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Oxman E, Li H, Wang HY, Zohn IE. Identification and functional analysis of rare HECTD1 missense variants in human neural tube defects. Hum Genet 2024; 143:263-277. [PMID: 38451291 PMCID: PMC11043113 DOI: 10.1007/s00439-024-02647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 01/20/2024] [Indexed: 03/08/2024]
Abstract
Neural tube defects (NTDs) are severe malformations of the central nervous system that arise from failure of neural tube closure. HECTD1 is an E3 ubiquitin ligase required for cranial neural tube closure in mouse models. NTDs in the Hectd1 mutant mouse model are due to the failure of cranial mesenchyme morphogenesis during neural fold elevation. Our earlier research has linked increased extracellular heat shock protein 90 (eHSP90) secretion to aberrant cranial mesenchyme morphogenesis in the Hectd1 model. Furthermore, overexpression of HECTD1 suppresses stress-induced eHSP90 secretion in cell lines. In this study, we report the identification of five rare HECTD1 missense sequence variants in NTD cases. The variants were found through targeted next-generation sequencing in a Chinese cohort of 352 NTD cases and 224 ethnically matched controls. We present data showing that HECTD1 is a highly conserved gene, extremely intolerant to loss-of-function mutations and missense changes. To evaluate the functional consequences of NTD-associated missense variants, functional assays in HEK293T cells were performed to examine protein expression and the ability of HECTD1 sequence variants to suppress eHSP90 secretion. One NTD-associated variant (A1084T) had significantly reduced expression in HEK293T cells. All five NTD-associated variants (p.M392V, p.T801I, p.I906V, p.A1084T, and p.P1835L) reduced regulation of eHSP90 secretion by HECTD1, while a putative benign variant (p.P2474L) did not. These findings are the first association of HECTD1 sequence variation with NTDs in humans.
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Affiliation(s)
- Elias Oxman
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Research and Innovation Campus, Children's National Hospital, Washington, DC, 20012, USA
| | - Huili Li
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Hong-Yan Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, State Key Laboratory of Genetic, Engineering at School of Life Sciences, Fudan University, Shanghai, 200011, China
| | - Irene E Zohn
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Research and Innovation Campus, Children's National Hospital, Washington, DC, 20012, USA.
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Oxman E, Li H, Wang HY, Zohn I. Identification and Functional Analysis of Rare HECTD1 Missense Variants in Human Neural Tube Defects. RESEARCH SQUARE 2024:rs.3.rs-3794712. [PMID: 38260607 PMCID: PMC10802691 DOI: 10.21203/rs.3.rs-3794712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neural tube defects (NTDs) are severe malformations of the central nervous system that arise from failure of neural tube closure. HECTD1 is an E3 ubiquitin ligase required for cranial neural tube closure in mouse models. NTDs in the Hectd1 mutant mouse model are due to the failure of cranial mesenchyme morphogenesis during neural fold elevation. Our earlier research has linked increased secretion of extracellular heat shock protein 90 (eHSP90) to aberrant cranial mesenchyme morphogenesis in the Hectd1 model. Furthermore, overexpression of HECTD1 suppresses stress-induced eHSP90 secretion in cell lines. In this study, we report the identification of five rare HECTD1 missense sequence variants in NTD cases. The variants were found through targeted next-generation sequencing in a Chinese cohort of 352 NTD cases and 224 ethnically matched controls. We present data showing that HECTD1 is a highly conserved gene, extremely intolerant to loss-of-function mutations and missense changes. To evaluate the functional consequences of NTD-associated missense variants, functional assays in HEK293T cells were performed to examine protein expression and the ability of HECTD1 sequence variants to suppress eHSP90 secretion. One NTD-associated variant (A1084T) had significantly reduced expression in HEK293T cells. All five NTD-associated variants (p.M392V, p.T801I, p.I906V, p.A1084T, and p.P1835L) reduced regulation of eHSP90 secretion by HECTD1, while a putative benign variant (p.P2474L) did not. These findings are the first association of HECTD1 sequence variation with human disease and suggest that sequence variation in HECTD1 may play a role in the etiology of human NTDs.
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Affiliation(s)
| | - Huili Li
- University of Colorado at Boulder
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Salas J, Garcia A, Zora V, Dornbush S, Mousa-Ibrahim F, Fogg H, Gromley Z, Gromley A. Centriolin interacts with HectD1 in a cell cycle dependent manner. BMC Res Notes 2023; 16:375. [PMID: 38115153 PMCID: PMC10731774 DOI: 10.1186/s13104-023-06670-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
OBJECTIVE The centrosome is universally recognized as the microtubule organizing center of animal cells, but emerging evidence suggests that it has other important functions including primary cilia formation, DNA damage checkpoints, and cell cycle progression. Despite this, the role of individual components of the centrosome remains unclear. Previous studies suggest that one component, centriolin, has an important function in cytokinesis and cell cycle progression, although its exact role in these processes is not known. To determine how centriolin influences the progression through the cell cycle, we sought to identify interacting partners that may be involved in regulating its function. RESULTS This study provides evidence that the ubiquitin E3 ligase HectD1 binds to centriolin and that this association likely accounts for our observation that HectD1 co-localizes with centriolin at the centrosome during mitosis. In addition to its centrosomal localization, we also show that the expression of HectD1 fluctuates throughout the cell cycle, with the highest levels during mitosis, coinciding with a marked reduction in centriolin expression. We propose that the interaction between HectD1 and centriolin may be necessary for normal cell cycle progression and we speculate that this function may involve HectD1-mediated degradation of centriolin.
