmer MC, Brennenstuhl H, Hirsch S, Dötsch L, Unser S, Caro P, Schaaf CP. Hao-Fountain syndrome: 32 novel patients reveal new insights into the clinical spectrum. Clin Genet 2024; 105:499-509. [PMID: 38221796 DOI: 10.1111/cge.14480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
Hao-Fountain syndrome (HAFOUS, OMIM: #616863) is a neurodevelopmental disorder caused by pathogenic variants in the gene USP7 coding for USP7, a protein involved in several crucial cellular homeostatic mechanisms and the recently described MUST complex. The phenotype of HAFOUS is insufficiently understood, yet there is a great need to better understand the spectrum of disease, genotype-phenotype correlations, and disease trajectories. We now present a larger cohort of 32 additional individuals and provide further clinical information about six previously reported individuals. A questionnaire-based study was performed to characterize the phenotype of Hao-Fountain syndrome more clearly, to highlight new traits, and to better distinguish the disease from related neurodevelopmental disorders. In addition to confirming previously described features, we report hyperphagia and increased body weight in a subset of individuals. HAFOUS patients present an increased rate of birth complications, congenital anomalies, and abnormal pain thresholds. Speech impairment emerges as a potential hallmark of Hao-Fountain syndrome. Cognitive testing reports reveal borderline intellectual functioning on average, although some individuals score in the range of intellectual disability. Finally, we created a syndrome-specific severity score. This score neither indicates a sex- nor age-specific difference of clinical severity, yet highlights a more severe outcome when amino acid changes colocalize to the catalytic domain of the USP7 protein.
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Affiliation(s)
| | | | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Laura Dötsch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Samy Unser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Christian Patrick Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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2
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Kong L, Jin X. Dysregulation of deubiquitination in breast cancer. Gene 2024; 902:148175. [PMID: 38242375 DOI: 10.1016/j.gene.2024.148175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Breast cancer (BC) is a highly frequent malignant tumor that poses a serious threat to women's health and has different molecular subtypes, histological subtypes, and biological features, which act by activating oncogenic factors and suppressing cancer inhibitors. The ubiquitin-proteasome system (UPS) is the main process contributing to protein degradation, and deubiquitinases (DUBs) are reverse enzymes that counteract this process. There is growing evidence that dysregulation of DUBs is involved in the occurrence of BC. Herein, we review recent research findings in BC-associated DUBs, describe their nature, classification, and functions, and discuss the potential mechanisms of DUB-related dysregulation in BC. Furthermore, we present the successful treatment of malignant cancer with DUB inhibitors, as well as analyzing the status of targeting aberrant DUBs in BC.
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Affiliation(s)
- Lili Kong
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China.
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Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Nunez IR, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst ACE, Korf BR, Schmutz J, Grimwood J, Cooper GM. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. medRxiv 2024:2024.03.22.24304633. [PMID: 38585854 PMCID: PMC10996728 DOI: 10.1101/2024.03.22.24304633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, eight of which (8/96, 8.33%) harbored pathogenic or likely pathogenic variants. Newly identified variants were visible in both srGS and lrGS in nine probands (~9.4%) and resulted from changes to interpretation mostly from recent gene-disease association discoveries. Seven cases included variants that were only interpretable in lrGS, including copy-number variants, an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either: not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality-control and filtration. Thus, while reanalysis of older data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS datasets grow allowing for better variant frequency annotation, the additional lrGS-only rare disease yield will grow over time.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Donald R. Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | | | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Michael A. Lopez
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
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Migale R, Neumann M, Mitter R, Rafiee MR, Wood S, Olsen J, Lovell-Badge R. FOXL2 interaction with different binding partners regulates the dynamics of ovarian development. Sci Adv 2024; 10:eadl0788. [PMID: 38517962 PMCID: PMC10959415 DOI: 10.1126/sciadv.adl0788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2's role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (Usp7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
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Affiliation(s)
- Roberta Migale
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Michelle Neumann
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics core, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mahmoud-Reza Rafiee
- RNA Networks Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophie Wood
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jessica Olsen
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robin Lovell-Badge
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
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van der Laan L, Karimi K, Rooney K, Lauffer P, McConkey H, Caro P, Relator R, Levy MA, Bhai P, Mignot C, Keren B, Briuglia S, Sobering AK, Li D, Vissers LELM, Dingemans AJM, Valenzuela I, Verberne EA, Misra-Isrie M, Zwijnenburg PJG, Waisfisz Q, Alders M, Sailer S, Schaaf CP, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. DNA methylation episignature, extension of the clinical features, and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7. Genet Med 2024; 26:101050. [PMID: 38126281 DOI: 10.1016/j.gim.2023.101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE Hao-Fountain syndrome (HAFOUS) is a neurodevelopmental disorder caused by pathogenic variants in USP7. HAFOUS is characterized by developmental delay, intellectual disability, speech delay, behavioral abnormalities, autism spectrum disorder, seizures, hypogonadism, and mild dysmorphic features. We investigated the phenotype of 18 participants with HAFOUS and performed DNA methylation (DNAm) analysis, aiming to generate a diagnostic biomarker. Furthermore, we performed comparative analysis with known episignatures to gain more insight into the molecular pathophysiology of HAFOUS. METHODS We assessed genomic DNAm profiles of 18 individuals with pathogenic variants and variants of uncertain significance (VUS) in USP7 to map and validate a specific episignature. The comparison between the USP7 cohort and 56 rare genetic disorders with earlier reported DNAm episignatures was performed with statistical and functional correlation. RESULTS We mapped a sensitive and specific DNAm episignature for pathogenic variants in USP7 and utilized this to reclassify the VUS. Comparative epigenomic analysis showed evidence of HAFOUS similarity to a number of other rare genetic episignature disorders. CONCLUSION We discovered a sensitive and specific DNAm episignature as a robust diagnostic biomarker for HAFOUS that enables VUS reclassification in USP7. We also expand the phenotypic spectrum of 9 new and 5 previously reported individuals with HAFOUS.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Hôpital Armand Trousseau, Paris, France AND Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Silvana Briuglia
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Andrew K Sobering
- AU/UGA Medical Partnership Campus of the Medical College of Georgia, Athens, Georgia; Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada; St. George's University School of Medicine, Department of Biochemistry, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, University of Pennsylvania Perelman school of Medicine, Philadelphia, PA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Irene Valenzuela
- Àrea de Genètica Clínica i Malalties Minoritàries, Hospital Vall d'Hebron, Barcelona, Spain
| | - Eline A Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Sailer
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Bolhuis DL, Emanuele MJ, Brown NG. Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases. Biochem Soc Trans 2024; 52:BST20230454. [PMID: 38414432 DOI: 10.1042/bst20230454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.
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Affiliation(s)
- Derek L Bolhuis
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
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Chen H, Ferguson CJ, Mitchell DC, Titus A, Paulo JA, Hwang A, Lin TH, Yano H, Gu W, Song SK, Yuede CM, Gygi SP, Bonni A, Kim AH. The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway. bioRxiv 2024:2023.10.24.563880. [PMID: 37961719 PMCID: PMC10634808 DOI: 10.1101/2023.10.24.563880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Precise control of protein ubiquitination is essential for brain development, and hence, disruption of ubiquitin signaling networks can lead to neurological disorders. Mutations of the deubiquitinase USP7 cause the Hao-Fountain syndrome (HAFOUS), characterized by developmental delay, intellectual disability, autism, and aggressive behavior. Here, we report that conditional deletion of USP7 in excitatory neurons in the mouse forebrain triggers diverse phenotypes including sensorimotor deficits, learning and memory impairment, and aggressive behavior, resembling clinical features of HAFOUS. USP7 deletion induces neuronal apoptosis in a manner dependent of the tumor suppressor p53. However, most behavioral abnormalities in USP7 conditional mice persist despite p53 loss. Strikingly, USP7 deletion in the brain perturbs the synaptic proteome and dendritic spine morphogenesis independently of p53. Integrated proteomics analysis reveals that the neuronal USP7 interactome is enriched for proteins implicated in neurodevelopmental disorders and specifically identifies the RNA splicing factor Ppil4 as a novel neuronal substrate of USP7. Knockdown of Ppil4 in cortical neurons impairs dendritic spine morphogenesis, phenocopying the effect of USP7 loss on dendritic spines. These findings reveal a novel USP7-Ppil4 ubiquitin signaling link that regulates neuronal connectivity in the developing brain, with implications for our understanding of the pathogenesis of HAFOUS and other neurodevelopmental disorders.
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Sun M, Li Q, Zhang Y, Cai Y, Dong Y, Shu J, Li D, Cai C. Identification of Two Variants c.2697A > C and c.3305A > C in USP7 by Analysis of Whole-Exome Sequencing in Chinese Patients with Hao-Fountain Syndrome. Glob Med Genet 2024; 11:13-19. [PMID: 38229971 PMCID: PMC10791489 DOI: 10.1055/s-0043-1778089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Background Variants of ubiquitin-specific protease 7 ( USP7 ) gene in humans are associated with a neurodevelopmental disorder-Hao-Fountain syndrome, its core symptoms including developmental delay, intellectual disability, and speech delay. Other variable symptoms can affect multiple systems. In present study, we report two patients with core features from two unrelated consanguineous families originating from the Tianjin Children's Hospital. Methods and Results Genomic DNA was extracted from the peripheral blood samples collected from the probands with their family members and whole-exome sequencing (WES) was used to detect the pathogenic genes in the probands. Suspected variants were subsequently validated by Sanger sequencing. In family 1, WES revealed that the proband carried the de novo variant c.2697A > C (p.Leu899Phe) in USP7 (NM_003470.3). In family 2, WES identified the variant c.3305A > C (p.Asn1102Thr) in USP7 (NM_003470.3) from the proband. Conclusion We reported two cases of Hao-Fountain syndrome caused by novel USP7 variants. In addition, we report the first case of mosaicism with a USP7 variant in Chinese family. Our findings demonstrate the importance of WES in diagnosis of genetic diseases and expands the USP7 variants spectrum in Hao-Fountain syndrome. Moreover, we summarize the cases caused by USP7 variants in the literature. Our study can provide a vital reference for the diagnosis of future cases.
