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Bay S, Digwal CS, Rodilla Martín AM, Sharma S, Stanisavljevic A, Rodina A, Attaran A, Roychowdhury T, Parikh K, Toth E, Panchal P, Rosiek E, Pasala C, Arancio O, Fraser PE, Alldred MJ, Prado MAM, Ginsberg SD, Chiosis G. Synthesis and Characterization of Click Chemical Probes for Single-Cell Resolution Detection of Epichaperomes in Neurodegenerative Disorders. Biomedicines 2024; 12:1252. [PMID: 38927459 PMCID: PMC11201208 DOI: 10.3390/biomedicines12061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Neurodegenerative disorders, including Alzheimer's disease (AD) and Parkinson's disease (PD), represent debilitating conditions with complex, poorly understood pathologies. Epichaperomes, pathologic protein assemblies nucleated on key chaperones, have emerged as critical players in the molecular dysfunction underlying these disorders. In this study, we introduce the synthesis and characterization of clickable epichaperome probes, PU-TCO, positive control, and PU-NTCO, negative control. Through comprehensive in vitro assays and cell-based investigations, we establish the specificity of the PU-TCO probe for epichaperomes. Furthermore, we demonstrate the efficacy of PU-TCO in detecting epichaperomes in brain tissue with a cellular resolution, underscoring its potential as a valuable tool for dissecting single-cell responses in neurodegenerative diseases. This clickable probe is therefore poised to address a critical need in the field, offering unprecedented precision and versatility in studying epichaperomes and opening avenues for novel insights into their role in disease pathology.
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Affiliation(s)
- Sadik Bay
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Chander S. Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Ananda M. Rodilla Martín
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | | | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Anoosha Attaran
- Department of Physiology and Pharmacology, Schulich School of Medicine, Robarts Research Institute, The University of Western Ontario, London, ON N6A 3K7, Canada; (A.A.); (M.A.M.P.)
- Department of Anatomy and Cell Biology, Schulich School of Medicine, Robarts Research Institute, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Kamya Parikh
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Eugene Toth
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Eric Rosiek
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Chiranjeevi Pasala
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
| | - Ottavio Arancio
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY 10032, USA;
- Department of Medicine, Columbia University, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Paul E. Fraser
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medical Biophysics, University of Toronto, Toronto, ON M5R 0A3, Canada;
| | - Melissa J. Alldred
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA; (A.S.); (M.J.A.)
- Departments of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marco A. M. Prado
- Department of Physiology and Pharmacology, Schulich School of Medicine, Robarts Research Institute, The University of Western Ontario, London, ON N6A 3K7, Canada; (A.A.); (M.A.M.P.)
- Department of Anatomy and Cell Biology, Schulich School of Medicine, Robarts Research Institute, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Stephen D. Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA; (A.S.); (M.J.A.)
- Departments of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, USA
- Neuroscience & Physiology & the NYU Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (S.B.); (C.S.D.); (A.M.R.M.); (S.S.); (A.R.); (T.R.); (K.P.); (E.T.); (P.P.); (C.P.)
