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Seefelder M, Kochanek S, Klein FAC. ProteinCoLoc streamlines Bayesian analysis of colocalization in microscopic images. Sci Rep 2024; 14:13277. [PMID: 38858475 PMCID: PMC11164984 DOI: 10.1038/s41598-024-63884-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
Colocalization, the spatial overlap of molecular entities, is often key to support their involvement in common functions. Existing colocalization tools, however, face limitations, particularly because of their basic statistical analysis and their low-throughput manual entry processes making them unsuitable for automation and potentially introducing bias. These shortcomings underscore the need for user-friendly tools streamlining colocalization assessments and enabling their robust and automated quantitative analyses. We have developed ProteinCoLoc, an innovative software designed for automated high-throughput colocalization analyses and incorporating advanced statistical features such as Bayesian modelling, automatic background detection and localised correlation analysis. ProteinCoLoc rationalises colocalization assessments without manual input, comes with a user-friendly graphical user interface and provides various analytics allowing to study and locally quantify colocalization. This easy-to-use application presents numerous advantages, including a direct comparison with controls employing a Bayesian model and the analysis of local correlation patterns, while reducing hands-on time through automatic background detection. The software was validated while studying the colocalization pattern of two proteins forming a stable complex: the huntingtin protein (HTT) and its partner huntingtin-associated protein 40 (HAP40). Our results showcase the software's capacity to quantitatively assess colocalizations. ProteinCoLoc is available both as a Julia package and as a compiled software ( https://github.com/ma-seefelder/ProteinCoLoc ).
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany.
| | - Stefan Kochanek
- Department of Gene Therapy, Ulm University, 89081, Ulm, Germany
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Chen L, Qin Y, Guo T, Zhu W, Lin J, Xing T, Duan X, Zhang Y, Ruan E, Li X, Yin P, Li S, Li XJ, Yang S. HAP40 modulates mutant Huntingtin aggregation and toxicity in Huntington's disease mice. Cell Death Dis 2024; 15:337. [PMID: 38744826 PMCID: PMC11094052 DOI: 10.1038/s41419-024-06716-4] [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: 09/08/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a monogenic neurodegenerative disease, caused by the CAG trinucleotide repeat expansion in exon 1 of the Huntingtin (HTT) gene. The HTT gene encodes a large protein known to interact with many proteins. Huntingtin-associated protein 40 (HAP40) is one that shows high binding affinity with HTT and functions to maintain HTT conformation in vitro. However, the potential role of HAP40 in HD pathogenesis remains unknown. In this study, we found that the expression level of HAP40 is in parallel with HTT but inversely correlates with mutant HTT aggregates in mouse brains. Depletion of endogenous HAP40 in the striatum of HD140Q knock-in (KI) mice leads to enhanced mutant HTT aggregation and neuronal loss. Consistently, overexpression of HAP40 in the striatum of HD140Q KI mice reduced mutant HTT aggregation and ameliorated the behavioral deficits. Mechanistically, HAP40 preferentially binds to mutant HTT and promotes Lysine 48-linked ubiquitination of mutant HTT. Our results revealed that HAP40 is an important regulator of HTT protein homeostasis in vivo and hinted at HAP40 as a therapeutic target in HD treatment.
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Affiliation(s)
- Laiqiang Chen
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Yiyang Qin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Tingting Guo
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Wenzhen Zhu
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jingpan Lin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Tingting Xing
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xuezhi Duan
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yiran Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Eshu Ruan
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiang Li
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Peng Yin
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China.
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
| | - Su Yang
- Guangdong Key Laboratory of Non-human Primate Research, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China.
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, China.
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Seefelder M, Klein FAC, Landwehrmeyer B, Fernández-Busnadiego R, Kochanek S. Huntingtin and Its Partner Huntingtin-Associated Protein 40: Structural and Functional Considerations in Health and Disease. J Huntingtons Dis 2022; 11:227-242. [PMID: 35871360 PMCID: PMC9484127 DOI: 10.3233/jhd-220543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the discovery of the mutation causing Huntington’s disease (HD) in 1993, it has been debated whether an expanded polyglutamine (polyQ) stretch affects the properties of the huntingtin (HTT) protein and thus contributes to the pathological mechanisms responsible for HD. Here we review the current knowledge about the structure of HTT, alone (apo-HTT) or in a complex with Huntingtin-Associated Protein 40 (HAP40), the influence of polyQ-length variation on apo-HTT and the HTT-HAP40 complex, and the biology of HAP40. Phylogenetic analyses suggest that HAP40 performs essential functions. Highlighting the relevance of its interaction with HTT, HAP40 is one of the most abundant partners copurifying with HTT and is rapidly degraded, when HTT levels are reduced. As the levels of both proteins decrease during disease progression, HAP40 could also be a biomarker for HD. Whether declining HAP40 levels contribute to disease etiology is an open question. Structural studies have shown that the conformation of apo-HTT is less constrained but resembles that adopted in the HTT-HAP40 complex, which is exceptionally stable because of extensive interactions between HAP40 and the three domains of HTT. The complex— and to some extent apo-HTT— resists fragmentation after limited proteolysis. Unresolved regions of apo-HTT, constituting about 25% of the protein, are the main sites of post-translational modifications and likely have major regulatory functions. PolyQ elongation does not substantially alter the structure of HTT, alone or when associated with HAP40. Particularly, polyQ above the disease length threshold does not induce drastic conformational changes in full-length HTT. Therefore, models of HD pathogenesis stating that polyQ expansion drastically alters HTT properties should be reconsidered.