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Affiliation(s)
- Mei Sun
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, Peoples' Republic of China
| | - Qing Li
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, Peoples' Republic of China
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, Peoples' Republic of China
| | - Ying Zhang
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, Peoples' Republic of China
| | - Yingzi Cai
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, Peoples' Republic of China
| | - Yan Dong
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, Peoples' Republic of China
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, Peoples' Republic of China
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, Peoples' Republic of China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children Hosptial, Tianjin, Peoples' Republic of China
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, Peoples' Republic of China
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, Peoples' Republic of China
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, Peoples' Republic of China
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, Peoples' Republic of China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children Hosptial, Tianjin, Peoples' Republic of China
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9
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Park HB, Baek KH. Current and future directions of USP7 interactome in cancer study. Biochim Biophys Acta Rev Cancer 2023; 1878:188992. [PMID: 37775071 DOI: 10.1016/j.bbcan.2023.188992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The ubiquitin-proteasome system (UPS) is an essential protein quality controller for regulating protein homeostasis and autophagy. Ubiquitination is a protein modification process that involves the binding of one or more ubiquitins to substrates through a series of enzymatic processes. These include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Conversely, deubiquitination is a reverse process that removes ubiquitin from substrates via deubiquitinating enzymes (DUBs). Dysregulation of ubiquitination-related enzymes can lead to various human diseases, including cancer, through the modulation of protein ubiquitination. The most structurally and functionally studied DUB is the ubiquitin-specific protease 7 (USP7). Both the TRAF and UBL domains of USP7 are known to bind to the [P/A/E]-X-X-S or K-X-X-X-K motif of substrates. USP7 has been shown to be involved in cancer pathogenesis by binding with numerous substrates. Recently, a novel substrate of USP7 was discovered through a systemic analysis of its binding motif. This review summarizes the currently discovered substrates and cellular functions of USP7 in cancer and suggests putative substrates of USP7 through a comprehensive systemic analysis.
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Affiliation(s)
- Hong-Beom Park
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea; International Ubiquitin Center(,) CHA University, Gyeonggi-Do 13488, Republic of Korea.
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Štepihar D, Florke Gee RR, Hoyos Sanchez MC, Fon Tacer K. Cell-specific secretory granule sorting mechanisms: the role of MAGEL2 and retromer in hypothalamic regulated secretion. Front Cell Dev Biol 2023; 11:1243038. [PMID: 37799273 PMCID: PMC10548473 DOI: 10.3389/fcell.2023.1243038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Intracellular protein trafficking and sorting are extremely arduous in endocrine and neuroendocrine cells, which synthesize and secrete on-demand substantial quantities of proteins. To ensure that neuroendocrine secretion operates correctly, each step in the secretion pathways is tightly regulated and coordinated both spatially and temporally. At the trans-Golgi network (TGN), intrinsic structural features of proteins and several sorting mechanisms and distinct signals direct newly synthesized proteins into proper membrane vesicles that enter either constitutive or regulated secretion pathways. Furthermore, this anterograde transport is counterbalanced by retrograde transport, which not only maintains membrane homeostasis but also recycles various proteins that function in the sorting of secretory cargo, formation of transport intermediates, or retrieval of resident proteins of secretory organelles. The retromer complex recycles proteins from the endocytic pathway back to the plasma membrane or TGN and was recently identified as a critical player in regulated secretion in the hypothalamus. Furthermore, melanoma antigen protein L2 (MAGEL2) was discovered to act as a tissue-specific regulator of the retromer-dependent endosomal protein recycling pathway and, by doing so, ensures proper secretory granule formation and maturation. MAGEL2 is a mammalian-specific and maternally imprinted gene implicated in Prader-Willi and Schaaf-Yang neurodevelopmental syndromes. In this review, we will briefly discuss the current understanding of the regulated secretion pathway, encompassing anterograde and retrograde traffic. Although our understanding of the retrograde trafficking and sorting in regulated secretion is not yet complete, we will review recent insights into the molecular role of MAGEL2 in hypothalamic neuroendocrine secretion and how its dysregulation contributes to the symptoms of Prader-Willi and Schaaf-Yang patients. Given that the activation of many secreted proteins occurs after they enter secretory granules, modulation of the sorting efficiency in a tissue-specific manner may represent an evolutionary adaptation to environmental cues.
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Affiliation(s)
- Denis Štepihar
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Rebecca R. Florke Gee
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
| | - Maria Camila Hoyos Sanchez
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
| | - Klementina Fon Tacer
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX, United States
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Itani KN, Elfaki S. A Rare Case of Hao-Fountain Syndrome Mimicking Fragile X Syndrome. Cureus 2023; 15:e45332. [PMID: 37849578 PMCID: PMC10577392 DOI: 10.7759/cureus.45332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Hao-Fountain syndrome (HAFOUS) is a rare neurodevelopmental disorder caused by mutations in the ubiquitin-specific protease 7 (USP7) gene for endosomal recycling. The diagnosis is often challenging due to the nonspecific presentation of intellectual disability and developmental delay, often accompanied by dysmorphic facies. In this case, we present an 18-year-old female with intellectual disability (ID), attention-deficit/hyperactivity disorder (ADHD), and dysmorphic facies who had undergone single nucleotide polymorphism (SNP) microarray and fragile X polymerase chain reaction (PCR) testing five years prior to diagnosis, both returning with negative results for genetic anomalies. The patient was managed symptomatically for ADHD until recently when the topic of a possible genetic condition was reintroduced to the family, who were agreeable to a referral to a medical geneticist and repeat genetic testing. Repeat testing, but now with whole-exome sequence (WES) analysis, revealed a pathogenic variant of the USP7 gene, prompting the diagnosis of Hao-Fountain syndrome. Our patient continues to be symptomatically managed for ADHD and intellectual disability. Educational resources and support group information were also shared and discussed with the patient and her family in the wake of this rare diagnosis.
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Affiliation(s)
- Khaled N Itani
- Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, USA
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12
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Hoyos Sanchez MC, Bayat T, Gee RRF, Fon Tacer K. Hormonal Imbalances in Prader-Willi and Schaaf-Yang Syndromes Imply the Evolution of Specific Regulation of Hypothalamic Neuroendocrine Function in Mammals. Int J Mol Sci 2023; 24:13109. [PMID: 37685915 PMCID: PMC10487939 DOI: 10.3390/ijms241713109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
The hypothalamus regulates fundamental aspects of physiological homeostasis and behavior, including stress response, reproduction, growth, sleep, and feeding, several of which are affected in patients with Prader-Willi (PWS) and Schaaf-Yang syndrome (SYS). PWS is caused by paternal deletion, maternal uniparental disomy, or imprinting defects that lead to loss of expression of a maternally imprinted region of chromosome 15 encompassing non-coding RNAs and five protein-coding genes; SYS patients have a mutation in one of them, MAGEL2. Throughout life, PWS and SYS patients suffer from musculoskeletal deficiencies, intellectual disabilities, and hormonal abnormalities, which lead to compulsive behaviors like hyperphagia and temper outbursts. Management of PWS and SYS is mostly symptomatic and cures for these debilitating disorders do not exist, highlighting a clear, unmet medical need. Research over several decades into the molecular and cellular roles of PWS genes has uncovered that several impinge on the neuroendocrine system. In this review, we will discuss the expression and molecular functions of PWS genes, connecting them with hormonal imbalances in patients and animal models. Besides the observed hormonal imbalances, we will describe the recent findings about how the loss of individual genes, particularly MAGEL2, affects the molecular mechanisms of hormone secretion. These results suggest that MAGEL2 evolved as a mammalian-specific regulator of hypothalamic neuroendocrine function.
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Affiliation(s)
- Maria Camila Hoyos Sanchez
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Tara Bayat
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Rebecca R. Florke Gee
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
| | - Klementina Fon Tacer
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
- Texas Center for Comparative Cancer Research (TC3R), Amarillo, TX 79106, USA
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13
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Liu H, Han J, Lv Y, Zhao Z, Zheng S, Sun Y, Sun T. Isorhamnetin and anti-PD-L1 antibody dual-functional mesoporous silica nanoparticles improve tumor immune microenvironment and inhibit YY1-mediated tumor progression. J Nanobiotechnology 2023; 21:208. [PMID: 37408047 DOI: 10.1186/s12951-023-01967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/24/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND The immune checkpoint inhibitor (ICI) anti-PD-L1 monoclonal antibody can inhibit the progress of hepatocellular carcinoma (HCC). Epithelial-mesenchymal transformation (EMT) can promote tumor migration and the formation of immune-suppression microenvironment, which affects the therapeutic effect of ICI. Yin-yang-1 (YY1) is an important transcription factor regulating proliferation, migration and EMT of tumor cells. This work proposed a drug-development strategy that combined the regulation of YY1-mediated tumor progression with ICIs for the treatment of HCC. METHODS We first studied the proteins that regulated YY1 expression by using pull-down, co-immunoprecipitation, and duo-link assay. The active compound regulating YY1 content was screened by virtual screening and cell-function assay. Isorhamnetin (ISO) and anti-PD-L1 antibody dual-functional mesoporous silica nanoparticles (HMSN-ISO@ProA-PD-L1 Ab) were prepared as an antitumor drug to play a synergistic anti-tumor role. RESULTS YY1 can specifically bind with the deubiquitination enzyme USP7. USP7 can prevent YY1 from ubiquitin-dependent degradation and stabilize YY1 expression, which can promote the proliferation, migration and EMT of HCC cells. Isorhamnetin (ISO) were screened out, which can target USP7 and promote YY1 ubiquitin-dependent degradation. The cell experiments revealed that the HMSN-ISO@ProA-PD-L1 Ab nanoparticles can specifically target tumor cells and play a role in the controlled release of ISO. HMSN-ISO@ProA-PD-L1 Ab nanoparticles inhibited the growth of Hepa1-6 transplanted tumors and the effect was better than that of PD-L1 Ab treatment group and ISO treatment group. HMSN-ISO@ProA-PD-L1 Ab nanoparticles also exerted a promising effect on reducing MDSC content in the tumor microenvironment and promoting T-cell infiltration in tumors. CONCLUSIONS The isorhamnetin and anti-PD-L1 antibody dual-functional nanoparticles can improve tumor immune microenvironment and inhibit YY1-mediated tumor progression. This study demonstrated the possibility of HCC treatment strategies based on inhibiting USP7-mediated YY1 deubiquitination combined with anti-PD-L1 monoclonal Ab.
