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Garfinkle EAR, Nallagatla P, Sahoo B, Dang J, Balood M, Cotton A, Franke C, Mitchell S, Wilson T, Gruber TA. CBFA2T3-GLIS2 mediates transcriptional regulation of developmental pathways through a gene regulatory network. Nat Commun 2024; 15:8747. [PMID: 39384814 PMCID: PMC11464917 DOI: 10.1038/s41467-024-53158-9] [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: 03/06/2023] [Accepted: 10/03/2024] [Indexed: 10/11/2024] Open
Abstract
CBFA2T3-GLIS2 is a fusion oncogene found in pediatric acute megakaryoblastic leukemia that is associated with a poor prognosis. We establish a model of CBFA2T3-GLIS2 driven acute megakaryoblastic leukemia that allows the distinction of fusion specific changes from those that reflect the megakaryoblast lineage of this leukemia. Using this model, we map fusion genome wide binding that in turn imparts the characteristic transcriptional signature. A network of transcription factor genes bound and upregulated by the fusion are found to have downstream effects that result in dysregulated signaling of developmental pathways including NOTCH, Hedgehog, TGFβ, and WNT. Transcriptional regulation is mediated by homo-dimerization and binding of the ETO transcription factor through the nervy homology region 2. Loss of nerve homology region 2 abrogated the development of leukemia, leading to downregulation of JAK/STAT, Hedgehog, and NOTCH transcriptional signatures. These data contribute to the understanding of CBFA2T3-GLIS2 mediated leukemogenesis and identify potential therapeutic vulnerabilities for future studies.
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Affiliation(s)
| | - Pratima Nallagatla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Binay Sahoo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jinjun Dang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohammad Balood
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anitria Cotton
- Division of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Camryn Franke
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharnise Mitchell
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taylor Wilson
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Curley M, Rai M, Chuang CL, Pagala V, Stephan A, Coleman Z, Robles-Murguia M, Wang YD, Peng J, Demontis F. Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging. CELL REPORTS METHODS 2024:100875. [PMID: 39383859 DOI: 10.1016/j.crmeth.2024.100875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/01/2024] [Accepted: 09/12/2024] [Indexed: 10/11/2024]
Abstract
Loss of proteostasis is a hallmark of aging that underlies many age-related diseases. Different cell compartments experience distinctive challenges in maintaining protein quality control, but how aging regulates subcellular proteostasis remains underexplored. Here, by targeting the misfolding-prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we established transgenic sensors to examine subcellular proteostasis in Drosophila. Analysis of detergent-insoluble and -soluble levels of compartment-targeted FlucDM variants indicates that thermal stress, cold shock, and pro-longevity inter-organ signaling differentially affect subcellular proteostasis during aging. Moreover, aggregation-prone proteins that cause different neurodegenerative diseases induce a diverse range of outcomes on FlucDM insolubility, suggesting that subcellular proteostasis is impaired in a disease-specific manner. Further analyses with FlucDM and mass spectrometry indicate that pathogenic tauV337M produces an unexpectedly complex regulation of solubility for different FlucDM variants and protein subsets. Altogether, compartment-targeted FlucDM sensors pinpoint a diverse modulation of subcellular proteostasis by aging regulators.
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Affiliation(s)
- Michelle Curley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mamta Rai
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Chia-Lung Chuang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zane Coleman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Maricela Robles-Murguia
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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3
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Tate M, Wijeratne HRS, Kim B, Philtjens S, You Y, Lee DH, Gutierrez DA, Sharify D, Wells M, Perez-Cardelo M, Doud EH, Fernandez-Hernando C, Lasagna-Reeves C, Mosley AL, Kim J. Deletion of miR-33, a regulator of the ABCA1-APOE pathway, ameliorates neuropathological phenotypes in APP/PS1 mice. Alzheimers Dement 2024. [PMID: 39345217 DOI: 10.1002/alz.14243] [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: 04/25/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 10/01/2024]
Abstract
INTRODUCTION Rare variants in ABCA1 increase the risk of developing Alzheimer's disease (AD). ABCA1 facilitates the lipidation of apolipoprotein E (apoE). This study investigated whether microRNA-33 (miR-33)-mediated regulation of this ABCA1-APOE pathway affects phenotypes of an amyloid mouse model. METHODS We generated mir-33+/+;APP/PS1 and mir-33-/-;APP/PS1 mice to determine changes in amyloid pathology using biochemical and histological analyses. We used RNA sequencing and mass spectrometry to identify the transcriptomic and proteomic changes between our genotypes. We also performed mechanistic experiments by determining the role of miR-33 in microglial migration and amyloid beta (Aβ) phagocytosis. RESULTS Mir-33 deletion increases ABCA1 levels and reduces Aβ accumulation and glial activation. Multi-omics studies suggested miR-33 regulates the activation and migration of microglia. We confirm that the inhibition of miR-33 significantly increases microglial migration and Aβ phagocytosis. DISCUSSION These results suggest that miR-33 might be a potential drug target by modulating ABCA1 level, apoE lipidation, Aβ level, and microglial function. HIGHLIGHTS Loss of microRNA-33 (miR-33) increased ABCA1 protein levels and the lipidation of apolipoprotein E. Loss of miR-33 reduced amyloid beta (Aβ) levels, plaque deposition, and gliosis. mRNAs and proteins dysregulated by miR-33 loss relate to microglia and Alzheimer's disease. Inhibition of miR-33 increased microglial migration and Aβ phagocytosis in vitro.
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Affiliation(s)
- Mason Tate
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - H R Sagara Wijeratne
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Byungwook Kim
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stéphanie Philtjens
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yanwen You
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Do-Hun Lee
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Daniela A Gutierrez
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Daniel Sharify
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Megan Wells
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Magdalena Perez-Cardelo
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Carlos Fernandez-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Molecular and System Metabolism, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cristian Lasagna-Reeves
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amber L Mosley
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jungsu Kim
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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4
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He M, Zong X, Xu B, Qi W, Huang W, Djekidel MN, Zhang Y, Pagala VR, Li J, Hao X, Guy C, Bai L, Cross R, Li C, Peng J, Feng Y. Dynamic Foxp3-chromatin interaction controls tunable Treg cell function. J Exp Med 2024; 221:e20232068. [PMID: 38935023 PMCID: PMC11211070 DOI: 10.1084/jem.20232068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here, we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncover dynamic proteins within Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at the Foxp3 DNA-binding domain destabilize the Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.
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Affiliation(s)
- Minghong He
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xinying Zong
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjun Huang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R. Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Li
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xiaolei Hao
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Clifford Guy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lu Bai
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Cross
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structure Biology and Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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5
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Yang S, Guo J, Xiong Y, Han G, Luo T, Peng S, Liu J, Hu T, Zha Y, Lin X, Tan Y, Zhang J. Unraveling the genetic and molecular landscape of sepsis and acute kidney injury: A comprehensive GWAS and machine learning approach. Int Immunopharmacol 2024; 137:112420. [PMID: 38851159 DOI: 10.1016/j.intimp.2024.112420] [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: 03/11/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
OBJECTIVES This study aimed to explore the underlying mechanisms of sepsis and acute kidney injury (AKI), including sepsis-associated AKI (SA-AKI), a frequent complication in critically ill sepsis patients. METHODS GWAS data was analyzed for genetic association between AKI and sepsis. Then, we systematically applied three distinct machine learning algorithms (LASSO, SVM-RFE, RF) to rigorously identify and validate signature genes of SA-AKI, assessing their diagnostic and prognostic value through ROC curves and survival analysis. The study also examined the functional and immunological aspects of these genes, potential drug targets, and ceRNA networks. A mouse model of sepsis was created to test the reliability of these signature genes. RESULTS LDSC confirmed a positive genetic correlation between AKI and sepsis, although no significant shared loci were found. Bidirectional MR analysis indicated mutual increased risks of AKI and sepsis. Then, 311 key genes common to sepsis and AKI were identified, with 42 significantly linked to sepsis prognosis. Six genes, selected through LASSO, SVM-RFE, and RF algorithms, showed excellent predictive performance for sepsis, AKI, and SA-AKI. The models demonstrated near-perfect AUCs in both training and testing datasets, and a perfect AUC in a sepsis mouse model. Significant differences in immune cells, immune-related pathways, HLA, and checkpoint genes were found between high- and low-risk groups. The study identified 62 potential drug treatments for sepsis and AKI and constructed a ceRNA network. CONCLUSIONS The identified signature genes hold potential clinical applications, including prognostic evaluation and targeted therapeutic strategies for sepsis and AKI. However, further research is needed to confirm these findings.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
| | - Jing Guo
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China
| | - Yunbiao Xiong
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Guoqiang Han
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Tao Luo
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Shuo Peng
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Jian Liu
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China; Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Tieyi Hu
- Department of Neurology, the Affiliated Dazu Hospital of Chongqing Medical University , China
| | - Yan Zha
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China; Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Xin Lin
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China.
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China.
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People's Hospital, Guiyang, China.