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Yan H, Lu C, Lan C, Wang S, Zhang W, He Z, Hu J, Ai J, Liu GH, Ma S, Zhou Y, Qu J. Degeneration Directory: a multi-omics web resource for degenerative diseases. Protein Cell 2024; 15:385-392. [PMID: 38153694 DOI: 10.1093/procel/pwad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023] Open
Affiliation(s)
- Haoteng Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
| | - Changfa Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Chenyang Lan
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
- The Fifth People's Hospital of Chongqing, Chongqing 400062, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- Aging Biomarker Consortium, Beijing 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China NationalCenter for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zan He
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
| | - Jinghao Hu
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
| | - Jiaqi Ai
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu HospitalCapital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, XuanwuHospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanchun Zhou
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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3
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Yin DE, Palin AC, Lombo TB, Mahon RN, Poon B, Wu DY, Atala A, Brooks KM, Chen S, Coyne CB, D’Souza MP, Fackler OT, Furler O’Brien RL, Garcia-de-Alba C, Jean-Philippe P, Karn J, Majji S, Muotri AR, Ozulumba T, Sakatis MZ, Schlesinger LS, Singh A, Spiegel HM, Struble E, Sung K, Tagle DA, Thacker VV, Tidball AM, Varthakavi V, Vunjak-Novakovic G, Wagar LE, Yeung CK, Ndhlovu LC, Ott M. 3D human tissue models and microphysiological systems for HIV and related comorbidities. Trends Biotechnol 2024; 42:526-543. [PMID: 38071144 PMCID: PMC11065605 DOI: 10.1016/j.tibtech.2023.10.008] [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: 07/03/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 03/03/2024]
Abstract
Three-dimensional (3D) human tissue models/microphysiological systems (e.g., organs-on-chips, organoids, and tissue explants) model HIV and related comorbidities and have potential to address critical questions, including characterization of viral reservoirs, insufficient innate and adaptive immune responses, biomarker discovery and evaluation, medical complexity with comorbidities (e.g., tuberculosis and SARS-CoV-2), and protection and transmission during pregnancy and birth. Composed of multiple primary or stem cell-derived cell types organized in a dedicated 3D space, these systems hold unique promise for better reproducing human physiology, advancing therapeutic development, and bridging the human-animal model translational gap. Here, we discuss the promises and achievements with 3D human tissue models in HIV and comorbidity research, along with remaining barriers with respect to cell biology, virology, immunology, and regulatory issues.
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Amartumur S, Nguyen H, Huynh T, Kim TS, Woo RS, Oh E, Kim KK, Lee LP, Heo C. Neuropathogenesis-on-chips for neurodegenerative diseases. Nat Commun 2024; 15:2219. [PMID: 38472255 PMCID: PMC10933492 DOI: 10.1038/s41467-024-46554-8] [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: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Developing diagnostics and treatments for neurodegenerative diseases (NDs) is challenging due to multifactorial pathogenesis that progresses gradually. Advanced in vitro systems that recapitulate patient-like pathophysiology are emerging as alternatives to conventional animal-based models. In this review, we explore the interconnected pathogenic features of different types of ND, discuss the general strategy to modelling NDs using a microfluidic chip, and introduce the organoid-on-a-chip as the next advanced relevant model. Lastly, we overview how these models are being applied in academic and industrial drug development. The integration of microfluidic chips, stem cells, and biotechnological devices promises to provide valuable insights for biomedical research and developing diagnostic and therapeutic solutions for NDs.
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Affiliation(s)
- Sarnai Amartumur
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Huong Nguyen
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Thuy Huynh
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Testaverde S Kim
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea
| | - Ran-Sook Woo
- Department of Anatomy and Neuroscience, College of Medicine, Eulji University, Daejeon, 34824, Korea
| | - Eungseok Oh
- Department of Neurology, Chungnam National University Hospital, Daejeon, 35015, Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Luke P Lee
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Harvard Medical School, Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, 94720, USA.
| | - Chaejeong Heo
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea.
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5
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He C, Gu J, Wang D, Wang K, Wang Y, You Q, Wang L. Small molecules targeting molecular chaperones for tau regulation: Achievements and challenges. Eur J Med Chem 2023; 261:115859. [PMID: 37839344 DOI: 10.1016/j.ejmech.2023.115859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
Abnormal post-translational modification of microtubule-associated protein Tau (MAPT) is a prominent pathological feature in Alzheimer's disease (AD). Previous research has focused on designing small molecules to target Tau modification, aiming to restore microtubule stability and regulate Tau levels in vivo. However, progress has been hindered, and no effective Tau-targeted drugs have been successfully marketed, which urgently requires more strategies. Heat shock proteins (HSPs), especially Hsp90 and Hsp70, have been found to play a crucial role in Tau maturation and degradation. This review explores innovative approaches using small molecules that interact with the chaperone system to regulate Tau levels. We provide a comprehensive overview of the mechanisms involving HSPs and their co-chaperones in the Tau regulation cycle. Additionally, we analyze small molecules targeting these chaperone systems to modulate Tau function. By understanding the characteristics of the molecular chaperone system and its specific impact on Tau, we aim to provide a perspective that seeks to regulate Tau levels through the manipulation of the molecular chaperone system and ultimately develop effective treatments for AD.