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Affiliation(s)
- Huijuan Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
| | - Jingxia Han
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Ying Lv
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Zihan Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Shaoting Zheng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Yu Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Tao Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
- Tianjin Key Laboratory of Early Druggability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, China.
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14
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Castilla-Vallmanya L, Centeno-Pla M, Serrano M, Franco-Valls H, Martínez-Cabrera R, Prat-Planas A, Rojano E, Ranea JAG, Seoane P, Oliva C, Paredes-Fuentes AJ, Marfany G, Artuch R, Grinberg D, Rabionet R, Balcells S, Urreizti R. Advancing in Schaaf-Yang syndrome pathophysiology: from bedside to subcellular analyses of truncated MAGEL2. J Med Genet 2023; 60:406-415. [PMID: 36243518 PMCID: PMC10086475 DOI: 10.1136/jmg-2022-108690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Schaaf-Yang syndrome (SYS) is caused by truncating mutations in MAGEL2, mapping to the Prader-Willi region (15q11-q13), with an observed phenotype partially overlapping that of Prader-Willi syndrome. MAGEL2 plays a role in retrograde transport and protein recycling regulation. Our aim is to contribute to the characterisation of SYS pathophysiology at clinical, genetic and molecular levels. METHODS We performed an extensive phenotypic and mutational revision of previously reported patients with SYS. We analysed the secretion levels of amyloid-β 1-40 peptide (Aβ1-40) and performed targeted metabolomic and transcriptomic profiles in fibroblasts of patients with SYS (n=7) compared with controls (n=11). We also transfected cell lines with vectors encoding wild-type (WT) or mutated MAGEL2 to assess stability and subcellular localisation of the truncated protein. RESULTS Functional studies show significantly decreased levels of secreted Aβ1-40 and intracellular glutamine in SYS fibroblasts compared with WT. We also identified 132 differentially expressed genes, including non-coding RNAs (ncRNAs) such as HOTAIR, and many of them related to developmental processes and mitotic mechanisms. The truncated form of MAGEL2 displayed a stability similar to the WT but it was significantly switched to the nucleus, compared with a mainly cytoplasmic distribution of the WT MAGEL2. Based on the updated knowledge, we offer guidelines for the clinical management of patients with SYS. CONCLUSION A truncated MAGEL2 protein is stable and localises mainly in the nucleus, where it might exert a pathogenic neomorphic effect. Aβ1-40 secretion levels and HOTAIR mRNA levels might be promising biomarkers for SYS. Our findings may improve SYS understanding and clinical management.
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Affiliation(s)
- Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Mónica Centeno-Pla
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mercedes Serrano
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Neurology Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Héctor Franco-Valls
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raúl Martínez-Cabrera
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Aina Prat-Planas
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Juan A G Ranea
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Pedro Seoane
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Department of Molecular Biology and Biochemistry; Institute of Biomedical Research in Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Clara Oliva
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Abraham J Paredes-Fuentes
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Rafael Artuch
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, IBUB, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
| | - Roser Urreizti
- Institut de Recerca Sant Joan de Déu, Espluques de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instiuto de Salud Carlos III, Madrid, Spain
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
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15
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Xu N, Shi W, Cao X, Zhou X, Huang H, Chen S, Xu C. Preimplantation Genetic Testing (PGT) and Prenatal Diagnosis of Schaaf-Yang Syndrome: A Report of Three Families and a Research on Genotype-Phenotype Correlations. J Clin Med 2023; 12. [PMID: 36836222 DOI: 10.3390/jcm12041688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Schaaf-Yang Syndrome (SYS) is a genetic disorder caused by truncating pathogenic variants in the paternal allele of the maternally imprinted, paternally expressed gene MAGEL2 and is characterized by genital hypoplasia, neonatal hypotonia, developmental delay, intellectual disability, autism spectrum disorder (ASD), and other features. In this study, eleven SYS patients from three families were enrolled and comprehensive clinical features were gathered regarding each family. Whole-exome sequencing (WES) was performed for the definitive molecular diagnosis of the disease. Identified variants were validated using Sanger sequencing. Three couples underwent PGT for monogenic diseases (PGT-M) and/or a prenatal diagnosis. Haplotype analysis was performed to deduce the embryo's genotype by using the short tandem repeats (STRs) identified in each sample. The prenatal diagnosis results showed that the fetus in each case did not carry pathogenic variants, and all the babies of the three families were born at full term and were healthy. We also performed a review of SYS cases. In addition to the 11 patients in our study, a total of 127 SYS patients were included in 11 papers. We summarized all variant sites and clinical symptoms thus far, and conducted a genotype-phenotype correlation analysis. Our results also indicated that the variation in phenotypic severity may depend on the specific location of the truncating variant, suggestive of a genotype-phenotype association.
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16
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Alur V, Raju V, Vastrad B, Vastrad C, Kavatagimath S, Kotturshetti S. Bioinformatics Analysis of Next Generation Sequencing Data Identifies Molecular Biomarkers Associated With Type 2 Diabetes Mellitus. Clin Med Insights Endocrinol Diabetes 2023; 16:11795514231155635. [PMID: 36844983 PMCID: PMC9944228 DOI: 10.1177/11795514231155635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder. The aim of the present investigation was to identify gene signature specific to T2DM. Methods The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes. Results A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1 were screened out as the critical genes. ROC analysis provides prognostic value of hub genes. Conclusion The potential crucial genes, especially APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1, might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets.
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Affiliation(s)
- Varun Alur
- Department of Endocrinology, J.J.M
Medical College, Davanagere, Karnataka, India
| | - Varshita Raju
- Department of Obstetrics and
Gynecology, J.J.M Medical College, Davanagere, Karnataka, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry,
K.L.E. College of Pharmacy, Gadag, Karnataka, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics,
Chanabasava Nilaya, Dharwad, Karnataka, India,Chanabasayya Vastrad, Biostatistics and
Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka 580001,
India.
| | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E.
College of Pharmacy, Belagavi, Karnataka, India
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17
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Garcia-Garcia J, Berge AKM, Overå KS, Larsen KB, Bhujabal Z, Brech A, Abudu YP, Lamark T, Johansen T, Sjøttem E. TRIM27 is an autophagy substrate facilitating mitochondria clustering and mitophagy via phosphorylated TBK1. FEBS J 2023; 290:1096-1116. [PMID: 36111389 DOI: 10.1111/febs.16628] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/02/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022]
Abstract
Tripartite motif-containing protein 27 (TRIM27/also called RFP) is a multifunctional ubiquitin E3 ligase involved in numerous cellular functions, such as proliferation, apoptosis, regulation of the NF-kB pathway, endosomal recycling and the innate immune response. TRIM27 interacts directly with TANK-binding kinase 1 (TBK1) and regulates its stability. TBK1 in complex with autophagy receptors is recruited to ubiquitin chains assembled on the mitochondrial outer membrane promoting mitophagy. Here, we identify TRIM27 as an autophagy substrate, depending on ATG7, ATG9 and autophagy receptors for its lysosomal degradation. We show that TRIM27 forms ubiquitylated cytoplasmic bodies that co-localize with autophagy receptors. Surprisingly, we observed that induced expression of EGFP-TRIM27 in HEK293 FlpIn TRIM27 knockout cells mediates mitochondrial clustering. TRIM27 interacts with autophagy receptor SQSTM1/p62, and the TRIM27-mediated mitochondrial clustering is facilitated by SQSTM/p62. We show that phosphorylated TBK1 is recruited to the clustered mitochondria. Moreover, induced mitophagy activity is reduced in HEK293 FlpIn TRIM27 knockout cells, while re-introduction of EGFP-TRIM27 completely restores the mitophagy activity. Inhibition of TBK1 reduces mitophagy in HEK293 FlpIn cells and in the reconstituted EGFP-TRIM27-expressing cells, but not in HEK293 FlpIn TRIM27 knockout cells. Altogether, these data reveal novel roles for TRIM27 in mitophagy, facilitating mitochondrial clustering via SQSTM1/p62 and mitophagy via stabilization of phosphorylated TBK1 on mitochondria.
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Affiliation(s)
- Juncal Garcia-Garcia
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Anne Kristin McLaren Berge
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Katrine Stange Overå
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Kenneth Bowitz Larsen
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Zambarlal Bhujabal
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Andreas Brech
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Yakubu Princely Abudu
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Trond Lamark
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Terje Johansen
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
| | - Eva Sjøttem
- Department of Medical Biology, Autophagy Research Group, University of Tromsø -The Arctic University of Norway, Norway
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Reznik DL, Yang MV, Albelda de la Haza P, Jain A, Spanjaard M, Theiss S, Schaaf CP, Malovannaya A, Strong TV, Veeraragavan S, Samaco RC. Magel2 truncation alters select behavioral and physiological outcomes in a rat model of Schaaf-Yang syndrome. Dis Model Mech 2023; 16:286598. [PMID: 36637363 PMCID: PMC9922728 DOI: 10.1242/dmm.049829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
Previous studies in mice have utilized Magel2 gene deletion models to examine the consequences of its absence. We report the generation, molecular validation and phenotypic characterization of a novel rat model with a truncating Magel2 mutation modeling variants associated with Schaaf-Yang syndrome-causing mutations. Within the hypothalamus, a brain region in which human MAGEL2 is paternally expressed, we demonstrated, at the level of transcript and peptide detection, that rat Magel2 exhibits a paternal, parent-of-origin effect. In evaluations of behavioral features across several domains, juvenile Magel2 mutant rats displayed alterations in anxiety-like behavior and sociability measures. Moreover, the analysis of peripheral organ systems detected alterations in body composition, cardiac structure and function, and breathing irregularities in Magel2 mutant rats. Several of these findings are concordant with reported mouse phenotypes, indicating the conservation of MAGEL2 function across rodent species. Our comprehensive analysis revealing impairments across multiple domains demonstrates the tractability of this model system for the study of truncating MAGEL2 mutations.