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6
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Cutrona MB, Wu J, Yang K, Peng J, Chen T. Pancreatic cancer organoid-screening captures personalized sensitivity and chemoresistance suppression upon cytochrome P450 3A5-targeted inhibition. iScience 2024; 27:110289. [PMID: 39055940 PMCID: PMC11269815 DOI: 10.1016/j.isci.2024.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/12/2024] [Accepted: 06/13/2024] [Indexed: 07/28/2024] Open
Abstract
Cytochrome P450 3A5 (CYP3A5) has been proposed as a predictor of therapy response in subtypes of pancreatic ductal adenocarcinoma cancer (PDAC). To validate CYP3A5 as a therapeutic target, we developed a high-content image organoid-based screen to quantify the phenotypic responses to the selective inhibition of CYP3A5 enzymatic activity by clobetasol propionate (CBZ), using a cohort of PDAC-derived organoids (PDACOs). The chemoresistance of PDACOs to a panel of standard-of-care drugs, alone or in combination with CBZ, was investigated. PDACO pharmaco-profiling revealed CBZ to have anti-cancer activity that was dependent on the CYP3A5 level. In addition, CBZ restored chemo-vulnerability to cisplatin in a subset of PDACOs. A correlative proteomic analysis established that CBZ caused the suppression of multiple cancer pathways sustained by or associated with a mutant form of p53. Limiting the active pool of CYP3A5 enables targeted and personalized therapy to suppress pro-oncogenic mechanisms that fuel chemoresistance in some PDAC tumors.
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Affiliation(s)
- Meritxell B. Cutrona
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Ka Yang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA
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7
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Peng J, Zaman M, Yang S, Huang Y, Yarbro J, Wang Z, Liu D, Soliman H, Hemphill A, Harvey S, Pruett-Miller S, Stewart V, Tanwar A, Kalathur R, Grace C, Turk M, Chittori S, Jiao Y, Wu Z, High A, Wang X, Serrano G, Beach T, Yu G, Yang Y, Chen PC. Midkine Attenuates Aβ Fibril Assembly and AmyloidPlaque Formation. RESEARCH SQUARE 2024:rs.3.rs-4361125. [PMID: 38883748 PMCID: PMC11177971 DOI: 10.21203/rs.3.rs-4361125/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Proteomic profiling of Alzheimer's disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with Aβ since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates Aβ assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both Aβ40 and Aβ42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdkgene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and aggregated proteome in these mouse models indicates significant accumulation of Aβ and Aβ-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Shu Yang
- St Jude Children's Research Hospital
| | - Ya Huang
- St Jude Children's Research Hospital
| | | | - Zhen Wang
- St Jude Children's Research Hospital
| | | | | | | | | | | | | | | | | | | | | | | | - Yun Jiao
- St Jude Children's Research Hospital
| | | | | | | | | | | | - Gang Yu
- University of Texas Southwestern Medical Center
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8
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Wang J, Tan H, Fu Y, Mishra A, Sun H, Wang Z, Wu Z, Wang X, Serrano GE, Beach TG, Peng J, High AA. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1253-1260. [PMID: 38754071 DOI: 10.1021/jasms.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min). To further improve the identification of proteins in low-amount samples, we utilized different column settings and introduced 0.02% n-dodecyl-β-d-maltoside (DDM) in the sample reconstitution solution, resulting in a remarkable 19-fold increase in protein identification at the single-cell-equivalent level. Moreover, a comprehensive comparison of protein quantification using a tandem mass tag reporter (TMT-reporter), complement TMT ions (TMTc), and diaPASEF revealed a strong correlation between these methods. Both diaPASEF and TMTc have effectively addressed the issue of ratio compression, highlighting the diaPASEF method's effectiveness in achieving accurate quantification data compared to TMT reporter quantification. Additionally, an in-depth analysis of in-group variation positioned diaPASEF between the TMT-reporter and TMTc methods. Therefore, diaPASEF quantification on the timsTOF SCP instrument emerges as a precise and accurate methodology for quantitative proteomics, especially for samples with small amounts.
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Affiliation(s)
- Ju Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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9
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Reisman EG, Hawley JA, Hoffman NJ. Exercise-Regulated Mitochondrial and Nuclear Signalling Networks in Skeletal Muscle. Sports Med 2024; 54:1097-1119. [PMID: 38528308 PMCID: PMC11127882 DOI: 10.1007/s40279-024-02007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2024] [Indexed: 03/27/2024]
Abstract
Exercise perturbs energy homeostasis in skeletal muscle and engages integrated cellular signalling networks to help meet the contraction-induced increases in skeletal muscle energy and oxygen demand. Investigating exercise-associated perturbations in skeletal muscle signalling networks has uncovered novel mechanisms by which exercise stimulates skeletal muscle mitochondrial biogenesis and promotes whole-body health and fitness. While acute exercise regulates a complex network of protein post-translational modifications (e.g. phosphorylation) in skeletal muscle, previous investigations of exercise signalling in human and rodent skeletal muscle have primarily focused on a select group of exercise-regulated protein kinases [i.e. 5' adenosine monophosphate-activated protein kinase (AMPK), protein kinase A (PKA), Ca2+/calmodulin-dependent protein kinase (CaMK) and mitogen-activated protein kinase (MAPK)] and only a small subset of their respective protein substrates. Recently, global mass spectrometry-based phosphoproteomic approaches have helped unravel the extensive complexity and interconnection of exercise signalling pathways and kinases beyond this select group and phosphorylation and/or translocation of exercise-regulated mitochondrial and nuclear protein substrates. This review provides an overview of recent advances in our understanding of the molecular events associated with acute endurance exercise-regulated signalling pathways and kinases in skeletal muscle with a focus on phosphorylation. We critically appraise recent evidence highlighting the involvement of mitochondrial and nuclear protein phosphorylation and/or translocation in skeletal muscle adaptive responses to an acute bout of endurance exercise that ultimately stimulate mitochondrial biogenesis and contribute to exercise's wider health and fitness benefits.
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Affiliation(s)
- Elizabeth G Reisman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - Nolan J Hoffman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia.
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10
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Zhou X, Lee YK, Li X, Kim H, Sanchez-Priego C, Han X, Tan H, Zhou S, Fu Y, Purtell K, Wang Q, Holstein GR, Tang B, Peng J, Yang N, Yue Z. Integrated proteomics reveals autophagy landscape and an autophagy receptor controlling PKA-RI complex homeostasis in neurons. Nat Commun 2024; 15:3113. [PMID: 38600097 PMCID: PMC11006854 DOI: 10.1038/s41467-024-47440-z] [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: 12/01/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Autophagy is a conserved, catabolic process essential for maintaining cellular homeostasis. Malfunctional autophagy contributes to neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we report a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and brain LC3-interactome reveals roles of neuronal autophagy in targeting proteins of multiple cellular organelles/pathways, including endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) for degradation. By combining phosphoproteomics and functional analysis in human and mouse neurons, we uncovered a function of neuronal autophagy in controlling cAMP-PKA and c-FOS-mediated neuronal activity through selective degradation of the protein kinase A - cAMP-binding regulatory (R)-subunit I (PKA-RI) complex. Lack of AKAP11 causes accumulation of the PKA-RI complex in the soma and neurites, demonstrating a constant clearance of PKA-RI complex through AKAP11-mediated degradation in neurons. Our study thus reveals the landscape of autophagy degradation in human neurons and identifies a physiological function of autophagy in controlling homeostasis of PKA-RI complex and specific PKA activity in neurons.
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Affiliation(s)
- Xiaoting Zhou
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - You-Kyung Lee
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xianting Li
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Kim
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Sanchez-Priego
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xian Han
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Haiyan Tan
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kerry Purtell
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qian Wang
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gay R Holstein
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Nan Yang
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zhenyu Yue
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center of Parkinson's Disease Neurobiology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
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11
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Shrestha HK, Lee D, Wu Z, Wang Z, Fu Y, Wang X, Serrano GE, Beach TG, Peng J. Profiling Protein-Protein Interactions in the Human Brain by Refined Cofractionation Mass Spectrometry. J Proteome Res 2024; 23:1221-1231. [PMID: 38507900 PMCID: PMC11065482 DOI: 10.1021/acs.jproteome.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Proteins usually execute their biological functions through interactions with other proteins and by forming macromolecular complexes, but global profiling of protein complexes directly from human tissue samples has been limited. In this study, we utilized cofractionation mass spectrometry (CF-MS) to map protein complexes within the postmortem human brain with experimental replicates. First, we used concatenated anion and cation Ion Exchange Chromatography (IEX) to separate native protein complexes in 192 fractions and then proceeded with Data-Independent Acquisition (DIA) mass spectrometry to analyze the proteins in each fraction, quantifying a total of 4,804 proteins with 3,260 overlapping in both replicates. We improved the DIA's quantitative accuracy by implementing a constant amount of bovine serum albumin (BSA) in each fraction as an internal standard. Next, advanced computational pipelines, which integrate both a database-based complex analysis and an unbiased protein-protein interaction (PPI) search, were applied to identify protein complexes and construct protein-protein interaction networks in the human brain. Our study led to the identification of 486 protein complexes and 10054 binary protein-protein interactions, which represents the first global profiling of human brain PPIs using CF-MS. Overall, this study offers a resource and tool for a wide range of human brain research, including the identification of disease-specific protein complexes in the future.