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Affiliation(s)
- Chenxi He
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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Whitney K, Song WM, Sharma A, Dangoor DK, Farrell K, Krassner MM, Ressler HW, Christie TD, Walker RH, Nirenberg MJ, Zhang B, Frucht SJ, Riboldi GM, Crary JF, Pereira AC. Single-cell transcriptomic and neuropathologic analysis reveals dysregulation of the integrated stress response in progressive supranuclear palsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567587. [PMID: 38014079 PMCID: PMC10680842 DOI: 10.1101/2023.11.17.567587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Progressive supranuclear palsy (PSP) is a sporadic neurodegenerative tauopathy variably affecting brainstem and cortical structures and characterized by tau inclusions in neurons and glia. The precise mechanism whereby these protein aggregates lead to cell death remains unclear. To investigate the contribution of these different cellular abnormalities to PSP pathogenesis, we performed single-nucleus RNA sequencing and analyzed 45,559 high quality nuclei targeting the subthalamic nucleus and adjacent structures from human post-mortem PSP brains with varying degrees of pathology compared to controls. Cell-type specific differential expression and pathway analysis identified both common and discrete changes in numerous pathways previously implicated in PSP and other neurodegenerative disorders. This included EIF2 signaling, an adaptive pathway activated in response to diverse stressors, which was the top activated pathway in vulnerable cell types. Using immunohistochemistry, we found that activated eIF2α was positively correlated with tau pathology burden in vulnerable brain regions. Multiplex immunofluorescence localized activated eIF2α positivity to hyperphosphorylated tau (p-tau) positive neurons and ALDH1L1-positive astrocytes, supporting the increased transcriptomic EIF2 activation observed in these vulnerable cell types. In conclusion, these data provide insights into cell-type-specific pathological changes in PSP and support the hypothesis that failure of adaptive stress pathways play a mechanistic role in the pathogenesis and progression of PSP.
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7
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Chiosis G, Digwal CS, Trepel JB, Neckers L. Structural and functional complexity of HSP90 in cellular homeostasis and disease. Nat Rev Mol Cell Biol 2023; 24:797-815. [PMID: 37524848 PMCID: PMC10592246 DOI: 10.1038/s41580-023-00640-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
Heat shock protein 90 (HSP90) is a chaperone with vital roles in regulating proteostasis, long recognized for its function in protein folding and maturation. A view is emerging that identifies HSP90 not as one protein that is structurally and functionally homogeneous but, rather, as a protein that is shaped by its environment. In this Review, we discuss evidence of multiple structural forms of HSP90 in health and disease, including homo-oligomers and hetero-oligomers, also termed epichaperomes, and examine the impact of stress, post-translational modifications and co-chaperones on their formation. We describe how these variations influence context-dependent functions of HSP90 as well as its interaction with other chaperones, co-chaperones and proteins, and how this structural complexity of HSP90 impacts and is impacted by its interaction with small molecule modulators. We close by discussing recent developments regarding the use of HSP90 inhibitors in cancer and how our new appreciation of the structural and functional heterogeneity of HSP90 invites a re-evaluation of how we discover and implement HSP90 therapeutics for disease treatment.
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Affiliation(s)
- Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Institute, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Institute, New York, NY, USA.
