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Her Y, Pascual DM, Goldstone-Joubert Z, Marcogliese PC. Variant functional assessment in Drosophila by overexpression: what can we learn? Genome 2024; 67:158-167. [PMID: 38412472 DOI: 10.1139/gen-2023-0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The last decade has been highlighted by the increased use of next-generation DNA sequencing technology to identify novel human disease genes. A critical downstream part of this process is assigning function to a candidate gene variant. Functional studies in Drosophila melanogaster, the common fruit fly, have made a prominent contribution in annotating variant impact in an in vivo system. The use of patient-derived knock-in flies or rescue-based, "humanization", approaches are novel and valuable strategies in variant testing but have been recently widely reviewed. An often-overlooked strategy for determining variant impact has been GAL4/upstream activation sequence-mediated tissue-defined overexpression in Drosophila. This mini-review will summarize the recent contribution of ectopic overexpression of human reference and variant cDNA in Drosophila to assess variant function, interpret the consequence of the variant, and in some cases infer biological mechanisms.
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Affiliation(s)
- Yina Her
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, Winnipeg, MB, Canada
| | - Danielle M Pascual
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, Winnipeg, MB, Canada
| | - Zoe Goldstone-Joubert
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, Winnipeg, MB, Canada
| | - Paul C Marcogliese
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), University of Manitoba, Winnipeg, MB, Canada
- Excellence in Neurodevelopment and Rehabilitation Research in Child Health (ENRRICH) Theme, Winnipeg, MB, Canada
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Zhang X, Yao S, Zhang L, Yang L, Yang M, Guo Q, Li Y, Wang Z, Lei B, Jin X. Mechanisms underlying morphological and functional changes of cilia in fibroblasts derived from patients bearing ARL3 T31A and ARL3 T31A/C118F mutations. FASEB J 2024; 38:e23519. [PMID: 38457249 DOI: 10.1096/fj.202301906r] [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: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/10/2024]
Abstract
ARL3 is essential for cilia development, and mutations in ARL3 are closely associated with ciliopathies. In a previous study, we observed distinct phenotypes of retinal dystrophy in patients with heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, indicating that different mutation types may exert diverse effects on their functions. Here, we generated transformed immortal fibroblast cells from patients carrying heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, and systematically evaluated their cilia morphology and function, which were further validated in ARPE-19 cells. Results showed that both ARL3T31A and ARL3T31A/C118F mutations led to a decrease in cilium formation. The ARL3T31A/C118F mutations caused significantly elongated cilia and impaired retrograde transport, whereas the ARL3T31A mutation did not induce significant changes in fibroblasts. RNA-sequencing results indicated that compared to ARL3T31A , ARL3T31A/C118F fibroblasts exhibited a higher enrichment of biological processes related to neuron projection development, tissue morphogenesis, and extracellular matrix (ECM) organization, with noticeable alterations in pathways such as ECM-receptor interaction, focal adhesion, and TGF-β signaling. Similar changes were observed in the proteomic results in ARPE-19 cells. Core regulated genes including IQUB, UNC13D, RAB3IP, and GRIP1 were specifically downregulated in the ARL3T31A/C118F group, and expressions of IQUB, NPM2, and SLC38A4 were further validated. Additionally, IQUB showed a rescuing effect on the overlong cilia observed in ARL3T31A/C118F fibroblasts. Our results not only enhance our understanding of ARL3-related diseases but also provide new insights into the analysis of heterozygous and compound heterozygous mutations in genetics.
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Affiliation(s)
- Xiaoli Zhang
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
| | - Shun Yao
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Lujia Zhang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin Yang
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhu Yang
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Qingge Guo
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Yan Li
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhongfeng Wang
- Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Bo Lei
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
| | - Xiuxiu Jin
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, China
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Ledvin L, Gassaway BM, Tawil J, Urso O, Pizzo D, Welsh KA, Bolhuis DL, Fisher D, Bonni A, Gygi SP, Brown NG, Ferguson CJ. The anaphase-promoting complex controls a ubiquitination-phosphoprotein axis in chromatin during neurodevelopment. Dev Cell 2023; 58:2666-2683.e9. [PMID: 37875116 PMCID: PMC10872926 DOI: 10.1016/j.devcel.2023.10.002] [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: 12/13/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Mutations in the degradative ubiquitin ligase anaphase-promoting complex (APC) alter neurodevelopment by impairing proteasomal protein clearance, but our understanding of their molecular and cellular pathogenesis remains limited. Here, we employ the proteomic-based discovery of APC substrates in APC mutant mouse brain and human cell lines and identify the chromosome-passenger complex (CPC), topoisomerase 2a (Top2a), and Ki-67 as major chromatin factors targeted by the APC during neuronal differentiation. These substrates accumulate in phosphorylated form, suggesting that they fail to be eliminated after mitosis during terminal differentiation. The accumulation of the CPC kinase Aurora B within constitutive heterochromatin and hyperphosphorylation of its target histone 3 are corrected in the mutant brain by pharmacologic Aurora B inhibition. Surprisingly, the reduction of Ki-67, but not H3S10ph, rescued the function of constitutive heterochromatin in APC mutant neurons. These results expand our understanding of how ubiquitin signaling regulates chromatin during neurodevelopment and identify potential therapeutic targets in APC-related disorders.