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Affiliation(s)
- Him K. Shrestha
- Departments of Structural Biology and Developmental Neurobiology
| | - DongGeun Lee
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, USA
| | | | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology
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12
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Hunt LC, Nyamkondiwa K, Stephan A, Jiao J, Kavdia K, Pagala V, Peng J, Demontis F. The ubiquitin-conjugating enzyme UBE2D/eff maintains a youthful proteome and ensures protein quality control during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571303. [PMID: 38168249 PMCID: PMC10759998 DOI: 10.1101/2023.12.12.571303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Ubiquitin-conjugating enzymes (E2s) are key for regulating protein function and turnover via ubiquitination but it remains undetermined which E2s maintain proteostasis during aging. Here, we find that E2s have diverse roles in handling a model aggregation-prone protein (huntingtin-polyQ) in the Drosophila retina: while some E2s mediate aggregate assembly, UBE2D/effete (eff) and other E2s are required for huntingtin-polyQ degradation. UBE2D/eff is key for proteostasis also in skeletal muscle: eff protein levels decline with aging, and muscle-specific eff knockdown causes an accelerated buildup in insoluble poly-ubiquitinated proteins (which progressively accumulate with aging) and shortens lifespan. Transgenic expression of human UBE2D2, homologous to eff, partially rescues the lifespan and proteostasis deficits caused by muscle-specific effRNAi by re-establishing the physiological levels of effRNAi-regulated proteins, which include several regulators of proteostasis. Interestingly, UBE2D/eff knockdown in young age reproduces part of the proteomic changes that normally occur in old muscles, suggesting that the decrease in UBE2D/eff protein levels that occurs with aging contributes to reshaping the composition of the muscle proteome. Altogether, these findings indicate that UBE2D/eff is a key E2 ubiquitin-conjugating enzyme that ensures protein quality control and helps maintain a youthful proteome composition during aging.
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Affiliation(s)
- Liam C. Hunt
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kudzai Nyamkondiwa
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jianqin Jiao
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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13
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Nishiguchi G, Mascibroda LG, Young SM, Caine EA, Abdelhamed S, Kooijman JJ, Miller DJ, Das S, McGowan K, Mayasundari A, Shi Z, Barajas JM, Hiltenbrand R, Aggarwal A, Chang Y, Mishra V, Narina S, Thomas M, Loughran AJ, Kalathur R, Yu K, Zhou S, Wang X, High AA, Peng J, Pruett-Miller SM, Daniels DL, Urh M, Shelat AA, Mullighan CG, Riching KM, Zaman GJR, Fischer M, Klco JM, Rankovic Z. Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines. Nat Commun 2024; 15:482. [PMID: 38228616 PMCID: PMC10791743 DOI: 10.1038/s41467-024-44698-1] [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: 05/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.
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Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lauren G Mascibroda
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sarah M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | | | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhe Shi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Juan M Barajas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anup Aggarwal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Melvin Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Memphis, TN, 38105, USA
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Guido J R Zaman
- Oncolines B.V., Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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14
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Shrestha HK, Sun H, Wang J, Peng J. Profiling Mouse Brain Single-Cell-Type Proteomes Via Adeno-Associated Virus-Mediated Proximity Labeling and Mass Spectrometry. Methods Mol Biol 2024; 2817:115-132. [PMID: 38907151 DOI: 10.1007/978-1-0716-3934-4_10] [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: 06/23/2024]
Abstract
Single-cell-type proteomics is an emerging field of research that combines cell-type specificity with the comprehensive proteome coverage offered by bulk proteomics. However, the extraction of single-cell-type proteomes remains a challenge, particularly for hard-to-isolate cells like neurons. In this chapter, we present an innovative technique for profiling single-cell-type proteomes using adeno-associated virus (AAV)-mediated proximity labeling (PL) and tandem-mass-tag (TMT) mass spectrometry. This technique eliminates the need for cell isolation and offers a streamlined workflow, including AAV delivery to express TurboID (an engineered biotin ligase) controlled by cell-type-specific promoters, biotinylated protein purification, on-bead digestion, TMT labeling, and liquid chromatography-mass spectrometry (LC-MS). We examined this method by analyzing distinct brain cell types in mice. Initially, recombinant AAVs were used to concurrently express TurboID and mCherry proteins driven by neuron- or astrocyte-specific promoters, which was validated through co-immunostaining with cellular markers. With biotin purification and TMT analysis, we successfully identified around 10,000 unique proteins from a few micrograms of protein samples with high reproducibility. Our statistical analyses revealed that these proteomes encompass cell-type-specific cellular pathways. By utilizing this technique, researchers can explore the proteomic landscape of specific cell types, paving the way for new insights into cellular processes, deciphering disease mechanisms, and identifying therapeutic targets in neuroscience and beyond.
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Affiliation(s)
- Him K Shrestha
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huan Sun
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ju Wang
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [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: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
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Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
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16
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Coleman C, Wang M, Wang E, Micallef C, Shao Z, Vicari JM, Li Y, Yu K, Cai D, Peng J, Haroutunian V, Fullard JF, Bendl J, Zhang B, Roussos P. Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease. Sci Data 2023; 10:602. [PMID: 37684260 PMCID: PMC10491684 DOI: 10.1038/s41597-023-02507-2] [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: 05/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia worldwide, with a projection of 151 million cases by 2050. Previous genetic studies have identified three main genes associated with early-onset familial Alzheimer's disease, however this subtype accounts for less than 5% of total cases. Next-generation sequencing has been well established and holds great promise to assist in the development of novel therapeutics as well as biomarkers to prevent or slow the progression of this devastating disease. Here we present a public resource of functional genomic data from the parahippocampal gyrus of 201 postmortem control, mild cognitively impaired (MCI) and AD individuals from the Mount Sinai brain bank, of which whole-genome sequencing (WGS), and bulk RNA sequencing (RNA-seq) were previously published. The genomic data include bulk proteomics and DNA methylation, as well as cell-type-specific RNA-seq and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) data. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource available on the Synapse platform at https://doi.org/10.7303/syn51180043.2 .
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Affiliation(s)
- Claire Coleman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Courtney Micallef
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James M Vicari
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dongming Cai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA.
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17
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Zaman M, Fu Y, Chen PC, Sun H, Yang S, Wu Z, Wang Z, Poudel S, Serrano GE, Beach TG, Li L, Wang X, Peng J. Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry. Mol Cell Proteomics 2023; 22:100608. [PMID: 37356496 PMCID: PMC10392608 DOI: 10.1016/j.mcpro.2023.100608] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023] Open
Abstract
Protein aggregation of amyloid-β peptides and tau are pathological hallmarks of Alzheimer's disease (AD), which are often resistant to detergent extraction and thus enriched in the insoluble proteome. However, additional proteins that coaccumulate in the detergent-insoluble AD brain proteome remain understudied. Here, we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples using differential extraction, tandem mass tag (TMT) labeling, and two-dimensional LC-tandem mass spectrometry. To improve quantification accuracy of the TMT method, we developed a complement TMT-based strategy to correct for ratio compression. Through the meta-analysis of two independent detergent-insoluble AD proteome datasets (8914 and 8917 proteins), we identified 190 differentially expressed proteins in AD compared with control brains, highlighting the pathways of amyloid cascade, RNA splicing, endocytosis/exocytosis, protein degradation, and synaptic activity. To differentiate the truly detergent-insoluble proteins from copurified background during protein extraction, we analyzed the fold of enrichment for each protein by comparing the detergent-insoluble proteome with the whole proteome from the same AD samples. Among the 190 differentially expressed proteins, 84 (51%) proteins of the upregulated proteins (n = 165) were enriched in the insoluble proteome, whereas all downregulated proteins (n = 25) were not enriched, indicating that they were copurified components. The vast majority of these enriched 84 proteins harbor low-complexity regions in their sequences, including amyloid-β, Tau, TARDBP/TAR DNA-binding protein 43, SNRNP70/U1-70K, MDK, PTN, NTN1, NTN3, and SMOC1. Moreover, many of the enriched proteins in AD were validated in the detergent-insoluble proteome by five steps of differential extraction, proteomic analysis, or immunoblotting. Our study reveals a resource list of proteins and pathways that are exclusively present in the detergent-insoluble proteome, providing novel molecular insights to the formation of protein pathology in AD.
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Affiliation(s)
- Masihuz Zaman
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingxue Fu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ping-Chung Chen
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Huan Sun
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shu Yang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zhiping Wu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zhen Wang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ling Li
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
| | - Junmin Peng
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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18
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Min J, Yang S, Cai Y, Vanderwall DR, Wu Z, Li S, Liu S, Liu B, Wang J, Ding Y, Chen J, Jiang C, Wren JD, Csiszar A, Ungvari Z, Greco C, Kanie T, Peng J, Zhang XA. Tetraspanin Tspan8 restrains interferon signaling to stabilize intestinal epithelium by directing endocytosis of interferon receptor. Cell Mol Life Sci 2023; 80:154. [PMID: 37204469 PMCID: PMC10484302 DOI: 10.1007/s00018-023-04803-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Inflammation can impair intestinal barrier, while increased epithelial permeability can lead to inflammation. In this study, we found that the expression of Tspan8, a tetraspanin expressed specifically in epithelial cells, is downregulated in mouse model of ulcerative disease (UC) but correlated with those of cell-cell junction components, such as claudins and E-cadherin, suggesting that Tspan8 supports intestinal epithelial barrier. Tspan8 removal increases intestinal epithelial permeability and upregulates IFN-γ-Stat1 signaling. We also demonstrated that Tspan8 coalesces with lipid rafts and facilitates IFNγ-R1 localization at or near lipid rafts. As IFN-γ induces its receptor undergoing clathrin- or lipid raft-dependent endocytosis and IFN-γR endocytosis plays an important role in Jak-Stat1 signaling, our analysis on IFN-γR endocytosis revealed that Tspan8 silencing impairs lipid raft-mediated but promotes clathrin-mediated endocytosis of IFN-γR1, leading to increased Stat1 signaling. These changes in IFN-γR1 endocytosis upon Tspan8 silencing correlates with fewer lipid raft component GM1 at the cell surface and more clathrin heavy chain in the cells. Our findings indicate that Tspan8 determines the IFN-γR1 endocytosis route, to restrain Stat1 signaling, stabilize intestine epithelium, and subsequently prevent intestine from inflammation. Our finding also implies that Tspan8 is needed for proper endocytosis through lipid rafts.