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Affiliation(s)
- Derek L Reznik
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Mingxiao V Yang
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Pedro Albelda de la Haza
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Antrix Jain
- Baylor College of Medicine, Mass Spectrometry Proteomics Core, Houston, TX 77030, USA
| | - Melanie Spanjaard
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Susanne Theiss
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian P Schaaf
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Anna Malovannaya
- Baylor College of Medicine, Mass Spectrometry Proteomics Core, Houston, TX 77030, USA.,Baylor College of Medicine, Verna and Marrs McLean Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Houston, TX 77030, USA.,Baylor College of Medicine, Dan L. Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
| | - Theresa V Strong
- Foundation for Prader-Willi Research, Walnut, CA 91789, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Surabi Veeraragavan
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Rodney C Samaco
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
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19
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Smits DJ, Dekker J, Schot R, Tabarki B, Alhashem A, Demmers JAA, Dekkers DHW, Romito A, van der Spek PJ, van Ham TJ, Bertoli-Avella AM, Mancini GMS. CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment. Hum Genet 2023; 142:379-397. [PMID: 36538041 PMCID: PMC9950183 DOI: 10.1007/s00439-022-02511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
CLEC16A is a membrane-associated C-type lectin protein that functions as a E3-ubiquitin ligase. CLEC16A regulates autophagy and mitophagy, and reportedly localizes to late endosomes. GWAS studies have associated CLEC16A SNPs to various auto-immune and neurological disorders, including multiple sclerosis and Parkinson disease. Studies in mouse models imply a role for CLEC16A in neurodegeneration. We identified bi-allelic CLEC16A truncating variants in siblings from unrelated families presenting with a severe neurodevelopmental disorder including microcephaly, brain atrophy, corpus callosum dysgenesis, and growth retardation. To understand the function of CLEC16A in neurodevelopment we used in vitro models and zebrafish embryos. We observed CLEC16A localization to early endosomes in HEK293T cells. Mass spectrometry of human CLEC16A showed interaction with endosomal retromer complex subunits and the endosomal ubiquitin ligase TRIM27. Expression of the human variant leading to C-terminal truncated CLEC16A, abolishes both its endosomal localization and interaction with TRIM27, suggesting a loss-of-function effect. CLEC16A knockdown increased TRIM27 adhesion to early endosomes and abnormal accumulation of endosomal F-actin, a sign of disrupted vesicle sorting. Mutagenesis of clec16a by CRISPR-Cas9 in zebrafish embryos resulted in accumulated acidic/phagolysosome compartments, in neurons and microglia, and dysregulated mitophagy. The autophagocytic phenotype was rescued by wild-type human CLEC16A but not the C-terminal truncated CLEC16A. Our results demonstrate that CLEC16A closely interacts with retromer components and regulates endosomal fate by fine-tuning levels of TRIM27 and polymerized F-actin on the endosome surface. Dysregulation of CLEC16A-mediated endosomal sorting is associated with neurodegeneration, but it also causes accumulation of autophagosomes and unhealthy mitochondria during brain development.
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Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Jordy Dekker
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands.
| | - Rachel Schot
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Brahim Tabarki
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, 12233, Saudi Arabia
| | - Amal Alhashem
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, 12233, Saudi Arabia
| | - Jeroen A A Demmers
- Department of Molecular Genetics, Proteomics Center, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Dick H W Dekkers
- Department of Molecular Genetics, Proteomics Center, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Clinical Bioinformatics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
| | | | - Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center, 3015 CN, Rotterdam, the Netherlands
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20
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Sakamoto T, Kuboki S, Furukawa K, Takayashiki T, Takano S, Yoshizumi A, Ohtsuka M. TRIM27-USP7 complex promotes tumour progression via STAT3 activation in human hepatocellular carcinoma. Liver Int 2023; 43:194-207. [PMID: 35753056 DOI: 10.1111/liv.15346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/31/2022] [Accepted: 06/23/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND & AIMS TRIM27 is stabilized by binding to USP7 and mediates tumour progression in several cancers; however, the roles of TRIM27-USP7 complex on STAT3 activation in HCC are unknown. METHODS Regulations and functions of TRIM27 for activating STAT3 in HCC were assessed using 207 HCC samples or HCC cells. RESULTS TRIM27 expression was increased in some cases of HCC. High TRIM27 expression was an independent predictor for poor prognosis in HCC after surgery. It was correlated with the expression of EpCAM, vimentin, MMP-9, and activation of STAT3 in HCC. TRIM27 expression was correlated with USP7 expression, and HCC with high TRIM27 expression together with high USP7 expression showed enhanced STAT3 activation, resulting in poorer prognosis. p-JAK1 expression was correlated with STAT3 activation in HCC with high TRIM27 expression. In vitro, USP7 knockdown decreased TRIM27 expression, suggesting that USP7 was essential for TRIM27 stabilization. Knocking down of TRIM27 or USP7 suppressed STAT3 activation and overexpression of TRIM27 accelerated STAT3 activation; therefore, the formation of TRIM27-USP7 complex was needed for STAT3 activation, which led to aggressive tumour proliferation and invasion by enhancing EMT and CSC-like property. Binding of JAK1 to TRIM27-USP7 complex was confirmed in vitro. Deletion of TRIM27-USP7 complex by USP7 inhibitor significantly inhibited tumour cell invasion by suppressing STAT3 activation. CONCLUSIONS TRIM27 is stabilized by binding to USP7 and is related to aggressive tumour progression in HCC via STAT3 activation, resulting in poor prognosis after operation. Therefore, TRIM27-USP7 complex is a useful prognostic predictor and a promising therapeutic target for HCC.
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Affiliation(s)
- Toshiya Sakamoto
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Kuboki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Katsunori Furukawa
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tsukasa Takayashiki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigetsugu Takano
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Arihito Yoshizumi
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
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21
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Elu N, Osinalde N, Ramirez J, Presa N, Rodriguez JA, Prieto G, Mayor U. Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders. Semin Cell Dev Biol 2022; 132:120-131. [PMID: 35042675 DOI: 10.1016/j.semcdb.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022]
Abstract
Similar to the reversal of kinase-mediated protein phosphorylation by phosphatases, deubiquitinating enzymes (DUBs) oppose the action of E3 ubiquitin ligases and reverse the ubiquitination of proteins. A total of 99 human DUBs, classified in 7 families, allow in this way for a precise control of cellular function and homeostasis. Ubiquitination regulates a myriad of cellular processes, and is altered in many pathological conditions. Thus, ubiquitination-regulating enzymes are increasingly regarded as potential candidates for therapeutic intervention. In this context, given the predicted easier pharmacological control of DUBs relative to E3 ligases, a significant effort is now being directed to better understand the processes and substrates regulated by each DUB. Classical studies have identified specific DUB substrate candidates by traditional molecular biology techniques in a case-by-case manner. Lately, single experiments can identify thousands of ubiquitinated proteins at a specific cellular context and narrow down which of those are regulated by a given DUB, thanks to the development of new strategies to isolate and enrich ubiquitinated material and to improvements in mass spectrometry detection capabilities. Here we present an overview of both types of studies, discussing the criteria that, in our view, need to be fulfilled for a protein to be considered as a high-confidence substrate of a given DUB. Applying these criteria, we have manually reviewed the relevant literature currently available in a systematic manner, and identified 650 high-confidence substrates of human DUBs. We make this information easily accessible to the research community through an updated version of the DUBase website (https://ehubio.ehu.eus/dubase/). Finally, in order to illustrate how this information can contribute to a better understanding of the physiopathological role of DUBs, we place a special emphasis on a subset of these enzymes that have been associated with neurodevelopmental disorders.
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Affiliation(s)
- Nagore Elu
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Natalia Presa
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao 48013, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.
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22
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Zheng H, Mei S, Li F, Wei L, Wang Y, Huang J, Zhang F, Huang J, Liu Y, Gu W, Liu H. Expansion of the mutation spectrum and phenotype of USP7-related neurodevelopmental disorder. Front Mol Neurosci 2022; 15:970649. [PMID: 36466803 PMCID: PMC9708884 DOI: 10.3389/fnmol.2022.970649] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/20/2022] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Hao-fountain syndrome (HAFOUS) is a neurodevelopmental syndrome characterized by global developmental and severe language delays, behavioral abnormalities (including autism), and mild dysmorphic impairment of intellectual development. It is a dominant genetic disease caused by USP7 gene (*602519) mutations on chromosome 16p13.2. So far, only 15 cases with 14 deleterious variants in the USP7 gene have been reported. MATERIALS AND METHODS This study describes three unrelated patients with USP7 variants. Besides, we identified novel de novo heterozygous USP7 variants using trio-whole exome sequencing and verified by Sanger sequencing. Furthermore, clinical characteristics were evaluated by reviewing the medical records. RESULTS The three identified variants, i.e., one frameshift variant (c.247_250del, p.Glu83Argfs × 18) and two missense variants (c.992A > G, p.Tyr331Cys; c.835T > G, p.Leu279Val) are unreported. The predominant clinical manifestations of the three patients included: DD/ID; language impairment; abnormal behavior; abnormal brain magnetic resonance (dilation of lateral ventricles, dilation of Virchow-Robin spaces, dilated the third ventricle, abnormal cerebral white matter morphology in bilateral occipital lobes, hypodysplasia of the corpus callosum, arachnoid cyst, delayed myelination, and widened subarachnoid space); some also had facial abnormalities. CONCLUSION In summary, DD/ID is the most prevalent clinical phenotype of HAFOUS, although some patients also exhibit language and behavioral abnormalities. For the first time in China, we identified three variants of the USP7 gene using whole-genome sequence data. This work expands the USP7 gene mutation spectrum and provides additional clinical data on the clinical phenotype of HAFOUS.
