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Arnskötter F, da Silva PBG, Schouw ME, Lukasch C, Bianchini L, Sieber L, Garcia-Lopez J, Ahmad ST, Li Y, Lin H, Joshi P, Spänig L, Radoš M, Roiuk M, Sepp M, Zuckermann M, Northcott PA, Patrizi A, Kutscher LM. Loss of Elp1 in cerebellar granule cell progenitors models ataxia phenotype of Familial Dysautonomia. Neurobiol Dis 2024; 199:106600. [PMID: 38996985 DOI: 10.1016/j.nbd.2024.106600] [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] [Received: 04/18/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
Familial Dysautonomia (FD) is an autosomal recessive disorder caused by a splice site mutation in the gene ELP1, which disproportionally affects neurons. While classically characterized by deficits in sensory and autonomic neurons, neuronal defects in the central nervous system have also been described. Although ELP1 expression remains high in the normal developing and adult cerebellum, its role in cerebellar development is unknown. To explore the role of Elp1 in the cerebellum, we knocked out Elp1 in cerebellar granule cell progenitors (GCPs) and examined the outcome on animal behavior and cellular composition. We found that GCP-specific conditional knockout of Elp1 (Elp1cKO) resulted in ataxia by 8 weeks of age. Cellular characterization showed that the animals had smaller cerebella with fewer granule cells. This defect was already apparent as early as 7 days after birth, when Elp1cKO animals also had fewer mitotic GCPs and shorter Purkinje dendrites. Through molecular characterization, we found that loss of Elp1 was associated with an increase in apoptotic cell death and cell stress pathways in GCPs. Our study demonstrates the importance of ELP1 in the developing cerebellum, and suggests that loss of Elp1 in the GC lineage may also play a role in the progressive ataxia phenotypes of FD patients.
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Affiliation(s)
- Frederik Arnskötter
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Patricia Benites Goncalves da Silva
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Mackenna E Schouw
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Chiara Lukasch
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Luca Bianchini
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Laura Sieber
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Jesus Garcia-Lopez
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA; Department of In vivo Pharmacology-Immunology, Tempest Therapeutics, Brisbane, CA, USA
| | - Shiekh Tanveer Ahmad
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiran Li
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Lin
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Piyush Joshi
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Lisa Spänig
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Magdalena Radoš
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany
| | - Mykola Roiuk
- Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany; Division of Pediatric Neuro-Oncology, Preclinical Modeling Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA; Center of Excellence in Neuro-Oncology Sciences (CENOS), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena M Kutscher
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; National Center for Tumor Diseases (NCT), NCT Heidelberg, A partnership between DKFZ and Heidelberg University Hospital, Germany.
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Xie X, Zhang O, Yeo MJR, Lee C, Harry SA, Paul L, Li Y, Payne NC, Nam E, Kwok HS, Jiang H, Mao H, Hadley JL, Lin H, Batts M, Gosavi PM, D'Angiolella V, Cole PA, Mazitschek R, Northcott PA, Zheng N, Liau BB. KBTBD4 Cancer Hotspot Mutations Drive Neomorphic Degradation of HDAC1/2 Corepressor Complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.593970. [PMID: 38798357 PMCID: PMC11118371 DOI: 10.1101/2024.05.14.593970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cancer mutations can create neomorphic protein-protein interactions to drive aberrant function 1 . As a substrate receptor of the CULLIN3-RBX1 E3 ubiquitin ligase complex, KBTBD4 is recurrently mutated in medulloblastoma (MB) 2 , the most common embryonal brain tumor in children, and pineoblastoma 3 . These mutations impart gain-of-function to KBTBD4 to induce aberrant degradation of the transcriptional corepressor CoREST 4 . However, their mechanism of action remains unresolved. Here, we elucidate the mechanistic basis by which KBTBD4 mutations promote CoREST degradation through engaging HDAC1/2, the direct neomorphic target of the substrate receptor. Using deep mutational scanning, we systematically map the mutational landscape of the KBTBD4 cancer hotspot, revealing distinct preferences by which insertions and substitutions can promote gain-of-function and the critical residues involved in the hotspot interaction. Cryo-electron microscopy (cryo-EM) analysis of two distinct KBTBD4 cancer mutants bound to LSD1-HDAC1-CoREST reveals that a KBTBD4 homodimer asymmetrically engages HDAC1 with two KELCH-repeat propeller domains. The interface between HDAC1 and one of the KBTBD4 propellers is stabilized by the MB mutations, which directly insert a bulky side chain into the active site pocket of HDAC1. Our structural and mutational analyses inform how this hotspot E3-neo-substrate interface can be chemically modulated. First, our results unveil a converging shape complementarity-based mechanism between gain-of-function E3 mutations and a molecular glue degrader, UM171. Second, we demonstrate that HDAC1/2 inhibitors can block the mutant KBTBD4-HDAC1 interface, the aberrant degradation of CoREST, and the growth of KBTBD4-mutant MB models. Altogether, our work reveals the structural and mechanistic basis of cancer mutation-driven neomorphic protein-protein interactions and pharmacological strategies to modulate their action for therapeutic applications.