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Affiliation(s)
- Jiang Min
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Shenglan Yang
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Yang Cai
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - David R Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shuping Li
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Songlan Liu
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Beibei Liu
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Jie Wang
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Yingjun Ding
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Junxiong Chen
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Chao Jiang
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | | | - Anna Csiszar
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Zoltan Ungvari
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Céline Greco
- Department of Pain and Palliative Care Unit, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Tomoharu Kanie
- University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xin A Zhang
- University of Oklahoma Health Sciences Center, Oklahoma City, USA.
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19
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Garg A, Sanchez AM, Miele M, Schwer B, Shuman S. Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis. Nucleic Acids Res 2023; 51:3094-3115. [PMID: 36794724 PMCID: PMC10123115 DOI: 10.1093/nar/gkad063] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Inorganic phosphate is an essential nutrient acquired by cells from their environment. Here, we characterize the adaptative responses of fission yeast to chronic phosphate starvation, during which cells enter a state of quiescence, initially fully reversible upon replenishing phosphate after 2 days but resulting in gradual loss of viability during 4 weeks of starvation. Time-resolved analyses of changes in mRNA levels revealed a coherent transcriptional program in which phosphate dynamics and autophagy were upregulated, while the machineries for rRNA synthesis and ribosome assembly, and for tRNA synthesis and maturation, were downregulated in tandem with global repression of genes encoding ribosomal proteins and translation factors. Consistent with the transcriptome changes, proteome analysis highlighted global depletion of 102 ribosomal proteins. Concomitant with this ribosomal protein deficit, 28S and 18S rRNAs became vulnerable to site-specific cleavages that generated temporally stable rRNA fragments. The finding that Maf1, a repressor of RNA polymerase III transcription, was upregulated during phosphate starvation prompted a hypothesis that its activity might prolong lifespan of the quiescent cells by limiting production of tRNAs. Indeed, we found that deletion of maf1 results in precocious death of phosphate-starved cells via a distinctive starvation-induced pathway associated with tRNA overproduction and dysfunctional tRNA biogenesis.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ana M Sanchez
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Matthew Miele
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Beate Schwer
- Correspondence may also be addressed to Beate Schwer. Tel: +1 212 746 6518;
| | - Stewart Shuman
- To whom correspondence should be addressed. Tel: +1 212 639 7145;
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20
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Wei JJ, Li XJ, Liu W, Chai XJ, Zhu XY, Sun PH, Liu F, Zhao YK, Huang JL, Liu YF, Zhao ST. Eucommia Polysaccharides Ameliorate Aging-Associated Gut Dysbiosis: A Potential Mechanism for Life Extension in Drosophila. Int J Mol Sci 2023; 24:ijms24065881. [PMID: 36982954 PMCID: PMC10054339 DOI: 10.3390/ijms24065881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The gut microbiota is increasingly considered to play a key role in human immunity and health. The aging process alters the microbiota composition, which is associated with inflammation, reactive oxygen species (ROS), decreased tissue function, and increased susceptibility to age-related diseases. It has been demonstrated that plant polysaccharides have beneficial effects on the gut microbiota, particularly in reducing pathogenic bacteria abundance and increasing beneficial bacteria populations. However, there is limited evidence of the effect of plant polysaccharides on age-related gut microbiota dysbiosis and ROS accumulation during the aging process. To explore the effect of Eucommiae polysaccharides (EPs) on age-related gut microbiota dysbiosis and ROS accumulation during the aging process of Drosophila, a series of behavioral and life span assays of Drosophila with the same genetic background in standard medium and a medium supplemented with EPs were performed. Next, the gut microbiota composition and protein composition of Drosophila in standard medium and the medium supplemented with EPs were detected using 16S rRNA gene sequencing analysis and quantitative proteomic analysis. Here, we show that supplementation of Eucommiae polysaccharides (EPs) during development leads to the life span extension of Drosophila. Furthermore, EPs decreased age-related ROS accumulation and suppressed Gluconobacter, Providencia, and Enterobacteriaceae in aged Drosophila. Increased Gluconobacter, Providencia, and Enterobacteriaceae in the indigenous microbiota might induce age-related gut dysfunction in Drosophila and shortens their life span. Our study demonstrates that EPs can be used as prebiotic agents to prevent aging-associated gut dysbiosis and reactive oxidative stress.
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Affiliation(s)
- Jing-Jing Wei
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Xiu-Juan Li
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Wei Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Xue-Jun Chai
- College of Basic Medicine, Xi'an Medical University, Xi'an 710068, China
| | - Xiao-Yan Zhu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Peng-Hao Sun
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Feng Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Yong-Kang Zhao
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Jun-Lang Huang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Ya-Fei Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Shan-Ting Zhao
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
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21
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Kamens JL, Nance S, Koss C, Xu B, Cotton A, Lam JW, Garfinkle EAR, Nallagatla P, Smith AMR, Mitchell S, Ma J, Currier D, Wright WC, Kavdia K, Pagala VR, Kim W, Wallace LM, Cho JH, Fan Y, Seth A, Twarog N, Choi JK, Obeng EA, Hatley ME, Metzger ML, Inaba H, Jeha S, Rubnitz JE, Peng J, Chen T, Shelat AA, Guy RK, Gruber TA. Proteasome inhibition targets the KMT2A transcriptional complex in acute lymphoblastic leukemia. Nat Commun 2023; 14:809. [PMID: 36781850 PMCID: PMC9925443 DOI: 10.1038/s41467-023-36370-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.
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Affiliation(s)
- Jennifer L Kamens
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephanie Nance
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cary Koss
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anitria Cotton
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeannie W Lam
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratima Nallagatla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Amelia M R Smith
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharnise Mitchell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Duane Currier
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William C Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wonil Kim
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - LaShanale M Wallace
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aman Seth
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nathaniel Twarog
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John K Choi
- Department of Pathology, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Monika L Metzger
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - R Kiplin Guy
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
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22
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Sun H, Yang K, Zhang X, Fu Y, Yarbro J, Wu Z, Chen PC, Chen T, Peng J. Evaluation of a Pooling Chemoproteomics Strategy with an FDA-Approved Drug Library. Biochemistry 2023; 62:624-632. [PMID: 35969671 PMCID: PMC9905291 DOI: 10.1021/acs.biochem.2c00256] [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: 02/08/2023]
Abstract
Chemoproteomics is a key platform for characterizing the mode of action for compounds, especially for targeted protein degraders such as proteolysis targeting chimeras (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy for further enhancing the throughput and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing more than 15 000 unique proteins (> 12 000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by reprofiling the cells via treatment with individual drugs with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN, and LRRC58 with 7-hydroxystaurosporine; C6orf64, HMGCR, and RRM2 with Sorafenib; SYS1 and ALAS1 with Venetoclax; and ATF3, CLK1, and CLK4 with Palbocilib. Thus, pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.
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Affiliation(s)
- Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Xue Zhang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jay Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Chemical Biology & Therapeutics Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Correspondence:
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23
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Zeleke TZ, Pan Q, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ, Honan E, Yang M, Chia PL, Mukhopadhyay P, Kelly S, Wu R, Fenn K, Trivedi MS, Accordino M, Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano A, Kalinsky K, Yu J, Silva J. Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. NATURE CANCER 2023; 4:257-275. [PMID: 36585452 PMCID: PMC9992270 DOI: 10.1038/s43018-022-00489-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 11/10/2022] [Indexed: 12/31/2022]
Abstract
Inhibiting individual histone deacetylase (HDAC) is emerging as well-tolerated anticancer strategy compared with pan-HDAC inhibitors. Through preclinical studies, we demonstrated that the sensitivity to the leading HDAC6 inhibitor (HDAC6i) ricolinstat can be predicted by a computational network-based algorithm (HDAC6 score). Analysis of ~3,000 human breast cancers (BCs) showed that ~30% of them could benefice from HDAC6i therapy. Thus, we designed a phase 1b dose-escalation clinical trial to evaluate the activity of ricolinostat plus nab-paclitaxel in patients with metastatic BC (MBC) (NCT02632071). Study results showed that the two agents can be safely combined, that clinical activity is identified in patients with HR+/HER2- disease and that the HDAC6 score has potential as predictive biomarker. Analysis of other tumor types also identified multiple cohorts with predicted sensitivity to HDAC6i's. Mechanistically, we have linked the anticancer activity of HDAC6i's to their ability to induce c-Myc hyperacetylation (ac-K148) promoting its proteasome-mediated degradation in sensitive cancer cells.
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Affiliation(s)
- Tizita Z Zeleke
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Codruta Chiuzan
- Feinstein Institutes for Medical Research, Northwell Health, New York, USA
| | | | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.,DarwinHealth, Inc., New York, NY, USA
| | - Erin Honan
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Min Yang
- Acetylon Pharmaceuticals, Boston, MA, USA
| | - Pei Ling Chia
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Partha Mukhopadhyay
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Sean Kelly
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ruby Wu
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Kathleen Fenn
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Meghna S Trivedi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Melissa Accordino
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Katherine D Crew
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Dawn L Hershman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | - Simon Jones
- Regenacy Pharmaceuticals, Inc., Waltham, MA, USA
| | - Anthony High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kevin Kalinsky
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA.
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jose Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA.