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Affiliation(s)
- Hong Zheng
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
- School of Pediatrics, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Fuwei Li
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | - Liwan Wei
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | | | - Jinrong Huang
- Ganzhou Women and Children’s Health Care Hospital, Ganzhou, China
| | - Feng Zhang
- Ganzhou Women and Children’s Health Care Hospital, Ganzhou, China
| | - Jia Huang
- Department of Medical Genetics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Yanping Liu
- Department of Pediatrics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Weiyue Gu
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | - Hongyan Liu
- Department of Medical Genetics, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
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23
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González-García A, Garrido A, Carrera AC. Targeting PTEN Regulation by Post Translational Modifications. Cancers (Basel) 2022; 14. [PMID: 36428706 DOI: 10.3390/cancers14225613] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphatidylinositol-3,4,5-triphosphate (PIP3) is a lipidic second messenger present at very low concentrations in resting normal cells. PIP3 levels, though, increase quickly and transiently after growth factor addition, upon activation of phosphatidylinositol 3-kinase (PI3-kinase). PIP3 is required for the activation of intracellular signaling pathways that induce cell proliferation, cell migration, and survival. Given the critical role of this second messenger for cellular responses, PIP3 levels must be tightly regulated. The lipid phosphatase PTEN (phosphatase and tensin-homolog in chromosome 10) is the phosphatase responsible for PIP3 dephosphorylation to PIP2. PTEN tumor suppressor is frequently inactivated in endometrium and prostate carcinomas, and also in glioblastoma, illustrating the contribution of elevated PIP3 levels for cancer development. PTEN biological activity can be modulated by heterozygous gene loss, gene mutation, and epigenetic or transcriptional alterations. In addition, PTEN can also be regulated by post-translational modifications. Acetylation, oxidation, phosphorylation, sumoylation, and ubiquitination can alter PTEN stability, cellular localization, or activity, highlighting the complexity of PTEN regulation. While current strategies to treat tumors exhibiting a deregulated PI3-kinase/PTEN axis have focused on PI3-kinase inhibition, a better understanding of PTEN post-translational modifications could provide new therapeutic strategies to restore PTEN action in PIP3-dependent tumors.
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24
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Sijm A, Atlasi Y, van der Knaap JA, Wolf van der Meer J, Chalkley GE, Bezstarosti K, Dekkers DHW, Doff WAS, Ozgur Z, van IJcken WFJ, Demmers JAA, Verrijzer CP. USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3. Sci Adv 2022; 8:eabq7598. [PMID: 36332031 PMCID: PMC9635827 DOI: 10.1126/sciadv.abq7598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/16/2022] [Indexed: 05/29/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
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Affiliation(s)
- Ayestha Sijm
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Jan A. van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Gillian E. Chalkley
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Bezstarosti
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Dick H. W. Dekkers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wouter A. S. Doff
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Zeliha Ozgur
- Center for Biomics, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Jeroen A. A. Demmers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - C. Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
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25
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Jolly LA, Kumar R, Penzes P, Piper M, Gecz J. The DUB Club: Deubiquitinating Enzymes and Neurodevelopmental Disorders. Biol Psychiatry 2022; 92:614-625. [PMID: 35662507 PMCID: PMC10084722 DOI: 10.1016/j.biopsych.2022.03.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 02/08/2023]
Abstract
Protein ubiquitination is a widespread, multifunctional, posttranslational protein modification, best known for its ability to direct protein degradation via the ubiquitin proteasome system (UPS). Ubiquitination is also reversible, and the human genome encodes over 90 deubiquitinating enzymes (DUBs), many of which appear to target specific subsets of ubiquitinated proteins. This review focuses on the roles of DUBs in neurodevelopmental disorders (NDDs). We present the current genetic evidence connecting 12 DUBs to a range of NDDs and the functional studies implicating at least 19 additional DUBs as candidate NDD genes. We highlight how the study of DUBs in NDDs offers critical insights into the role of protein degradation during brain development. Because one of the major known functions of a DUB is to antagonize the UPS, loss of function of DUB genes has been shown to culminate in loss of abundance of its protein substrates. The identification and study of NDD DUB substrates in the developing brain is revealing that they regulate networks of proteins that themselves are encoded by NDD genes. We describe the new technologies that are enabling the full resolution of DUB protein networks in the developing brain, with the view that this knowledge can direct the development of new therapeutic paradigms. The fact that the abundance of many NDD proteins is regulated by the UPS presents an exciting opportunity to combat NDDs caused by haploinsufficiency, because the loss of abundance of NDD proteins can be potentially rectified by antagonizing their UPS-based degradation.
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Affiliation(s)
- Lachlan A Jolly
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia.
| | - Raman Kumar
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael Piper
- School of Biomedical Sciences and Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Jozef Gecz
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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Valles G, Pozhidaeva A, Korzhnev DM, Bezsonova I. Backbone and ILV side-chain NMR resonance assignments of the catalytic domain of human deubiquitinating enzyme USP7. Biomol NMR Assign 2022; 16:197-203. [PMID: 35536398 PMCID: PMC9529858 DOI: 10.1007/s12104-022-10079-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin specific protease 7 (USP7) is a deubiquitinating enzyme, which removes ubiquitin tag from numerous protein substrates involved in diverse cellular processes such as cell cycle regulation, apoptosis and DNA damage response. USP7 affects stability, interaction network and cellular localization of its cellular and viral substrates by controlling their ubiquitination status. The large 41 kDa catalytic domain of USP7 harbors the active site of the enzyme. Here we present a nearly complete (93%) NMR resonance assignment of isoleucine, leucine and valine (ILV) side-chains of the USP7 catalytic domain along with a refined nearly complete (93%) assignment of its backbone resonances. The reported ILV methyl group assignment will facilitate further NMR investigations of structure, interactions and conformational dynamics of the USP7 enzyme.
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Affiliation(s)
- Gabrielle Valles
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Alexandra Pozhidaeva
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA.
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27
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | | | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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28
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Qiao H, Tian Y, Huo Y, Man HY. Role of the DUB enzyme USP7 in dendritic arborization, neuronal migration, and autistic-like behaviors in mice. iScience 2022; 25:104595. [PMID: 35800757 PMCID: PMC9253496 DOI: 10.1016/j.isci.2022.104595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/15/2022] [Accepted: 06/08/2022] [Indexed: 12/04/2022] Open
Abstract
Duplication and haploinsufficiency of the USP7 gene are implicated in autism spectrum disorders (ASD), but the role for USP7 in neurodevelopment and contribution to ASD pathogenesis remain unknown. We find that in primary neurons, overexpression of USP7 increases dendritic branch number and total dendritic length, whereas knockdown leads to opposite alterations. Besides, USP7 deubiquitinates the X-linked inhibitor of apoptosis protein (XIAP). The USP7-induced increase in XIAP suppresses caspase 3 activity, leading to a reduction in tubulin cleavage and suppression of dendritic pruning. When USP7 is introduced into the brains of prenatal mice via in utero electroporation (IUE), it results in abnormal migration of newborn neurons and increased dendritic arborization. Importantly, intraventricular brain injection of AAV-USP7 in P0 mice leads to autistic-like phenotypes including aberrant social interactions, repetitive behaviors, as well as changes in somatosensory sensitivity. These findings provide new insights in USP7-related neurobiological functions and its implication in ASD. Overexpression of USP7 increases dendritic arborization USP7 targets XIAP for deubiquitination and regulates XIAP proteostasis in neurons USP7 regulates dendritic remodeling via the XIAP-caspase 3-tubulin pathway Prenatal overexpression of USP7 in mice leads to autistic-like behaviors
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Priolo M, Mancini C, Pizzi S, Chiriatti L, Radio FC, Cordeddu V, Pintomalli L, Mammì C, Dallapiccola B, Tartaglia M. Complex Presentation of Hao-Fountain Syndrome Solved by Exome Sequencing Highlighting Co-Occurring Genomic Variants. Genes (Basel) 2022; 13:genes13050889. [PMID: 35627274 PMCID: PMC9141324 DOI: 10.3390/genes13050889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/11/2022] [Indexed: 01/05/2023] Open
Abstract
Objective: The co-occurrence of pathogenic variants has emerged as a relatively common finding underlying complex phenotypes. Here, we used whole-exome sequencing (WES) to solve an unclassified multisystem clinical presentation. Patients and Methods: A 20-year-old woman affected by moderate intellectual disability (ID), dysmorphic features, hypertrichosis, scoliosis, recurrent bronchitis, and pneumonia with bronchiectasis, colelithiasis, chronic severe constipation, and a family history suggestive of autosomal dominant recurrence of polycystic kidney disease was analyzed by WES to identify the genomic events underlying the condition. Results: Four co-occurring genomic events fully explaining the proband’s clinical features were identified. A de novo truncating USP7 variant was disclosed as the cause of Hao–Fountain syndrome, a disorder characterized by syndromic ID and distinctive behavior. Compound heterozygosity for a major cystic fibrosis-causing variant and the modulator allele, IVS8-5T, in CFTR explained the recurrent upper and lower respiratory way infections, bronchiectasis, cholelithiasis, and chronic constipation. Finally, a truncating PKD2 variant co-segregating with polycystic kidney disease in the family allowed presymptomatic disease diagnosis. Conclusions: The co-occurring variants in USP7 and CFTR variants explained the multisystem disorder of the patient. The comprehensive dissection of the phenotype and early diagnosis of autosomal dominant polycystic kidney disease allowed us to manage the CFTR-related disorder symptoms and monitor renal function and other complications associated with PKD2 haploinsufficiency, addressing proper care and surveillance.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
- Correspondence: ; Tel.: +39-09-6539-7319
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Luigi Chiriatti
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
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Liu G, Liang J, Lou L, Tian M, Zhang X, Liu L, Zhao Q, Xia R, Wu Y, Xie Q, Yu F. The deubiquitinases UBP12 and UBP13 integrate with the E3 ubiquitin ligase XBAT35.2 to modulate VPS23A stability in ABA signaling. Sci Adv 2022; 8:eabl5765. [PMID: 35385312 PMCID: PMC8986106 DOI: 10.1126/sciadv.abl5765] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/11/2022] [Indexed: 06/01/2023]
Abstract
Ubiquitination-mediated protein degradation in both the 26S proteasome and vacuole is an important process in abscisic acid (ABA) signaling. However, the role of deubiquitination in this process remains elusive. Here, we demonstrate that two deubiquitinating enzymes (DUBs), ubiquitin-specific protease 12 (UBP12) and UBP13, modulate ABA signaling and drought tolerance by deubiquitinating and stabilizing the endosomal sorting complex required for transport-I (ESCRT-I) component vacuolar protein sorting 23A (VPS23A) and thereby affect the stability of ABA receptors in Arabidopsis thaliana. Genetic analysis showed that VPS23A overexpression could rescue the ABA hypersensitive and drought tolerance phenotypes of ubp12-2w or ubp13-1. In addition to the direct regulation of VPS23A, we found that UBP12 and UBP13 also stabilized the E3 ligase XB3 ortholog 5 in A. thaliana (XBAT35.2) in response to ABA treatment. Hence, we demonstrated that UBP12 and UBP13 are previously unidentified rheostatic regulators of ABA signaling and revealed a mechanism by which deubiquitination precisely monitors the XBAT35/VPS23A ubiquitination module in the ABA response.