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Zhang T, Kim BM, Lee TH. Death-associated protein kinase 1 as a therapeutic target for Alzheimer's disease. Transl Neurodegener 2024; 13:4. [PMID: 38195518 PMCID: PMC10775678 DOI: 10.1186/s40035-023-00395-5] [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: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia in the elderly and represents a major clinical challenge in the ageing society. Neuropathological hallmarks of AD include neurofibrillary tangles composed of hyperphosphorylated tau, senile plaques derived from the deposition of amyloid-β (Aβ) peptides, brain atrophy induced by neuronal loss, and synaptic dysfunctions. Death-associated protein kinase 1 (DAPK1) is ubiquitously expressed in the central nervous system. Dysregulation of DAPK1 has been shown to contribute to various neurological diseases including AD, ischemic stroke and Parkinson's disease (PD). We have established an upstream effect of DAPK1 on Aβ and tau pathologies and neuronal apoptosis through kinase-mediated protein phosphorylation, supporting a causal role of DAPK1 in the pathophysiology of AD. In this review, we summarize current knowledge about how DAPK1 is involved in various AD pathological changes including tau hyperphosphorylation, Aβ deposition, neuronal cell death and synaptic degeneration. The underlying molecular mechanisms of DAPK1 dysregulation in AD are discussed. We also review the recent progress regarding the development of novel DAPK1 modulators and their potential applications in AD intervention. These findings substantiate DAPK1 as a novel therapeutic target for the development of multifunctional disease-modifying treatments for AD and other neurological disorders.
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Affiliation(s)
- Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Byeong Mo Kim
- Research Center for New Drug Development, AgingTarget Inc., 10F Ace Cheonggye Tower, 53, Seonggogae-Ro, Uiwang-Si, 16006, Gyeonggi-Do, Korea.
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
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Wei X, Wang Y, Zhu W, Li J, Peng L, Gao Z, Bai B. Stable Plasma Sample Storage in Acetonitrile for Angiotensin and Aldosterone Analysis. Lab Med 2020; 52:352-356. [PMID: 33098298 DOI: 10.1093/labmed/lmaa079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Angiotensin I, II (AI, AII) and aldosterone are unstable in plasma specimens at room temperature, making it difficult for collect samples for remote regions in centralized and collaborative studies. Here we introduce a stable storage method which do not require cold conditions.. METHODS Acetonitrile was added to the plasma to 60%, and then the supernatants were kept at 4°C and room temperature for 0, 1, 2, 3, 10 and 30 days. AI, AII and aldosterone were extracted and analyzed by chemiluminescence immunoassays. RESULTS AI, AII and aldosterone were well retained in the supernatant under this method. The intra- and inter-day CVs of this method were all below 10%. The levels of AI, AII and aldosterone by this method remained stable for 30 days at room temperature. CONCLUSION Addition of 60% acetonitrile in the plasma provides a stable storage method for clinical AI, AII and aldosterone.