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24
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Zhang X, Sun H, Wang Z, Zhou S, Fu Y, Anthony HA, Peng J. In-Depth Blood Proteome Profiling by Extensive Fractionation and Multiplexed Quantitative Mass Spectrometry. Methods Mol Biol 2023; 2628:109-125. [PMID: 36781782 DOI: 10.1007/978-1-0716-2978-9_8] [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: 04/25/2023]
Abstract
Blood in the circulatory system carries information of physiological and pathological status of the human body, so blood proteins are often used as biomarkers for diagnosis, prognosis, and therapy. Human blood proteome can be explored by the latest technologies in mass spectrometry (MS), creating an opportunity of discovering new disease biomarkers. The extreme dynamic range of protein concentrations in blood, however, poses a challenge to detect proteins of low abundance, namely, tissue leakage proteins. Here, we describe a strategy to directly analyze undepleted blood samples by extensive liquid chromatography (LC) fractionation and 18-plex tandem-mass-tag (TMT) mass spectrometry. The proteins in blood specimens (e.g., plasma or serum) are isolated by acetone precipitation and digested into peptides. The resulting peptides are TMT-labeled, separated by basic pH reverse-phase (RP) LC into at least 40 fractions, and analyzed by acidic pH RPLC and high-resolution MS/MS, leading to the quantification of ~3000 unique proteins. Further increase of basic pH RPLC fractions and adjustment of the fraction concatenation strategy can enhance the proteomic coverage (up to ~5000 proteins). Finally, the combination of multiple batches of TMT experiments allows the profiling of hundreds of blood samples. This TMT-MS-based method provides a powerful platform for deep proteome profiling of human blood samples.
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Affiliation(s)
- Xue Zhang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - High A Anthony
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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25
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Huang X, Li L, Zhou S, Kong D, Luo J, Lu L, Xu HM, Wang X. Multi-omics analysis reveals expression complexity and functional diversity of mouse kinome. Proteomics 2022; 22:e2200120. [PMID: 35856475 DOI: 10.1002/pmic.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 12/29/2022]
Abstract
Protein kinases are a crucial component of signaling pathways involved in a wide range of cellular responses, including growth, proliferation, differentiation, and migration. Systematic investigation of protein kinases is critical to better understand phosphorylation-mediated signaling pathways and may provide insights into the development of potential therapeutic drug targets. Here we perform a systems-level analysis of the mouse kinome by analyzing multi-omics data. We used bulk and single-cell transcriptomic data from the C57BL/6J mouse strain to define tissue- and cell-type-specific expression of protein kinases, followed by investigating variations in sequence and expression between C57BL/6J and DBA/2J strains. We then profiled a deep brain phosphoproteome from C57BL/6J and DBA/2J strains as well as their reciprocal hybrids to infer the activity of the mouse kinome. Finally, we performed phenome-wide association analysis using the BXD recombinant inbred (RI) mice (a cross between C57BL/6J and DBA/2J strains) to identify any associations between variants in protein kinases and phenotypes. Collectively, our study provides a comprehensive analysis of the mouse kinome by investigating genetic sequence variation, tissue-specific expression patterns, and associations with downstream phenotypes.
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Affiliation(s)
- Xin Huang
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ling Li
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Dehui Kong
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Jie Luo
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hai-Ming Xu
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
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26
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Chen PC, Han X, Shaw TI, Fu Y, Sun H, Niu M, Wang Z, Jiao Y, Teubner BJW, Eddins D, Beloate LN, Bai B, Mertz J, Li Y, Cho JH, Wang X, Wu Z, Liu D, Poudel S, Yuan ZF, Mancieri A, Low J, Lee HM, Patton MH, Earls LR, Stewart E, Vogel P, Hui Y, Wan S, Bennett DA, Serrano GE, Beach TG, Dyer MA, Smeyne RJ, Moldoveanu T, Chen T, Wu G, Zakharenko SS, Yu G, Peng J. Alzheimer's disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment. NATURE AGING 2022; 2:923-940. [PMID: 36636325 PMCID: PMC9833817 DOI: 10.1038/s43587-022-00290-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/01/2022] [Indexed: 11/05/2022]
Abstract
Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, erroneous splicing events, neuronal degeneration and cognitive impairment. Specifically, N40K-Tg shows the reduction of GABAergic synapse components (e.g., the GABA receptor subunit of GABRA2), and concomitant postsynaptic hyperexcitability that is rescued by a GABA receptor agonist. Crossing of N40K-Tg and the 5xFAD amyloidosis model indicates that the RNA splicing defect synergizes with the amyloid cascade to remodel the brain transcriptome and proteome, deregulate synaptic proteins, and accelerate cognitive decline. Thus, our results support the contribution of U1 snRNP-mediated splicing dysfunction to AD pathogenesis.
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Affiliation(s)
- Ping-Chung Chen
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xian Han
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Timothy I. Shaw
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Yingxue Fu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Huan Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mingming Niu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zhen Wang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yun Jiao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brett J. W. Teubner
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Donnie Eddins
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lauren N. Beloate
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biomedical Engineering and Electrical Engineering, Penn State University, State College, PA 16801, USA
| | - Bing Bai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Laboratory Medicine, Center for Precision Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Joseph Mertz
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: GlaxoSmithKline, Rockville, MD 20850, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xusheng Wang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Present address: Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Zhiping Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Danting Liu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Suresh Poudel
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ariana Mancieri
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyeong-Min Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mary H. Patton
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laurie R. Earls
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biological Sciences, Loyola University of New Orleans, LA 70118, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yawei Hui
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David A. Bennett
- Department of Neurological Sciences, Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | | | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard J. Smeyne
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Present address: Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AK 72205, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Yu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Present address: Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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27
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Hu J, Jarusiewicz J, Du G, Nishiguchi G, Yoshimura S, Panetta JC, Li Z, Min J, Yang L, Chepyala D, Actis M, Reyes N, Smart B, Pui CH, Teachey DT, Rankovic Z, Yang JJ. Preclinical evaluation of proteolytic targeting of LCK as a therapeutic approach in T cell acute lymphoblastic leukemia. Sci Transl Med 2022; 14:eabo5228. [PMID: 36001679 PMCID: PMC9730446 DOI: 10.1126/scitranslmed.abo5228] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy, and there is an unmet need for targeted therapies, especially for patients with relapsed disease. We have recently identified pre-T cell receptor and lymphocyte-specific protein tyrosine kinase (LCK) signaling as a common therapeutic vulnerability in T-ALL. LCK inhibitor dasatinib showed efficacy against T-ALL in preclinical studies and in patients with T-ALL; however, this is transient in most cases. Leveraging the proteolysis targeting chimera (PROTAC) approach, we developed a series of LCK degraders using dasatinib as an LCK ligand and phenyl-glutarimide as a cereblon-directing moiety. Our lead compound SJ11646 exhibited marked efficiency in cereblon-mediated LCK degradation in T-ALL cells. Relative to dasatinib, SJ11646 showed up to three orders of magnitude higher cytotoxicity in LCK-activated T-ALL cell lines and primary leukemia samples in vitro, with drastically prolonged suppression of LCK signaling. In vivo pharmacokinetic and pharmacodynamic profiling indicated a 630% increase in the duration of LCK suppression by SJ11646 over dasatinib in patient-derived xenograft models of T-ALL, which translated into its extended leukemia-free survival over dasatinib in vivo. Last, SJ11646 retained a high binding affinity to 51 human kinases, particularly ABL1, KIT, and DDR1, all of which are known drug targets in other cancers. Together, our dasatinib-based phenyl-glutarimide PROTACs are promising therapeutic agents in T-ALL and valuable tools for developing degradation-based therapeutics for other cancers.
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Affiliation(s)
- Jianzhong Hu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Jamie Jarusiewicz
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Guoqing Du
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Gisele Nishiguchi
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - John C. Panetta
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Jaeki Min
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Divyabharathi Chepyala
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Marisa Actis
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Noemi Reyes
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Brandon Smart
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - David T. Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Zoran Rankovic
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA,,Correspondence to: Jun J. Yang Ph.D., Member, Department of Pharmacy and Pharmaceutical Sciences, Department of Oncology, ; Zoran Rankovic Ph.D., Director, CBT Chemistry Centers, Department of Chemical Biology & Therapeutics, ; St. Jude Children’s Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA,,Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA,,Correspondence to: Jun J. Yang Ph.D., Member, Department of Pharmacy and Pharmaceutical Sciences, Department of Oncology, ; Zoran Rankovic Ph.D., Director, CBT Chemistry Centers, Department of Chemical Biology & Therapeutics, ; St. Jude Children’s Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105
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28
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Labib D, Wang Z, Prakash P, Zimmer M, Smith MD, Frazel PW, Barbar L, Sapar ML, Calabresi PA, Peng J, Liddelow SA, Fossati V. Proteomic Alterations and Novel Markers of Neurotoxic Reactive Astrocytes in Human Induced Pluripotent Stem Cell Models. Front Mol Neurosci 2022; 15:870085. [PMID: 35592112 PMCID: PMC9113221 DOI: 10.3389/fnmol.2022.870085] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/29/2022] [Indexed: 12/20/2022] Open
Abstract
Astrocytes respond to injury, infection, and inflammation in the central nervous system by acquiring reactive states in which they may become dysfunctional and contribute to disease pathology. A sub-state of reactive astrocytes induced by proinflammatory factors TNF, IL-1α, and C1q ("TIC") has been implicated in many neurodegenerative diseases as a source of neurotoxicity. Here, we used an established human induced pluripotent stem cell (hiPSC) model to investigate the surface marker profile and proteome of TIC-induced reactive astrocytes. We propose VCAM1, BST2, ICOSL, HLA-E, PD-L1, and PDPN as putative, novel markers of this reactive sub-state. We found that several of these markers colocalize with GFAP+ cells in post-mortem samples from people with Alzheimer's disease. Moreover, our whole-cells proteomic analysis of TIC-induced reactive astrocytes identified proteins and related pathways primarily linked to potential engagement with peripheral immune cells. Taken together, our findings will serve as new tools to purify reactive astrocyte subtypes and to further explore their involvement in immune responses associated with injury and disease.