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Affiliation(s)
- Guangchao Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jiaxuan Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lijuan Lou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206 Beijing, China
| | - Miaomiao Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangyun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lijing Liu
- School of Life Sciences, Shandong University, Qingdao, 266237 Shandong, China
| | - Qingzhen Zhao
- College of Life Sciences, Liaocheng University, Liaocheng, 252000 Shandong, China
| | - Ran Xia
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
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Taylor JP, Malhotra A, Burns NJ, Clause AR, Brown CM, Burns BT, Chandrasekhar A, Schlachetzki Z, Bennett M, Thorpe E, Taft RJ, Perry DL, Coffey AJ. A clinical laboratory's experience using GeneMatcher - building stronger gene-disease relationships. Hum Mutat 2022; 43:765-771. [PMID: 35181961 DOI: 10.1002/humu.24356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/08/2022]
Abstract
The use of whole-genome sequencing (WGS) has accelerated the pace of gene discovery and highlighted the need for open and collaborative data sharing in the search for novel disease genes and variants. GeneMatcher (GM) is designed to facilitate connections between researchers, clinicians, health-care providers and others to help in the identification of additional patients with variants in the same candidate disease genes. The Illumina Clinical Services Laboratory offers a WGS test for patients with suspected rare and undiagnosed genetic disease and regularly submits potential candidate genes to GM to strengthen gene-disease relationships. We describe our experience with GM, including criteria for evaluation of candidate genes, and our workflow for the submission and review process. We have made 69 submissions, 36 of which are currently active. Ten per cent of submissions have resulted in publications, with an additional 14 submissions part of ongoing collaborations and expected to result in a publication. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Julie P Taylor
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alka Malhotra
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Nicole J Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Amanda R Clause
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Carolyn M Brown
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Brendan T Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Anjana Chandrasekhar
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Zina Schlachetzki
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Maren Bennett
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
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Sutus E, Henry S, Adorján L, Kovács G, Pirity MK. RYBP regulates Pax6 during in vitro neural differentiation of mouse embryonic stem cells. Sci Rep 2022; 12:2364. [PMID: 35149723 DOI: 10.1038/s41598-022-06228-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/19/2022] [Indexed: 12/05/2022] Open
Abstract
We have previously reported that RING1 and YY1 binding protein (RYBP) is important for central nervous system development in mice and that Rybp null mutant (Rybp−/−) mouse embryonic stem (ES) cells form more progenitors and less terminally differentiated neural cells than the wild type cells in vitro. Accelerated progenitor formation coincided with a high level of Pax6 expression in the Rybp−/− neural cultures. Since Pax6 is a retinoic acid (RA) inducible gene, we have analyzed whether altered RA signaling contributes to the accelerated progenitor formation and impaired differentiation ability of the Rybp−/− cells. Results suggested that elevated Pax6 expression was driven by the increased activity of the RA signaling pathway in the Rybp−/− neural cultures. RYBP was able to repress Pax6 through its P1 promoter. The repression was further attenuated when RING1, a core member of ncPRC1s was also present. According to this, RYBP and PAX6 were rarely localized in the same wild type cells during in vitro neural differentiation. These results suggest polycomb dependent regulation of Pax6 by RYBP during in vitro neural differentiation. Our results thus provide novel insights on the dynamic regulation of Pax6 and RA signaling by RYBP during mouse neural development.
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Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI. DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology (Basel) 2022; 11:260. [PMID: 35205126 PMCID: PMC8869715 DOI: 10.3390/biology11020260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 01/10/2023]
Abstract
High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging and often time-consuming. Here, we developed DRPPM-EASY, an R Shiny framework for integrative multi-omics analysis. We applied our application to analyze RNA-seq data generated from a USP7 knockdown in T-cell acute lymphoblastic leukemia (T-ALL) cell line, which identified upregulated expression of a TAL1-associated proliferative signature in T-cell acute lymphoblastic leukemia cell lines. Next, we performed proteomic profiling of the USP7 knockdown samples. Through DRPPM-EASY-Integration, we performed a concurrent analysis of the transcriptome and proteome and identified consistent disruption of the protein degradation machinery and spliceosome in samples with USP7 silencing. To further illustrate the utility of the R Shiny framework, we developed DRPPM-EASY-CCLE, a Shiny extension preloaded with the Cancer Cell Line Encyclopedia (CCLE) data. The DRPPM-EASY-CCLE app facilitates the sample querying and phenotype assignment by incorporating meta information, such as genetic mutation, metastasis status, sex, and collection site. As proof of concept, we verified the expression of TP53 associated DNA damage signature in TP53 mutated ovary cancer cells. Altogether, our open-source application provides an easy-to-use framework for omics exploration and discovery.
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Affiliation(s)
- Alyssa Obermayer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Li Dong
- Computational Biology Department, St Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Qianqian Hu
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | | | - Jerald D. Noble
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA; (J.D.N.); (T.J.R.)
| | - Paulo Rodriguez
- Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Timothy J. Robinson
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA; (J.D.N.); (T.J.R.)
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Aik-Choon Tan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
| | - Timothy I. Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (A.O.); (M.T.); (A.-C.T.)
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Li D, Dewey MG, Wang L, Falcinelli SD, Wong LM, Tang Y, Browne EP, Chen X, Archin NM, Margolis DM, Jiang G. Crotonylation sensitizes IAPi-induced disruption of latent HIV by enhancing p100 cleavage into p52. iScience 2022; 25:103649. [PMID: 35024584 PMCID: PMC8728431 DOI: 10.1016/j.isci.2021.103649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 01/08/2023] Open
Abstract
The eradication of HIV infection is difficult to achieve because of stable viral reservoirs. Here, we show that crotonylation enhances AZD5582-induced noncanonical NF-κB (ncNF-κB) signaling, further augmenting HIV latency reversal in Jurkat and U1 cell line models of latency, HIV latently infected primary CD4+ T cells and resting CD4+ T cells isolated from people living with HIV. Crotonylation upregulated the levels of the active p52 subunit of NF-κB following AZD5582. Biochemical analyses suggest that the ubiquitin E3 ligase TRIM27 is involved in enhanced p100 cleavage to p52. When TRIM27 was depleted, AZD5582-induced HIV latency reversal was reduced. TRIM27 small interfering RNA (siRNA) knockdown reduced both p100 and p52 levels without inhibiting p100 transcription, indicating that TRIM27 not only acts on p100 cleavage but also may impact p100/p52 stability. These observations reveal the complexity of HIV transcriptional machinery, particularly of NF-κB.
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Affiliation(s)
- Dajiang Li
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
| | - Morgan G. Dewey
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - Shane D. Falcinelli
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - Lilly M. Wong
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
| | - Yuyang Tang
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
| | - Edward P. Browne
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - David M. Margolis
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
| | - Guochun Jiang
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Genetic Medicine Building, Room 2111, Chapel Hill, NC 27599-7042, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7042, USA
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Abstract
The quality and quantity of membrane proteins are precisely and dynamically maintained through an endosomal recycling process. This endosomal recycling is executed by two protein complexes: retromer and recently identified retriever. Defects in the function of retromer or retriever cause dysregulation of many membrane proteins and result in several human disorders, including neurodegenerative disorders such as Alzheimer’s disease and Parkinson’s disease. Recently, neurodevelopmental disorders caused by pathogenic variants in genes associated with retriever were identified. This review focuses on the two recycling complexes and discuss their biological and developmental roles and the consequences of defects in endosomal recycling, especially in the nervous system. We also discuss future perspectives of a possible relationship of the dysfunction of retromer and retriever with neurodevelopmental disorders.
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Affiliation(s)
- Shinji Saitoh
- Department of Pediatrics and Neonatology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi 1, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
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Zhou L, Ouyang T, Li M, Hong T, Mhs A, Meng W, Zhang N. Ubiquitin-Specific Peptidase 7: A Novel Deubiquitinase That Regulates Protein Homeostasis and Cancers. Front Oncol 2021; 11:784672. [PMID: 34869041 PMCID: PMC8640129 DOI: 10.3389/fonc.2021.784672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin-Specific Peptidase 7 (USP7), or herpes virus-associated protease (HAUSP), is the largest family of the deubiquitinating enzymes (DUBs). Recent studies have shown that USP7 plays a vital role in regulating various physiological and pathological processes. Dysregulation of these processes mediated by USP7 may contribute to many diseases, such as cancers. Moreover, USP7 with aberrant expression levels and abnormal activity are found in cancers. Therefore, given the association between USP7 and cancers, targeting USP7 could be considered as an attractive and potential therapeutic approach in cancer treatment. This review describes the functions of USP7 and the regulatory mechanisms of its expression and activity, aiming to emphasize the necessity of research on USP7, and provide a better understanding of USP7-related biological processes and cancer.