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Institute, New York, NY, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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8
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Svirsky SE, Li Y, Henchir J, Rodina A, Carlson SW, Chiosis G, Dixon CE. Experimental traumatic brain injury increases epichaperome formation. Neurobiol Dis 2023; 188:106331. [PMID: 37863370 PMCID: PMC10698712 DOI: 10.1016/j.nbd.2023.106331] [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: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023] Open
Abstract
Under normal conditions, heat shock proteins work in unison through dynamic protein interactions collectively referred to as the "chaperome." Recent work revealed that during cellular stress, the functional interactions of the chaperome are modified to form the "epichaperome," which results in improper protein folding, degradation, aggregation, and transport. This study is the first to investigate this novel mechanism of protein dishomeostasis in traumatic brain injury (TBI). Male and female adult, Sprague-Dawley rats received a lateral controlled cortical impact (CCI) and the ipsilateral hippocampus was collected 24 h 1, 2, and 4 weeks after injury. The epichaperome complex was visualized by measuring HSP90, HSC70 and HOP expression in native-PAGE and normalized to monomeric protein expression. A two-way ANOVA examined the effect of injury and sex at each time-point. Native HSP90, HSC70 and HOP protein expression showed a significant effect of injury effect across all time-points. Additionally, HSC70 and HOP showed significant sex effects at 24 h and 4 weeks. Altogether, controlled cortical impact significantly increased formation of the epichaperome across all proteins measured. Further investigation of this pathological mechanism can lead to a greater understanding of the link between TBI and increased risk of neurodegenerative disease and targeting the epichaperome for therapeutics.
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Affiliation(s)
- Sarah E Svirsky
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Youming Li
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jeremy Henchir
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Shaun W Carlson
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - C Edward Dixon
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; V.A. Pittsburgh Healthcare System, Pittsburgh, PA, USA.
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9
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Sharma S, Joshi S, Kalidindi T, Digwal CS, Panchal P, Lee SG, Zanzonico P, Pillarsetty N, Chiosis G. Unraveling the Mechanism of Epichaperome Modulation by Zelavespib: Biochemical Insights on Target Occupancy and Extended Residence Time at the Site of Action. Biomedicines 2023; 11:2599. [PMID: 37892973 PMCID: PMC10604720 DOI: 10.3390/biomedicines11102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drugs with a long residence time at their target sites are often more efficacious in disease treatment. The mechanism, however, behind prolonged retention at the site of action is often difficult to understand for non-covalent agents. In this context, we focus on epichaperome agents, such as zelavespib and icapamespib, which maintain target binding for days despite rapid plasma clearance, minimal retention in non-diseased tissues, and rapid metabolism. They have shown significant therapeutic value in cancer and neurodegenerative diseases by disassembling epichaperomes, which are assemblies of tightly bound chaperones and other factors that serve as scaffolding platforms to pathologically rewire protein-protein interactions. To investigate their impact on epichaperomes in vivo, we conducted pharmacokinetic and target occupancy measurements for zelavespib and monitored epichaperome assemblies biochemically in a mouse model. Our findings provide evidence of the intricate mechanism through which zelavespib modulates epichaperomes in vivo. Initially, zelavespib becomes trapped when epichaperomes bound, a mechanism that results in epichaperome disassembly, with no change in the expression level of epichaperome constituents. We propose that the initial trapping stage of epichaperomes is a main contributing factor to the extended on-target residence time observed for this agent in clinical settings. Zelavespib's residence time in tumors seems to be dictated by target disassembly kinetics rather than by frank drug-target unbinding kinetics. The off-rate of zelavespib from epichaperomes is, therefore, much slower than anticipated from the recorded tumor pharmacokinetic profile or as determined in vitro using diluted systems. This research sheds light on the underlying processes that make epichaperome agents effective in the treatment of certain diseases.