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Affiliation(s)
- David Labib
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Zhen Wang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Priya Prakash
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
| | - Matthew Zimmer
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Matthew D. Smith
- Department of Neurology, Johns Hopkins University, Baltimore, MD, United States
| | - Paul W. Frazel
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
| | - Lilianne Barbar
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Maria L. Sapar
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University, Baltimore, MD, United States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, United States
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shane A. Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, United States
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, NY, United States
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, United States
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
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29
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Azevedo R, Jacquemin C, Villain N, Fenaille F, Lamari F, Becher F. Mass Spectrometry for Neurobiomarker Discovery: The Relevance of Post-Translational Modifications. Cells 2022; 11:1279. [PMID: 35455959 PMCID: PMC9031030 DOI: 10.3390/cells11081279] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
Neurodegenerative diseases are incurable, heterogeneous, and age-dependent disorders that challenge modern medicine. A deeper understanding of the pathogenesis underlying neurodegenerative diseases is necessary to solve the unmet need for new diagnostic biomarkers and disease-modifying therapy and reduce these diseases' burden. Specifically, post-translational modifications (PTMs) play a significant role in neurodegeneration. Due to its proximity to the brain parenchyma, cerebrospinal fluid (CSF) has long been used as an indirect way to measure changes in the brain. Mass spectrometry (MS) analysis in neurodegenerative diseases focusing on PTMs and in the context of biomarker discovery has improved and opened venues for analyzing more complex matrices such as brain tissue and blood. Notably, phosphorylated tau protein, truncated α-synuclein, APP and TDP-43, and many other modifications were extensively characterized by MS. Great potential is underlying specific pathological PTM-signatures for clinical application. This review focuses on PTM-modified proteins involved in neurodegenerative diseases and highlights the most important and recent breakthroughs in MS-based biomarker discovery.
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Affiliation(s)
- Rita Azevedo
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (C.J.); (N.V.); (F.F.)
| | - Chloé Jacquemin
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (C.J.); (N.V.); (F.F.)
| | - Nicolas Villain
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (C.J.); (N.V.); (F.F.)
- Institut du Cerveau (ICM), Pitié-Salpêtrière Hospital, 75013 Paris, France
- Department of Neurology, Institute of Memory and Alzheimer’s Disease, Pitié-Salpêtrière Hospital, AP-HP Sorbonne Université, CEDEX 13, 75651 Paris, France
| | - François Fenaille
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (C.J.); (N.V.); (F.F.)
| | - Foudil Lamari
- Department of Metabolic Biochemistry (AP-HP Sorbonne), Pitié-Salpêtrière Hospital, CEDEX 13, 75651 Paris, France;
| | - François Becher
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (C.J.); (N.V.); (F.F.)
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30
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Grecco GG, Huang JY, Muñoz B, Doud EH, Hines CD, Gao Y, Rodriguez B, Mosley AL, Lu HC, Atwood BK. Sex-Dependent Synaptic Remodeling of the Somatosensory Cortex in Mice With Prenatal Methadone Exposure. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10400. [PMID: 37829495 PMCID: PMC10569410 DOI: 10.3389/adar.2022.10400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Rising opioid use among pregnant women has led to a growing population of neonates exposed to opioids during the prenatal period, but how opioids affect the developing brain remains to be fully understood. Animal models of prenatal opioid exposure have discovered deficits in somatosensory behavioral development that persist into adolescence suggesting opioid exposure induces long lasting neuroadaptations on somatosensory circuitry such as the primary somatosensory cortex (S1). Using a mouse model of prenatal methadone exposure (PME) that displays delays in somatosensory milestone development, we performed an un-biased multi-omics analysis and investigated synaptic functioning in the primary somatosensory cortex (S1), where touch and pain sensory inputs are received in the brain, of early adolescent PME offspring. PME was associated with numerous changes in protein and phosphopeptide abundances that differed considerably between sexes in the S1. Although prominent sex effects were discovered in the multi-omics assessment, functional enrichment analyses revealed the protein and phosphopeptide differences were associated with synapse-related cellular components and synaptic signaling-related biological processes, regardless of sex. Immunohistochemical analysis identified diminished GABAergic synapses in both layer 2/3 and 4 of PME offspring. These immunohistochemical and proteomic alterations were associated with functional consequences as layer 2/3 pyramidal neurons revealed reduced amplitudes and a lengthened decay constant of inhibitory postsynaptic currents. Lastly, in addition to reduced cortical thickness of the S1, cell-type marker analysis revealed reduced microglia density in the upper layer of the S1 that was primarily driven by PME females. Taken together, our studies show the lasting changes on synaptic function and microglia in S1 cortex caused by PME in a sex-dependent manner.
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Affiliation(s)
- Gregory G. Grecco
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Medical Scientist Training Program, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Jui Yen Huang
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, United States
- Program in Neuroscience and Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States
| | - Braulio Muñoz
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Caliel D. Hines
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, United States
| | - Yong Gao
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Brooke Rodriguez
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Hui-Chen Lu
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, United States
- Program in Neuroscience and Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States
| | - Brady K. Atwood
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Stark Neurosciences Research Institute, School of Medicine, Indiana University, Indianapolis, IN, United States
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31
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Sun X, Sun H, Han X, Chen PC, Jiao Y, Wu Z, Zhang X, Wang Z, Niu M, Yu K, Liu D, Dey KK, Mancieri A, Fu Y, Cho JH, Li Y, Poudel S, Branon TC, Ting AY, Peng J. Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling. Anal Chem 2022; 94:5325-5334. [PMID: 35315655 DOI: 10.1021/acs.analchem.1c05212] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.
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Affiliation(s)
- Xiaojun Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xian Han
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Ping-Chung Chen
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yun Jiao
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Xue Zhang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Mingming Niu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Danting Liu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ariana Mancieri
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tess C Branon
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Alice Y Ting
- Department of Genetics, Department of Chemistry, Department of Biology, Stanford University, Stanford, California 94305, United States
| | - Junmin Peng
- Departments of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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32
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Zhang Y, Liu W, Feng W, Wang X, Lei T, Chen Z, Song W. Identification of 14 Differentially-Expressed Metabolism-Related Genes as Potential Targets of Gastric Cancer by Integrated Proteomics and Transcriptomics. Front Cell Dev Biol 2022; 10:816249. [PMID: 35265615 PMCID: PMC8899292 DOI: 10.3389/fcell.2022.816249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Although research on the metabolism related to gastric cancer (GC) is gradually gaining increasing interest, there are few studies regarding metabolism-related genes in GC. Understanding the characteristic changes of metabolism-related genes at the transcriptional and protein levels in GC will help us to identify new biomarkers and novel therapeutic targets. We harvested six pairs of samples from GC patients and evaluated the differentially expressed proteins using mass spectrometry-based proteomics. RNA sequencing was conducted simultaneously to detect the corresponding expression of mRNAs, and bioinformatics analysis was used to reveal the correlation of significant differentially expressed genes. A total of 57 genes were observed to be dysregulated both in proteomics and transcriptomics. Bioinformatics analysis showed that these differentially expressed genes were significantly associated with regulating metabolic activity. Further, 14 metabolic genes were identified as potential targets for GC patients and were related to immune cell infiltration. Moreover, we found that dysregulation of branched-chain amino acid transaminase 2 (BCAT2), one of the 14 differentially expressed metabolism-related genes, was associated with the overall survival time in GC patients. We believe that this study provides comprehensive information to better understand the mechanism underlying the progression of GC metastasis and explores the potential therapeutic and prognostic metabolism-related targets for GC.
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Affiliation(s)
- Yongxin Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenwei Liu
- Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Wei Feng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tianxiang Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zehong Chen
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wu Song
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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33
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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34
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Prenatal Opioid Exposure Impairs Endocannabinoid and Glutamate Transmission in the Dorsal Striatum. eNeuro 2022; 9:ENEURO.0119-22.2022. [PMID: 35396255 PMCID: PMC9034757 DOI: 10.1523/eneuro.0119-22.2022] [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] [Received: 03/20/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
The opioid crisis has contributed to a growing population of children exposed to opioids during fetal development; however, many of the long-term effects of opioid exposure on development are unknown. We previously demonstrated that opioids have deleterious effects on endocannabinoid plasticity at glutamate synapses in the dorsal striatum of adolescent rodents, but it is unclear whether prenatal opioid exposure produces similar neuroadaptations. Using a mouse model of prenatal methadone exposure (PME), we performed proteomics, phosphoproteomics, and patch-clamp electrophysiology in the dorsolateral striatum (DLS) and dorsomedial striatum (DMS) to examine synaptic functioning in adolescent PME offspring. PME impacted the proteome and phosphoproteome in a region- and sex-dependent manner. Many proteins and phosphorylated proteins associated with glutamate transmission were differentially abundant in PME offspring, which was associated with reduced glutamate release in the DLS and altered the rise time of excitatory events in the DMS. Similarly, the intrinsic excitability properties of DMS neurons were significantly affected by PME. Last, pathway analyses revealed an enrichment in retrograde endocannabinoid signaling in the DLS, but not in the DMS, of males. Electrophysiology studies confirmed that endocannabinoid-mediated synaptic depression was impaired in the DLS, but not DMS, of PME-males. These results indicate that PME induces persistent neuroadaptations in the dorsal striatum and could contribute to the aberrant behavioral development described in offspring with prenatal opioid exposure.