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Affiliation(s)
- Jesus Salas
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Alexander Garcia
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Vancy Zora
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Sean Dornbush
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Fady Mousa-Ibrahim
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Hanna Fogg
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Zeynep Gromley
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA
| | - Adam Gromley
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, USA.
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Frank D, Bergamasco M, Mlodzianoski MJ, Kueh A, Tsui E, Hall C, Kastrappis G, Voss AK, McLean C, Faux M, Rogers KL, Tran B, Vincan E, Komander D, Dewson G, Tran H. Trabid patient mutations impede the axonal trafficking of adenomatous polyposis coli to disrupt neurite growth. eLife 2023; 12:RP90796. [PMID: 38099646 PMCID: PMC10723793 DOI: 10.7554/elife.90796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
ZRANB1 (human Trabid) missense mutations have been identified in children diagnosed with a range of congenital disorders including reduced brain size, but how Trabid regulates neurodevelopment is not understood. We have characterized these patient mutations in cells and mice to identify a key role for Trabid in the regulation of neurite growth. One of the patient mutations flanked the catalytic cysteine of Trabid and its deubiquitylating (DUB) activity was abrogated. The second variant retained DUB activity, but failed to bind STRIPAK, a large multiprotein assembly implicated in cytoskeleton organization and neural development. Zranb1 knock-in mice harboring either of these patient mutations exhibited reduced neuronal and glial cell densities in the brain and a motor deficit consistent with fewer dopaminergic neurons and projections. Mechanistically, both DUB-impaired and STRIPAK-binding-deficient Trabid variants impeded the trafficking of adenomatous polyposis coli (APC) to microtubule plus-ends. Consequently, the formation of neuronal growth cones and the trajectory of neurite outgrowth from mutant midbrain progenitors were severely compromised. We propose that STRIPAK recruits Trabid to deubiquitylate APC, and that in cells with mutant Trabid, APC becomes hyperubiquitylated and mislocalized causing impaired organization of the cytoskeleton that underlie the neuronal and developmental phenotypes.
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Affiliation(s)
- Daniel Frank
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Maria Bergamasco
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Michael J Mlodzianoski
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Andrew Kueh
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Melbourne Advanced Genome Editing Centre, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Australia
| | - Ellen Tsui
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Histology Facility, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Cathrine Hall
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Georgios Kastrappis
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anne Kathrin Voss
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Catriona McLean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Maree Faux
- Neuro-Oncology Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Kelly L Rogers
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Bang Tran
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- The Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Grant Dewson
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hoanh Tran
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Julio AR, Shikwana F, Truong C, Burton NR, Dominguez E, Turmon AC, Cao J, Backus K. Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564067. [PMID: 38014036 PMCID: PMC10680658 DOI: 10.1101/2023.10.30.564067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of 'undruggable' protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.
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Ghosh A, Chakraborty P, Biswas D. Fine tuning of the transcription juggernaut: A sweet and sour saga of acetylation and ubiquitination. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194944. [PMID: 37236503 DOI: 10.1016/j.bbagrm.2023.194944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/26/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Among post-translational modifications of proteins, acetylation, phosphorylation, and ubiquitination are most extensively studied over the last several decades. Owing to their different target residues for modifications, cross-talk between phosphorylation with that of acetylation and ubiquitination is relatively less pronounced. However, since canonical acetylation and ubiquitination happen only on the lysine residues, an overlap of the same lysine residue being targeted for both acetylation and ubiquitination happens quite frequently and thus plays key roles in overall functional regulation predominantly through modulation of protein stability. In this review, we discuss the cross-talk of acetylation and ubiquitination in the regulation of protein stability for the functional regulation of cellular processes with an emphasis on transcriptional regulation. Further, we emphasize our understanding of the functional regulation of Super Elongation Complex (SEC)-mediated transcription, through regulation of stabilization by acetylation, deacetylation and ubiquitination and associated enzymes and its implication in human diseases.
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Affiliation(s)
- Avik Ghosh
- Laboratory of Transcription Biology Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Poushali Chakraborty
- Laboratory of Transcription Biology Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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Chen YH, Chen HH, Wang WJ, Chen HY, Huang WS, Kao CH, Lee SR, Yeat NY, Yan RL, Chan SJ, Wu KP, Chen RH. TRABID inhibition activates cGAS/STING-mediated anti-tumor immunity through mitosis and autophagy dysregulation. Nat Commun 2023; 14:3050. [PMID: 37237031 DOI: 10.1038/s41467-023-38784-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Activation of tumor-intrinsic innate immunity has been a major strategy for improving immunotherapy. Previously, we reported an autophagy-promoting function of the deubiquitinating enzyme TRABID. Here, we identify a critical role of TRABID in suppressing anti-tumor immunity. Mechanistically, TRABID is upregulated in mitosis and governs mitotic cell division by removing K29-linked polyubiquitin chain from Aurora B and Survivin, thereby stabilizing the entire chromosomal passenger complex. TRABID inhibition causes micronuclei through a combinatory defect in mitosis and autophagy and protects cGAS from autophagic degradation, thereby activating the cGAS/STING innate immunity pathway. Genetic or pharmacological inhibition of TRABID promotes anti-tumor immune surveillance and sensitizes tumors to anti-PD-1 therapy in preclinical cancer models in male mice. Clinically, TRABID expression in most solid cancer types correlates inversely with an interferon signature and infiltration of anti-tumor immune cells. Our study identifies a suppressive role of tumor-intrinsic TRABID in anti-tumor immunity and highlights TRABID as a promising target for sensitizing solid tumors to immunotherapy.
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Affiliation(s)
- Yu-Hsuan Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Han-Hsiun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Wei-Syun Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Chien-Han Kao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Sin-Rong Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Nai Yang Yeat
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ruei-Liang Yan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Shu-Jou Chan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 106, Taiwan.
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