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Affiliation(s)
- Xuefei Wei
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China
| | - Yanyang Wang
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China
| | - Wenbo Zhu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China
| | - Jingjing Li
- Center for Precision Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China
| | - Lu Peng
- Department of Laboratory Medicine, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhiwei Gao
- Department of Vascular Surgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, PR China
| | - Bing Bai
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China.,Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China.,Center for Precision Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, PR China
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Chen Y, Wang S, Jia J, Tian X, Xu H, Ning M, Bai B. Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis. Proteomics 2018; 18:e1700336. [PMID: 29740960 DOI: 10.1002/pmic.201700336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 04/25/2018] [Indexed: 12/30/2022]
Abstract
Long-term storage of protein samples for transportation is a challenge in the field of mass spectrometric analysis because the low temperature condition is not easy to be maintained. Here we introduce a simple method to preserve proteins at room temperature for at least one month. In this method, the protein sample is run shortly into a polyacrylamide gel which is then excised after Coomassie staining. The protein gel band is then dehydrated by 100% acetonitrile three times and kept in 100% acetonitrile for storage at room temperature. By the TMT 10-plex based quantitative proteomic analyses, we have found that these proteins are stable in their levels and modifications (phosphorylation, oxidation, and ubiquitination) for 30 days. Further analysis has revealed this storage method also well preserves proteins even at 45 °C. We therefore recommend to use acetonitrile to dehydrate and store protein gel pieces as an effective alternative for sample shipping over days. Therefore, it might facilitate worldwide collaborations in the mass spectrometry-based proteomic research.
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Affiliation(s)
- Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Sen Wang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Jia Jia
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Xinyu Tian
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Hongpan Xu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Mingzhe Ning
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
| | - Bing Bai
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008 Jiangsu, P. R. China
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Chen M, Lee HK, Moo L, Hanlon E, Stein T, Xia W. Common proteomic profiles of induced pluripotent stem cell-derived three-dimensional neurons and brain tissue from Alzheimer patients. J Proteomics 2018; 182:21-33. [PMID: 29709615 DOI: 10.1016/j.jprot.2018.04.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/03/2018] [Accepted: 04/24/2018] [Indexed: 01/21/2023]
Abstract
We established a unique platform for proteomic analysis of cultured three-dimensional (3D) neurons and brain tissue from Alzheimer's disease (AD) patients. We collected peripheral blood mononuclear cells (PBMC), converted PBMC to induced pluripotent stem cell (iPSC) lines, and differentiated the iPSC into human 3D neuro-spheroids. The postmortem brain tissue from the superior frontal cortex, inferior frontal cortex and cerebellum area of the AD patients was compared to the same regions from the control subjects. Proteomic analysis of 3D neuro-spheroids derived from AD subjects revealed the alteration of a number of proteins involved in axon growth, mitochondrial function, and antioxidant defense. Similar analysis of post-mortem AD brain tissue revealed significant alteration in proteins involved in oxidative stress, neuro-inflammation, along with proteins related to axonal injury. These results clearly indicate that the dysfunction of 3D neurons from AD patients in our in vitro environment is comparable to the post-mortem AD brain tissue in vivo. In conclusion, our study revealed a number of candidate proteins that have important implications in AD pathogenesis and supports the notion that the iPSC-derived 3D neuronal system functions as a model to examine novel aspects of AD pathology. SIGNIFICANCE In this study, we present a unique platform for proteomic analysis of induced pluripotent stem cell-derived three dimensional (3D) neurons and compare the results to those from three regions of post-mortem brain tissue from Alzheimer's disease patients and normal control subjects. Our results show that the dysfunction of 3D neurons from AD patients in our in vitro environment is comparable to the post-mortem AD brain tissue in vivo. Our results revealed several candidate proteins that have important implications in AD pathogenesis.
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Affiliation(s)
- Mei Chen
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States; Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA, United States
| | - Han-Kyu Lee
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States
| | - Lauren Moo
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States
| | - Eugene Hanlon
- Office of Research and Development, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States
| | - Thor Stein
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States; Department of Pathology, Boston University School of Medicine, Boston, MA, United States
| | - Weiming Xia
- Geriatric Research Education and Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, United States; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States.
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