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35
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Dey KK, Sun H, Wang Z, Niu M, Wang H, Jiao Y, Sun X, Li Y, Peng J. Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry. Methods Mol Biol 2022; 2420:21-37. [PMID: 34905163 PMCID: PMC8890903 DOI: 10.1007/978-1-0716-1936-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mass spectrometry (MS) has become a mainstream platform for comprehensive profiling of proteome, especially with the improvement of multiplexed tandem mass tag labeling coupled with two-dimensional liquid chromatography and tandem mass spectrometry (TMT-LC/LC-MS/MS). Recently, we have established a robust method for direct profiling of undepleted cerebrospinal fluid (CSF) proteome with the 16-plex TMTpro method, in which we optimized parameters in experimental steps of sample preparation, TMT labeling, LC/LC fractionation, tandem mass spectrometry, and computational data processing. The extensive LC fractionation not only enhances proteome coverage of the CSF but also alleviates ratio distortion of TMT quantification. The crucial quality control steps and improvements specific for the TMT16 analysis are highlighted. More than 3000 proteins can be quantified in a single experiment from 16 different CSF samples. This multiplexed method offers a powerful tool for profiling a variety of complex biofluids samples such as CSF, serum/plasma, and other clinical specimens.
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36
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Hunt LC, Graca FA, Pagala V, Wang YD, Li Y, Yuan ZF, Fan Y, Labelle M, Peng J, Demontis F. Integrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy. Cell Rep 2021; 37:109971. [PMID: 34758314 PMCID: PMC8852763 DOI: 10.1016/j.celrep.2021.109971] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/27/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle atrophy is a debilitating condition that occurs with aging and disease, but the underlying mechanisms are incompletely understood. Previous work determined that common transcriptional changes occur in muscle during atrophy induced by different stimuli. However, whether this holds true at the proteome level remains largely unexplored. Here, we find that, contrary to this earlier model, distinct atrophic stimuli (corticosteroids, cancer cachexia, and aging) induce largely different mRNA and protein changes during muscle atrophy in mice. Moreover, there is widespread transcriptome-proteome disconnect. Consequently, atrophy markers (atrogenes) identified in earlier microarray-based studies do not emerge from proteomics as generally induced by atrophy. Rather, we identify proteins that are distinctly modulated by different types of atrophy (herein defined as “atroproteins”) such as the myokine CCN1/Cyr61, which regulates myofiber type switching during sarcopenia. Altogether, these integrated analyses indicate that different catabolic stimuli induce muscle atrophy via largely distinct mechanisms. Skeletal muscle wasting is caused by many catabolic stimuli, which were thought to act via shared mechanisms. Hunt et al. now show that distinct catabolic stimuli induce muscle wasting via largely different molecular changes. The authors identify atrophy-associated proteins (“atroproteins”) that may represent diagnostic biomarkers and/or therapeutic targets.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Myriam Labelle
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Solid Tumor Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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37
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Bai B, Vanderwall D, Li Y, Wang X, Poudel S, Wang H, Dey KK, Chen PC, Yang K, Peng J. Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery. Mol Neurodegener 2021; 16:55. [PMID: 34384464 PMCID: PMC8359598 DOI: 10.1186/s13024-021-00474-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/18/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in "amyloidome" (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.
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Affiliation(s)
- Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Center for Precision Medicine, Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu 210008 Nanjing, China
| | - David Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Department of Biology, University of North Dakota, ND 58202 Grand Forks, USA
| | - Suresh Poudel
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
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38
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Maxwell BA, Gwon Y, Mishra A, Peng J, Nakamura H, Zhang K, Kim HJ, Taylor JP. Ubiquitination is essential for recovery of cellular activities after heat shock. Science 2021; 372:eabc3593. [PMID: 34739326 PMCID: PMC8574219 DOI: 10.1126/science.abc3593] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
Eukaryotic cells respond to stress through adaptive programs that include reversible shutdown of key cellular processes, the formation of stress granules, and a global increase in ubiquitination. The primary function of this ubiquitination is thought to be for tagging damaged or misfolded proteins for degradation. Here, working in mammalian cultured cells, we found that different stresses elicited distinct ubiquitination patterns. For heat stress, ubiquitination targeted specific proteins associated with cellular activities that are down-regulated during stress, including nucleocytoplasmic transport and translation, as well as stress granule constituents. Ubiquitination was not required for the shutdown of these processes or for stress granule formation but was essential for the resumption of cellular activities and for stress granule disassembly. Thus, stress-induced ubiquitination primes the cell for recovery after heat stress.
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Affiliation(s)
- Brian A. Maxwell
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Youngdae Gwon
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ashutosh Mishra
- Department of Structural Biology Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haruko Nakamura
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ke Zhang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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39
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Pagel O, Kollipara L, Sickmann A. Tandem Mass Tags for Comparative and Discovery Proteomics. Methods Mol Biol 2021; 2228:117-131. [PMID: 33950487 DOI: 10.1007/978-1-0716-1024-4_9] [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: 02/16/2023]
Abstract
Relative or comparative proteomics provides valuable insights about the altered protein abundances across different biological samples in a single (labeled) or series (label-free) of LC-MS measurement(s). Chemical labeling of peptides using isobaric mass tags for identification and quantification of different proteomes simultaneously has become a routine in the so-called discovery proteomics in the past decade. One of the earliest isobaric tags-based technologies is TMT (tandem mass tags), which relies on the comparison of the unique "reporter ions" intensities for relative peptide/protein quantification. This differential labeling approach has evolved over time with respect to its multiplexing capability, i.e., from just 2 samples (TMTduplex) to 10 samples (TMT10plex) and a nowadays of up to 16 samples (TMTpro 16plex). Here, we describe a straightforward protocol to perform relatively deep proteome quantitative analyses using TMT10plex.
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Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany. .,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland. .,Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.
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40
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Lyons CE, Zhou X, Razzoli M, Chen M, Xia W, Ashe K, Zhang B, Bartolomucci A. Lifelong chronic psychosocial stress induces a proteomic signature of Alzheimer's disease in wildtype mice. Eur J Neurosci 2021; 55:2971-2985. [PMID: 34048087 DOI: 10.1111/ejn.15329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/26/2021] [Accepted: 05/23/2021] [Indexed: 12/25/2022]
Abstract
Late onset, sporadic Alzheimer's disease (AD) accounts for the vast majority of cases. Unlike familial AD, the factors that drive the onset of sporadic AD are poorly understood, although aging and stress play a role. The early onset/severity of neuropathology observed in most genetic mouse models of AD hampers the study of the role of aging and environmental factors; thus alternate strategies are necessary to understand the contributions of these factors to sporadic AD. We demonstrate that mice acquiring a low social status (subordinate) in a lifelong chronic psychosocial stress (CPS) model, accrue widespread proteomic changes in the frontal/temporal cortex during aging. To better understand the significance of these stress-induced changes, we compared the differentially expressed proteins (DEPs) of subordinate mice to those of patients at varying stages of dementia. Sixteen and fifteen DEPs upregulated in subordinate mice were also upregulated in patients with mild cognitive impairment (MCI) and AD, respectively. Six of those upregulated proteins (CPE, ERC2, GRIN2B, SLC6A1, SYN1, WFS1) were shared by subordinate mice and patients with MCI or AD. Finally, comparison with a spatially detailed transcriptomic database revealed that the superior frontal gyrus and hippocampus had the greatest overlap between mice subjected to lifelong CPS and AD patients. Overall, most of the overlapping proteins were functionally associated with enhanced NMDA receptor mediated glutamatergic signaling, an excitotoxicity mechanism known to affect neurodegeneration. These findings support the association between stress and AD progression and provide valuable insight into potential early biomarkers and protein mediators of this relationship.
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Affiliation(s)
- Carey E Lyons
- Department of Integrative Physiology and Biology, University of Minnesota, Minneapolis, MN, USA.,Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Razzoli
- Department of Integrative Physiology and Biology, University of Minnesota, Minneapolis, MN, USA
| | - Mei Chen
- Geriatric Research Education Clinical Center, Bedford VA Healthcare System, Bedford, MA, USA
| | - Weiming Xia
- Geriatric Research Education Clinical Center, Bedford VA Healthcare System, Bedford, MA, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Karen Ashe
- Department of Neurology and N. Bud Grossman Center for Memory Research and Care, University of Minnesota, and Minneapolis VA Medical Center, Minneapolis, MN, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Bartolomucci
- Department of Integrative Physiology and Biology, University of Minnesota, Minneapolis, MN, USA
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41
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Nishiguchi G, Keramatnia F, Min J, Chang Y, Jonchere B, Das S, Actis M, Price J, Chepyala D, Young B, McGowan K, Slavish PJ, Mayasundari A, Jarusiewicz JA, Yang L, Li Y, Fu X, Garrett SH, Papizan JB, Kodali K, Peng J, Pruett Miller SM, Roussel MF, Mullighan C, Fischer M, Rankovic Z. Identification of Potent, Selective, and Orally Bioavailable Small-Molecule GSPT1/2 Degraders from a Focused Library of Cereblon Modulators. J Med Chem 2021; 64:7296-7311. [PMID: 34042448 PMCID: PMC8201443 DOI: 10.1021/acs.jmedchem.0c01313] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Whereas the PROTAC approach to target protein degradation greatly benefits from rational design, the discovery of small-molecule degraders relies mostly on phenotypic screening and retrospective target identification efforts. Here, we describe the design, synthesis, and screening of a large diverse library of thalidomide analogues against a panel of patient-derived leukemia and medulloblastoma cell lines. These efforts led to the discovery of potent and novel GSPT1/2 degraders displaying selectivity over classical IMiD neosubstrates, such as IKZF1/3, and high oral bioavailability in mice. Taken together, this study offers compound 6 (SJ6986) as a valuable chemical probe for studying the role of GSPT1/2 in vitro and in vivo, and it supports the utility of a diverse library of CRBN binders in the pursuit of targeting undruggable oncoproteins.