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Affiliation(s)
- Lin Zhou
- First Clinical Medical College, Nanchang University, Nanchang, China
| | - Taohui Ouyang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meihua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Alriashy Mhs
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Wei Meng
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Na Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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Abstract
The melanoma antigen gene (MAGE) protein family is a group of highly conserved proteins that share a common homology domain. Under normal circumstances, numerous MAGE proteins are only expressed in reproduction-related tissues; however, abnormal expression levels are observed in a variety of tumor tissues. The MAGE family consists of type I and II proteins, several of which are cancer-testis antigens that are highly expressed in cancer and serve a critical role in tumorigenesis. Therefore, this review will use the relationship between MAGEs and tumors as a starting point, focusing on the latest developments regarding the function of MAGEs as oncogenes, and preliminarily reveal their possible mechanisms.
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Affiliation(s)
- Sanyan Li
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xiang Shi
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Jingping Li
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
| | - Xianrong Zhou
- Department of Pathology, Qianjiang Central Hospital, Qianjiang, Hubei 433100, P.R. China
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Wilson P, Abdelmoti L, Norcross R, Jang ER, Palayam M, Galperin E. The role of USP7 in the Shoc2-ERK1/2 signaling axis and Noonan-like syndrome with loose anagen hair. J Cell Sci 2021; 134:272259. [PMID: 34553755 DOI: 10.1242/jcs.258922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
The ERK1/2 (also known as MAPK3 and MAPK1, respectively) signaling pathway is critical in organismal development and tissue morphogenesis. Deregulation of this pathway leads to congenital abnormalities with severe developmental dysmorphisms. The core ERK1/2 cascade relies on scaffold proteins, such as Shoc2 to guide and fine-tune its signals. Mutations in SHOC2 lead to the development of the pathology termed Noonan-like Syndrome with Loose Anagen Hair (NSLAH). However, the mechanisms underlying the functions of Shoc2 and its contributions to disease progression remain unclear. Here, we show that ERK1/2 pathway activation triggers the interaction of Shoc2 with the ubiquitin-specific protease USP7. We reveal that, in the Shoc2 module, USP7 functions as a molecular 'switch' that controls the E3 ligase HUWE1 and the HUWE1-induced regulatory feedback loop. We also demonstrate that disruption of Shoc2-USP7 binding leads to aberrant activation of the Shoc2-ERK1/2 axis. Importantly, our studies reveal a possible role for USP7 in the pathogenic mechanisms underlying NSLAH, thereby extending our understanding of how ubiquitin-specific proteases regulate intracellular signaling.
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Affiliation(s)
- Patricia Wilson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Lina Abdelmoti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Rebecca Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Eun Ryoung Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Malathy Palayam
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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40
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Ebstein F, Küry S, Papendorf JJ, Krüger E. Neurodevelopmental Disorders (NDD) Caused by Genomic Alterations of the Ubiquitin-Proteasome System (UPS): the Possible Contribution of Immune Dysregulation to Disease Pathogenesis. Front Mol Neurosci 2021; 14:733012. [PMID: 34566579 PMCID: PMC8455891 DOI: 10.3389/fnmol.2021.733012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over thirty years have passed since the first description of ubiquitin-positive structures in the brain of patients suffering from Alzheimer’s disease. Meanwhile, the intracellular accumulation of ubiquitin-modified insoluble protein aggregates has become an indisputable hallmark of neurodegeneration. However, the role of ubiquitin and a fortiori the ubiquitin-proteasome system (UPS) in the pathogenesis of neurodevelopmental disorders (NDD) is much less described. In this article, we review all reported monogenic forms of NDD caused by lesions in genes coding for any component of the UPS including ubiquitin-activating (E1), -conjugating (E2) enzymes, ubiquitin ligases (E3), ubiquitin hydrolases, and ubiquitin-like modifiers as well as proteasome subunits. Strikingly, our analysis revealed that a vast majority of these proteins have a described function in the negative regulation of the innate immune response. In this work, we hypothesize a possible involvement of autoinflammation in NDD pathogenesis. Herein, we discuss the parallels between immune dysregulation and neurodevelopment with the aim at improving our understanding the biology of NDD and providing knowledge required for the design of novel therapeutic strategies.
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Affiliation(s)
- Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'Institut du Thorax, CNRS, INSERM, CHU Nantes, Université de Nantes, Nantes, France
| | - Jonas Johannes Papendorf
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
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41
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Steger M, Demichev V, Backman M, Ohmayer U, Ihmor P, Müller S, Ralser M, Daub H. Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale. Nat Commun 2021; 12:5399. [PMID: 34518535 DOI: 10.1038/s41467-021-25454-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/11/2021] [Indexed: 11/08/2022] Open
Abstract
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA)-MS and neural network-based data processing specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples identification numbers to 70,000 ubiquitinated peptides in single MS runs, while significantly improving robustness and quantification precision. Upon inhibition of the oncology target USP7, we simultaneously record ubiquitination and consequent changes in abundance of more than 8,000 proteins at high temporal resolution. While ubiquitination of hundreds of proteins increases within minutes of USP7 inhibition, we find that only a small fraction of those are ever degraded, thereby dissecting the scope of USP7 action. Our method enables rapid mode-of-action profiling of candidate drugs targeting DUBs or ubiquitin ligases at high precision and throughput. Combining improved sample preparation, data-independent acquisition mass spectrometry and deep learning, the authors develop a workflow for more robust and precise quantitative ubiquitinome profiling. They use this method to characterize targets of the deubiquitinase USP7 and effects of USP7 inhibitors.
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42
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Pluciennik A, Liu Y, Molotsky E, Marsh GB, Ranxhi B, Arnold FJ, St-Cyr S, Davidson B, Pourshafie N, Lieberman AP, Gu W, Todi SV, Merry DE. Deubiquitinase USP7 contributes to the pathogenicity of spinal and bulbar muscular atrophy. J Clin Invest 2021; 131:134565. [PMID: 33170804 DOI: 10.1172/jci134565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
Polyglutamine (polyQ) diseases are devastating, slowly progressing neurodegenerative conditions caused by expansion of polyQ-encoding CAG repeats within the coding regions of distinct, unrelated genes. In spinal and bulbar muscular atrophy (SBMA), polyQ expansion within the androgen receptor (AR) causes progressive neuromuscular toxicity, the molecular basis of which is unclear. Using quantitative proteomics, we identified changes in the AR interactome caused by polyQ expansion. We found that the deubiquitinase USP7 preferentially interacts with polyQ-expanded AR and that lowering USP7 levels reduced mutant AR aggregation and cytotoxicity in cell models of SBMA. Moreover, USP7 knockdown suppressed disease phenotypes in SBMA and spinocerebellar ataxia type 3 (SCA3) fly models, and monoallelic knockout of Usp7 ameliorated several motor deficiencies in transgenic SBMA mice. USP7 overexpression resulted in reduced AR ubiquitination, indicating the direct action of USP7 on AR. Using quantitative proteomics, we identified the ubiquitinated lysine residues on mutant AR that are regulated by USP7. Finally, we found that USP7 also differentially interacts with mutant Huntingtin (HTT) protein in striatum and frontal cortex of a knockin mouse model of Huntington's disease. Taken together, our findings reveal a critical role for USP7 in the pathophysiology of SBMA and suggest a similar role in SCA3 and Huntington's disease.
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Affiliation(s)
- Anna Pluciennik
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Yuhong Liu
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Elana Molotsky
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Gregory B Marsh
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bedri Ranxhi
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Frederick J Arnold
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sophie St-Cyr
- Department of Pathology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Beverly Davidson
- Department of Pathology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA.,George Washington University, Institute of Biomedical Sciences, Washington, DC, USA
| | - Andrew P Lieberman
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Wei Gu
- Department of Pathology and Cell Biology and Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Sokol V Todi
- Department of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Diane E Merry
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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43
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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44
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MacDonald E, Savage B, Zech T. Connecting the dots: combined control of endocytic recycling and degradation. Biochem Soc Trans 2020; 48:2377-86. [PMID: 33300959 DOI: 10.1042/BST20180255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/29/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Endocytosis is an essential process where proteins and lipids are internalised from the plasma membrane in membrane-bound carriers, such as clathrin-coated vesicles. Once internalised into the cell these vesicles fuse with the endocytic network where their contents are sorted towards degradation in the lysosome or recycling to their origin. Initially, it was thought that cargo recycling is a passive process, but in recent years the identification and characterisation of specialised recycling complexes has established a hitherto unthought-of level of complexity that actively opposes degradation. This review will summarise recent developments regarding the composition and regulation of the recycling machineries and their relationship with the degradative pathways of the endosome.
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45
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Sanderson MR, Fahlman RP, Wevrick R. The N-terminal domain of the Schaaf-Yang syndrome protein MAGEL2 likely has a role in RNA metabolism. J Biol Chem 2021; 297:100959. [PMID: 34265304 PMCID: PMC8350409 DOI: 10.1016/j.jbc.2021.100959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/22/2021] [Accepted: 07/11/2021] [Indexed: 02/08/2023] Open
Abstract
MAGEL2 encodes the L2 member of the melanoma-associated antigen gene (MAGE) protein family, truncating mutations of which can cause Schaaf-Yang syndrome, an autism spectrum disorder. MAGEL2 is also inactivated in Prader-Willi syndrome, which overlaps clinically and mechanistically with Schaaf-Yang syndrome. Studies to date have only investigated the C-terminal portion of the MAGEL2 protein, containing the MAGE homology domain that interacts with RING-E3 ubiquitin ligases and deubiquitinases to form protein complexes that modify protein ubiquitination. In contrast, the N-terminal portion of the MAGEL2 protein has never been studied. Here, we find that MAGEL2 has a low-complexity intrinsically disordered N-terminus rich in Pro-Xn-Gly motifs that is predicted to mediate liquid-liquid phase separation to form biomolecular condensates. We used proximity-dependent biotin identification (BioID) and liquid chromatography-tandem mass spectrometry to identify MAGEL2-proximal proteins, then clustered these proteins into functional networks. We determined that coding mutations analogous to disruptive mutations in other MAGE proteins alter these networks in biologically relevant ways. Proteins identified as proximal to the N-terminal portion of MAGEL2 are primarily involved in mRNA metabolic processes and include three mRNA N 6-methyladenosine (m6A)-binding YTHDF proteins and two RNA interference-mediating TNRC6 proteins. We found that YTHDF2 coimmunoprecipitates with MAGEL2, and coexpression of MAGEL2 reduces the nuclear accumulation of YTHDF2 after heat shock. We suggest that the N-terminal region of MAGEL2 may have a role in RNA metabolism and in particular the regulation of mRNAs modified by m6A methylation. These results provide mechanistic insight into pathogenic MAGEL2 mutations associated with Schaaf-Yang syndrome and related disorders.