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Affiliation(s)
- Leya Ledvin
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brandon M Gassaway
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Tawil
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivia Urso
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Donald Pizzo
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kaeli A Welsh
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Azad Bonni
- Neuroscience Department, Washington University, St. Louis, MO 63110, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cole J Ferguson
- Pathology Department, University of California, San Diego, La Jolla, CA 92093, USA.
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Ma P, Wan LP, Li Y, He CH, Song NN, Zhao S, Wang H, Ding YQ, Mao B, Sheng N. RNF220 is an E3 ubiquitin ligase for AMPA receptors to regulate synaptic transmission. SCIENCE ADVANCES 2022; 8:eabq4736. [PMID: 36179027 PMCID: PMC9524831 DOI: 10.1126/sciadv.abq4736] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/15/2022] [Indexed: 06/12/2023]
Abstract
The accurate expression of postsynaptic AMPA receptors (AMPARs) is critical for information processing in the brain, and ubiquitination is a key regulator for this biological process. However, the roles of E3 ubiquitin ligases in the regulation of AMPARs are poorly understood. Here, we find that RNF220 directly interacts with AMPARs to meditate their polyubiquitination, and RNF220 knockout specifically increases AMPAR protein levels, thereby enhancing basal synaptic activity while impairing synaptic plasticity. Moreover, depending on its E3 ubiquitin ligase activity, RNF220 represses AMPAR-mediated excitatory synaptic responses and their neuronal surface expression. Furthermore, learning and memory are altered in forebrain RNF220-deficient mice. In addition, two neuropathology-related RNF220 variants fail to repress excitatory synaptic activity because of the incapability to regulate AMPAR ubiquitination due to their attenuated interaction. Together, we identify RNF220 as an E3 ubiquitin ligase for AMPARs and establish its substantial role in excitatory synaptic transmission and brain function.
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Affiliation(s)
- Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Pear Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Yuwei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Chun-Hui He
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Ning-Ning Song
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
- Department of Laboratory Animal Science, Fudan University, Shanghai 200032, China
| | - Shiping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Huishan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Yu-Qiang Ding
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai 200092, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
- Department of Laboratory Animal Science, Fudan University, Shanghai 200032, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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Fischer FP, Kasture AS, Hummel T, Sucic S. Molecular and Clinical Repercussions of GABA Transporter 1 Variants Gone Amiss: Links to Epilepsy and Developmental Spectrum Disorders. Front Mol Biosci 2022; 9:834498. [PMID: 35295842 PMCID: PMC7612498 DOI: 10.3389/fmolb.2022.834498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
The human γ-aminobutyric acid (GABA) transporter 1 (hGAT-1) is the first member of the solute carrier 6 (SLC6) protein superfamily. GAT-1 (SLC6A1) is one of the main GABA transporters in the central nervous system. Its principal physiological role is retrieving GABA from the synapse into neurons and astrocytes, thus swiftly terminating neurotransmission. GABA is a key inhibitory neurotransmitter and shifts in GABAergic signaling can lead to pathological conditions, from anxiety and epileptic seizures to schizophrenia. Point mutations in the SLC6A1 gene frequently give rise to epilepsy, intellectual disability or autism spectrum disorders in the afflicted individuals. The mechanistic routes underlying these are still fairly unclear. Some loss-of-function variants impair the folding and intracellular trafficking of the protein (thus retaining the transporter in the endoplasmic reticulum compartment), whereas others, despite managing to reach their bona fide site of action at the cell surface, nonetheless abolish GABA transport activity (plausibly owing to structural/conformational defects). Whatever the molecular culprit(s), the physiological aftermath transpires into the absence of functional transporters, which in turn perturbs GABAergic actions. Dozens of mutations in the kin SLC6 family members are known to exhort protein misfolding. Such events typically elicit severe ailments in people, e.g., infantile parkinsonism-dystonia or X-linked intellectual disability, in the case of dopamine and creatine transporters, respectively. Flaws in protein folding can be rectified by small molecules known as pharmacological and/or chemical chaperones. The search for such apt remedies calls for a systematic investigation and categorization of the numerous disease-linked variants, by biochemical and pharmacological means in vitro (in cell lines and primary neuronal cultures) and in vivo (in animal models). We here give special emphasis to the utilization of the fruit fly Drosophila melanogaster as a versatile model in GAT-1-related studies. Jointly, these approaches can portray indispensable insights into the molecular factors underlying epilepsy, and ultimately pave the way for contriving efficacious therapeutic options for patients harboring pathogenic mutations in hGAT-1.
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Affiliation(s)
- Florian P. Fischer
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
- Department of Epileptology and Neurology, University of Aachen, Aachen, Germany
| | - Ameya S. Kasture
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Thomas Hummel
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
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