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Affiliation(s)
- Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Teja Kalidindi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Chander S. Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Sang-Gyu Lee
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Pat Zanzonico
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Nagavarakishore Pillarsetty
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
- Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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10
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Cerneckis J, Bu G, Shi Y. Pushing the boundaries of brain organoids to study Alzheimer's disease. Trends Mol Med 2023:S1471-4914(23)00098-9. [PMID: 37353408 PMCID: PMC10374393 DOI: 10.1016/j.molmed.2023.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Progression of Alzheimer's disease (AD) entails deterioration or aberrant function of multiple brain cell types, eventually leading to neurodegeneration and cognitive decline. Defining how complex cell-cell interactions become dysregulated in AD requires novel human cell-based in vitro platforms that could recapitulate the intricate cytoarchitecture and cell diversity of the human brain. Brain organoids (BOs) are 3D self-organizing tissues that partially resemble the human brain architecture and can recapitulate AD-relevant pathology. In this review, we highlight the versatile applications of different types of BOs to model AD pathogenesis, including amyloid-β and tau aggregation, neuroinflammation, myelin breakdown, vascular dysfunction, and other phenotypes, as well as to accelerate therapeutic development for AD.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guojun Bu
- SciNeuro Pharmaceuticals, Rockville, MD 20850, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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11
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Jiang L, Chakraborty P, Zhang L, Wong M, Hill SE, Webber CJ, Libera J, Blair LJ, Wolozin B, Zweckstetter M. Chaperoning of specific tau structure by immunophilin FKBP12 regulates the neuronal resilience to extracellular stress. SCIENCE ADVANCES 2023; 9:eadd9789. [PMID: 36724228 PMCID: PMC9891691 DOI: 10.1126/sciadv.add9789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Alzheimer's disease and related tauopathies are characterized by the pathogenic misfolding and aggregation of the microtubule-associated protein tau. Understanding how endogenous chaperones modulate tau misfolding could guide future therapies. Here, we show that the immunophilin FKBP12, the 12-kDa FK506-binding protein (also known as FKBP prolyl isomerase 1A), regulates the neuronal resilience by chaperoning a specific structure in monomeric tau. Using a combination of mouse and cell experiments, in vitro aggregation experiments, nuclear magnetic resonance-based structural analysis of monomeric tau, site-specific phosphorylation and mutation, as well as structure-based analysis using the neural network-based structure prediction program AlphaFold, we define the molecular factors that govern the binding of FKBP12 to tau and its influence on tau-induced neurotoxicity. We further demonstrate that tyrosine phosphorylation of tau blocks the binding of FKBP12 to two highly specific structural motifs in tau. Our data together with previous results demonstrating FKBP12/tau colocalization in neurons and neurofibrillary tangles support a critical role of FKBP12 in regulating tau pathology.
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Affiliation(s)
- Lulu Jiang
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Pijush Chakraborty
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Lushuang Zhang
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Melissa Wong
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shannon E. Hill
- Department of Molecular Medicine, College of Medicine, Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33612, USA
| | - Chelsea Joy Webber
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jenna Libera
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura J. Blair
- Department of Molecular Medicine, College of Medicine, Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33612, USA
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
- Center for Neurophotonics, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02215, USA
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
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12
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Ginsberg SD, Sharma S, Norton L, Chiosis G. Targeting stressor-induced dysfunctions in protein-protein interaction networks via epichaperomes. Trends Pharmacol Sci 2023; 44:20-33. [PMID: 36414432 PMCID: PMC9789192 DOI: 10.1016/j.tips.2022.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022]
Abstract
Diseases are manifestations of complex changes in protein-protein interaction (PPI) networks whereby stressors, genetic, environmental, and combinations thereof, alter molecular interactions and perturb the individual from the level of cells and tissues to the entire organism. Targeting stressor-induced dysfunctions in PPI networks has therefore become a promising but technically challenging frontier in therapeutics discovery. This opinion provides a new framework based upon disrupting epichaperomes - pathological entities that enable dysfunctional rewiring of PPI networks - as a mechanism to revert context-specific PPI network dysfunction to a normative state. We speculate on the implications of recent research in this area for a precision medicine approach to detecting and treating complex diseases, including cancer and neurodegenerative disorders.
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Affiliation(s)
- Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA; Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA; NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sahil Sharma
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Larry Norton
- Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY 10065, USA; Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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