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Affiliation(s)
- Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
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46
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Correa‐da‐Silva F, Fliers E, Swaab DF, Yi C. Hypothalamic neuropeptides and neurocircuitries in Prader Willi syndrome. J Neuroendocrinol 2021; 33:e12994. [PMID: 34156126 PMCID: PMC8365683 DOI: 10.1111/jne.12994] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
Prader-Willi Syndrome (PWS) is a rare and incurable congenital neurodevelopmental disorder, resulting from the absence of expression of a group of genes on the paternally acquired chromosome 15q11-q13. Phenotypical characteristics of PWS include infantile hypotonia, short stature, incomplete pubertal development, hyperphagia and morbid obesity. Hypothalamic dysfunction in controlling body weight and food intake is a hallmark of PWS. Neuroimaging studies have demonstrated that PWS subjects have abnormal neurocircuitry engaged in the hedonic and physiological control of feeding behavior. This is translated into diminished production of hypothalamic effector peptides which are responsible for the coordination of energy homeostasis and satiety. So far, studies with animal models for PWS and with human post-mortem hypothalamic specimens demonstrated changes particularly in the infundibular and the paraventricular nuclei of the hypothalamus, both in orexigenic and anorexigenic neural populations. Moreover, many PWS patients have a severe endocrine dysfunction, e.g. central hypogonadism and/or growth hormone deficiency, which may contribute to the development of increased fat mass, especially if left untreated. Additionally, the role of non-neuronal cells, such as astrocytes and microglia in the hypothalamic dysregulation in PWS is yet to be determined. Notably, microglial activation is persistently present in non-genetic obesity. To what extent microglia, and other glial cells, are affected in PWS is poorly understood. The elucidation of the hypothalamic dysfunction in PWS could prove to be a key feature of rational therapeutic management in this syndrome. This review aims to examine the evidence for hypothalamic dysfunction, both at the neuropeptidergic and circuitry levels, and its correlation with the pathophysiology of PWS.
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Affiliation(s)
- Felipe Correa‐da‐Silva
- Department of Endocrinology and MetabolismAmsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Center (UMC)University of AmsterdamAmsterdamThe Netherlands
- Laboratory of EndocrinologyAmsterdam University Medical Center (UMC)University of AmsterdamAmsterdamThe Netherlands
- Department of Neuropsychiatric DisordersNetherlands Institute for NeuroscienceAn Institute of the Royal Netherlands Academy of Arts and SciencesAmsterdamThe Netherlands
| | - Eric Fliers
- Department of Endocrinology and MetabolismAmsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Center (UMC)University of AmsterdamAmsterdamThe Netherlands
| | - Dick F. Swaab
- Department of Neuropsychiatric DisordersNetherlands Institute for NeuroscienceAn Institute of the Royal Netherlands Academy of Arts and SciencesAmsterdamThe Netherlands
| | - Chun‐Xia Yi
- Department of Endocrinology and MetabolismAmsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Center (UMC)University of AmsterdamAmsterdamThe Netherlands
- Laboratory of EndocrinologyAmsterdam University Medical Center (UMC)University of AmsterdamAmsterdamThe Netherlands
- Department of Neuropsychiatric DisordersNetherlands Institute for NeuroscienceAn Institute of the Royal Netherlands Academy of Arts and SciencesAmsterdamThe Netherlands
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47
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Capitani N, Baldari CT. F-Actin Dynamics in the Regulation of Endosomal Recycling and Immune Synapse Assembly. Front Cell Dev Biol 2021; 9:670882. [PMID: 34249926 PMCID: PMC8265274 DOI: 10.3389/fcell.2021.670882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Membrane proteins endocytosed at the cell surface as vesicular cargoes are sorted at early endosomes for delivery to lysosomes for degradation or alternatively recycled to different cellular destinations. Cargo recycling is orchestrated by multimolecular complexes that include the retromer, retriever, and the WASH complex, which promote the polymerization of new actin filaments at early endosomes. These endosomal actin pools play a key role at different steps of the recycling process, from cargo segregation to specific endosomal subdomains to the generation and mobility of tubulo-vesicular transport carriers. Local F-actin pools also participate in the complex redistribution of endomembranes and organelles that leads to the acquisition of cell polarity. Here, we will present an overview of the contribution of endosomal F-actin to T-cell polarization during assembly of the immune synapse, a specialized membrane domain that T cells form at the contact with cognate antigen-presenting cells.
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Affiliation(s)
- Nagaja Capitani
- Department of Life Sciences, University of Siena, Siena, Italy
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48
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Hebach NR, Caro P, Martin-Giacalone BA, Lupo PJ, Marbach F, Choukair D, Schaaf CP. A retrospective analysis of growth hormone therapy in children with Schaaf-Yang syndrome. Clin Genet 2021; 100:298-307. [PMID: 34013972 DOI: 10.1111/cge.14000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022]
Abstract
Short stature is a common phenotype in children with Schaaf-Yang syndrome (SYS). Prader-Willi syndrome (PWS) and SYS share several phenotypic features including short stature, muscular hypotonia and developmental delay/intellectual disability. Evidence exists that similar to PWS, growth hormone (GH) deficiency may also be a feature of SYS. Recombinant human GH (rhGH) therapy has been approved for PWS, but the effects of rhGH therapy in individuals with SYS have not yet been documented. This retrospective, questionnaire-based study analyzes the prevalence of rhGH therapy in children with SYS, the effects of rhGH therapy on anthropometric measures, and parental perception of the treatment. Twenty-six individuals with SYS were sent a clinical questionnaire and a request for growth charts. We found a significant increase in height z-score (p* = 0.04) as well as a significant decrease in body mass index 6 months after rhGH therapy initiation (p* = 0.04). Furthermore, height z-scores of the treated group (mean z-score = -1.00) were significantly higher than those of the untreated group (mean z-score = -3.36, p = 0.01) at time of enrollment. All parents reported an increase in muscle strength and endurance, and several families noted beneficial effects such as improved cognition and motor development.
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Affiliation(s)
- Nils R Hebach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Bailey A Martin-Giacalone
- Department of Pediatrics Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Philip J Lupo
- Department of Pediatrics Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Felix Marbach
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Daniela Choukair
- Divison of Paediatric Endocrinology and Diabetology, University Children's Hospital, Heidelberg, Germany
| | - Christian Patrick Schaaf
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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49
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Basu-Shrivastava M, Kozoriz A, Desagher S, Lassot I. To Ubiquitinate or Not to Ubiquitinate: TRIM17 in Cell Life and Death. Cells 2021; 10:1235. [PMID: 34069831 PMCID: PMC8157266 DOI: 10.3390/cells10051235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
TRIM17 is a member of the TRIM family, a large class of RING-containing E3 ubiquitin-ligases. It is expressed at low levels in adult tissues, except in testis and in some brain regions. However, it can be highly induced in stress conditions which makes it a putative stress sensor required for the triggering of key cellular responses. As most TRIM members, TRIM17 can act as an E3 ubiquitin-ligase and promote the degradation by the proteasome of substrates such as the antiapoptotic protein MCL1. Intriguingly, TRIM17 can also prevent the ubiquitination of other proteins and stabilize them, by binding to other TRIM proteins and inhibiting their E3 ubiquitin-ligase activity. This duality of action confers several pivotal roles to TRIM17 in crucial cellular processes such as apoptosis, autophagy or cell division, but also in pathological conditions as diverse as Parkinson's disease or cancer. Here, in addition to recent data that endorse this duality, we review what is currently known from public databases and the literature about TRIM17 gene regulation and expression, TRIM17 protein structure and interactions, as well as its involvement in cell physiology and human disorders.
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Affiliation(s)
| | - Alina Kozoriz
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
| | - Solange Desagher
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
| | - Iréna Lassot
- Institut de Génétique Moléculaire de Montpellier, University Montpellier, CNRS, Montpellier, France
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50
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Walpole GFW, Plumb JD, Chung D, Tang B, Boulay B, Osborne DG, Piotrowski JT, Catz SD, Billadeau DD, Grinstein S, Jaumouillé V. Inactivation of Rho GTPases by Burkholderia cenocepacia Induces a WASH-Mediated Actin Polymerization that Delays Phagosome Maturation. Cell Rep 2021; 31:107721. [PMID: 32492429 PMCID: PMC7315377 DOI: 10.1016/j.celrep.2020.107721] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 02/02/2023] Open
Abstract
Burkholderia cenocepacia is an opportunistic bacterial pathogen that causes severe pulmonary infections in cystic fibrosis and chronic granulomatous disease patients. B. cenocepacia can survive inside infected macrophages within the B. cenocepacia-containing vacuole (BcCV) and to elicit a severe inflammatory response. By inactivating the host macrophage Rho GTPases, the bacterial effector TecA causes depolymerization of the cortical actin cytoskeleton. In this study, we find that B. cenocepacia induces the formation of large cytosolic F-actin clusters in infected macrophages. Cluster formation requires the nucleation-promoting factor WASH, the Arp2/3 complex, and TecA. Inactivation of Rho GTPases by bacterial toxins is necessary and sufficient to induce the formation of the cytosolic actin clusters. By hijacking WASH and Arp2/3 activity, B. cenocepacia disrupts interactions with the endolysosomal system, thereby delaying the maturation of the BcCV.
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Affiliation(s)
- Glenn F W Walpole
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan D Plumb
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniel Chung
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brandon Tang
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Benoit Boulay
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Douglas G Osborne
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Joshua T Piotrowski
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sergio D Catz
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB-215, La Jolla, CA 92037, USA
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sergio Grinstein
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Valentin Jaumouillé
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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