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Affiliation(s)
| | | | | | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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Barbier M, Fellmann D, Risold PY. Characterization of McDonald's intermediate part of the Central nucleus of the amygdala in the rat. J Comp Neurol 2018; 526:2165-2186. [PMID: 29893014 DOI: 10.1002/cne.24470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 11/12/2022]
Abstract
The actual organization of the central nucleus of the amygdala (CEA) in the rat is mostly based on cytoarchitecture and the distribution of several cell types, as described by McDonald in 1982. Four divisions were identified by this author. However, since this original work, one of these divisions, the intermediate part, has not been consistently recognized based on Nissl-stained material. In the present study, we observed that a compact condensation of retrogradely labeled cells is found in the CEA after fluorogold injection in the anterior region of the tuberal lateral hypothalamic area (LHA) in the rat. We then searched for neurochemical markers of this cell condensation and found that it is quite specifically labeled for calbindin (Cb), but also contains calretinin (Cr), tyrosine hydroxylase (TH) and methionine-enkephalin (Met-Enk) immunohistochemical signals. These neurochemical features are specific to this cell group which, therefore, is distinct from the other parts of the CEA. We then performed cholera toxin injections in the mouse LHA to identify this cell group in this species. We found that neurons exist in the medial and rostral CEAl that project into the LHA but they have a less tight organization than in the rat.
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Affiliation(s)
- Marie Barbier
- EA481, UFR Sciences Médicales et Pharmaceutiques, 19 rue Ambroise Paré, Université Bourgogne Franche-Comté, Besançon cedex, 25030, France
| | - Dominique Fellmann
- EA481, UFR Sciences Médicales et Pharmaceutiques, 19 rue Ambroise Paré, Université Bourgogne Franche-Comté, Besançon cedex, 25030, France
| | - Pierre-Yves Risold
- EA481, UFR Sciences Médicales et Pharmaceutiques, 19 rue Ambroise Paré, Université Bourgogne Franche-Comté, Besançon cedex, 25030, France
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Dragatsis I, Dietrich P, Ren H, Deng YP, Del Mar N, Wang HB, Johnson IM, Jones KR, Reiner A. Effect of early embryonic deletion of huntingtin from pyramidal neurons on the development and long-term survival of neurons in cerebral cortex and striatum. Neurobiol Dis 2017; 111:102-117. [PMID: 29274742 PMCID: PMC5821111 DOI: 10.1016/j.nbd.2017.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 11/07/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022] Open
Abstract
We evaluated the impact of early embryonic deletion of huntingtin (htt) from pyramidal neurons on cortical development, cortical neuron survival and motor behavior, using a cre-loxP strategy to inactivate the mouse htt gene (Hdh) in emx1-expressing cell lineages. Western blot confirmed substantial htt reduction in cerebral cortex of these Emx-httKO mice, with residual cortical htt in all likelihood restricted to cortical interneurons of the subpallial lineage and/or vascular endothelial cells. Despite the loss of htt early in development, cortical lamination was normal, as revealed by layer-specific markers. Cortical volume and neuron abundance were, however, significantly less than normal, and cortical neurons showed reduced brain-derived neurotrophic factor (BDNF) expression and reduced activation of BDNF signaling pathways. Nonetheless, cortical volume and neuron abundance did not show progressive age-related decline in Emx-httKO mice out to 24 months. Although striatal neurochemistry was normal, reductions in striatal volume and neuron abundance were seen in Emx-httKO mice, which were again not progressive. Weight maintenance was normal in Emx-httKO mice, but a slight rotarod deficit and persistent hyperactivity were observed throughout the lifespan. Our results show that embryonic deletion of htt from developing pallium does not substantially alter migration of cortical neurons to their correct laminar destinations, but does yield reduced cortical and striatal size and neuron numbers. The Emx-httKO mice were persistently hyperactive, possibly due to defects in corticostriatal development. Importantly, deletion of htt from cortical pyramidal neurons did not yield age-related progressive cortical or striatal pathology.
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Affiliation(s)
- I Dragatsis
- Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - P Dietrich
- Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - H Ren
- Department of Anatomy & Neurobiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Y P Deng
- Department of Anatomy & Neurobiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - N Del Mar
- Department of Anatomy & Neurobiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - H B Wang
- Department of Anatomy & Neurobiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - I M Johnson
- Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - K R Jones
- Department of Molecular, Cellular, & Developmental Biology, 347 UCB, University of Colorado, Boulder, CO 80309, United States
| | - A Reiner
- Department of Anatomy & Neurobiology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States; Department of Ophthalmology, The University of Tennessee Health Science Center, Memphis, TN 38163, United States.
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