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Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Fatemeh Keramatnia
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Barbara Jonchere
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jeanine Price
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Divyabharathi Chepyala
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jamie A Jarusiewicz
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xiang Fu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shalandus H Garrett
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - James B Papizan
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Kiran Kodali
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shondra M Pruett Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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42
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Jiao J, Kavdia K, Pagala V, Palmer L, Finkelstein D, Fan Y, Peng J, Demontis F. An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome. G3-GENES GENOMES GENETICS 2021; 11:6273667. [PMID: 33974070 PMCID: PMC8495913 DOI: 10.1093/g3journal/jkab165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022]
Abstract
Recent evidence indicates that the composition of the ribosome is heterogeneous and that multiple types of specialized ribosomes regulate the synthesis of specific protein subsets. In Drosophila, we find that expression of the ribosomal RpS28 protein variants RpS28a and RpS28-like preferentially occurs in the germline, a tissue resistant to aging and that it significantly declines in skeletal muscle during aging. Muscle-specific overexpression of RpS28a at levels similar to those seen in the germline decreases early mortality and promotes the synthesis of a subset of proteins with known anti-aging roles, some of which have preferential expression in the germline. These findings indicate a contribution of specialized ribosomal proteins to the regulation of the muscle proteome during aging.
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Affiliation(s)
- Jianqin Jiao
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kanisha Kavdia
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lance Palmer
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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43
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Zheng Z, Zhang L, Cui XL, Yu X, Hsu PJ, Lyu R, Tan H, Mandal M, Zhang M, Sun HL, Sanchez Castillo A, Peng J, Clark MR, He C, Huang H. Control of Early B Cell Development by the RNA N 6-Methyladenosine Methylation. Cell Rep 2021; 31:107819. [PMID: 32610122 DOI: 10.1016/j.celrep.2020.107819] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA N6-methyladenosine (m6A) methylation is installed by the METTL3-METTL14 methyltransferase complex. This modification has critical regulatory roles in various biological processes. Here, we report that deletion of Mettl14 dramatically reduces mRNA m6A methylation in developing B cells and severely blocks B cell development in mice. Deletion of Mettl14 impairs interleukin-7 (IL-7)-induced pro-B cell proliferation and the large-pre-B-to-small-pre-B transition and causes dramatic abnormalities in gene expression programs important for B cell development. Suppression of a group of transcripts by cytoplasmic m6A reader YTHDF2 is critical to the IL-7-induced pro-B cell proliferation. In contrast, the block in the large-pre-B-to-small-pre-B transition is independent of YTHDF1 or YTHDF2 but is associated with a failure to properly upregulate key transcription factors regulating this transition. Our data highlight the important regulatory roles of the RNA m6A methylation and its reader proteins in early B cell development.
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Affiliation(s)
- Zhong Zheng
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Linda Zhang
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Xiao-Long Cui
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xianbin Yu
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Phillip J Hsu
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
| | - Ruitu Lyu
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Haiyan Tan
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Michelle Zhang
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Arantxa Sanchez Castillo
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA.
| | - Haochu Huang
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA.
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44
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Tomar AK, Rajak SK, Aslam Mk M, Chhikara N, Ojha SK, Nayak S, Chhillar S, Kumaresan A, Yadav S. Sub-fertility in crossbred bulls: Identification of proteomic alterations in spermatogenic cells using high throughput comparative proteomics approach. Theriogenology 2021; 169:65-75. [PMID: 33940217 DOI: 10.1016/j.theriogenology.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/11/2021] [Accepted: 04/20/2021] [Indexed: 01/01/2023]
Abstract
The present study was carried out to compare the proteomic profiles of spermatogenic cells of crossbred and zebu cattle in an effort to understand the possible reasons for a higher incidence of sub-fertility in crossbred bulls. The spermatogenic cells collected from the testes of pre-pubertal (6 mo) and adult (24 mo) crossbred and zebu males through fine needle aspiration were proliferated in vitro, and proteomic profiling was done using a shotgun proteomics approach. The age- and species-specific variations in the expression level of proteins were identified in spermatogenic cells. The number of differentially expressed proteins (DEPs) identified in pre-pubertal zebu and crossbred was 546, while 579 DEPs were identified between adult zebu and crossbred bulls. Out of these, 194 DEPS were common to these groups and 40 DEPs displayed a fold change ≥2. However, only 20 proteins exhibited similar expression variation trends (upregulated or downregulated) among pre-pubertal as well as adult zebu and crossbred bulls. Out of these 20 DEPs, 13 proteins were upregulated, and 7 proteins were downregulated in spermatogenic cells of zebu compared to crossbred bulls. Among the upregulated proteins were RPLP2, PAXIP1, calumenin, prosaposin, GTF2F1, TMP2, ubiquitin conjugation factor E4A, COL1A2, vimentin, protein FAM13A, peripherin, GFPT2, and GRP78. Seven proteins that were downregulated in zebu bulls compared to crossbred included APOA1, G patch domain-containing protein 1, NAD P transhydrogenase mitochondrial, glutamyl aminopeptidase, synaptojanin 1 fragment, Arf GAP with SH3 domain ANK repeat and PH domain-containing protein 1, and protein transport protein sec16B. It was inferred that the proteins associated with sperm function and fertilization processes, such as calumenin, prosaposin, vimentin, GRP78, and APOA1 could be studied further to understand the precise cause of subfertility in crossbred bulls.
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Affiliation(s)
- Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Shailendra Kumar Rajak
- Theriogenology Laboratory, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Muhammad Aslam Mk
- Theriogenology Laboratory, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Nirmal Chhikara
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sanjay Kumar Ojha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Samiksha Nayak
- Theriogenology Laboratory, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Shivani Chhillar
- Theriogenology Laboratory, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Arumugam Kumaresan
- Theriogenology Laboratory, ICAR-National Dairy Research Institute, Karnal, 132001, India.
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
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45
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Fingleton E, Li Y, Roche KW. Advances in Proteomics Allow Insights Into Neuronal Proteomes. Front Mol Neurosci 2021; 14:647451. [PMID: 33935646 PMCID: PMC8084103 DOI: 10.3389/fnmol.2021.647451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
Protein–protein interaction networks and signaling complexes are essential for normal brain function and are often dysregulated in neurological disorders. Nevertheless, unraveling neuron- and synapse-specific proteins interaction networks has remained a technical challenge. New techniques, however, have allowed for high-resolution and high-throughput analyses, enabling quantification and characterization of various neuronal protein populations. Over the last decade, mass spectrometry (MS) has surfaced as the primary method for analyzing multiple protein samples in tandem, allowing for the precise quantification of proteomic data. Moreover, the development of sophisticated protein-labeling techniques has given MS a high temporal and spatial resolution, facilitating the analysis of various neuronal substructures, cell types, and subcellular compartments. Recent studies have leveraged these novel techniques to reveal the proteomic underpinnings of well-characterized neuronal processes, such as axon guidance, long-term potentiation, and homeostatic plasticity. Translational MS studies have facilitated a better understanding of complex neurological disorders, such as Alzheimer’s disease (AD), Schizophrenia (SCZ), and Autism Spectrum Disorder (ASD). Proteomic investigation of these diseases has not only given researchers new insight into disease mechanisms but has also been used to validate disease models and identify new targets for research.
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Affiliation(s)
- Erin Fingleton
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, United States
| | - Yan Li
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, United States
| | - Katherine W Roche
- National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, United States
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46
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Yu K, Niu M, Wang H, Li Y, Wu Z, Zhang B, Haroutunian V, Peng J. Global Profiling of Lysine Accessibility to Evaluate Protein Structure Changes in Alzheimer's Disease. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:936-945. [PMID: 33683887 PMCID: PMC8255072 DOI: 10.1021/jasms.0c00450] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The linear sequence of amino acids in a protein folds into a 3D structure to execute protein activity and function, but it is still challenging to profile the 3D structure at the proteome scale. Here, we present a method of native protein tandem mass tag (TMT) profiling of Lys accessibility and its application to investigate structural alterations in human brain specimens of Alzheimer's disease (AD). In this method, proteins are extracted under a native condition, labeled by TMT reagents, followed by trypsin digestion and peptide analysis using two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). The method quantifies Lys labeling efficiency to evaluate its accessibility on the protein surface, which may be affected by protein conformations, protein modifications, and/or other molecular interactions. We systematically optimized the amount of TMT reagents, reaction time, and temperature and then analyzed protein samples under multiple conditions, including different labeling time (5 and 30 min), heat treatment, AD and normal human cases. The experiment profiled 15370 TMT-labeled peptides in 4475 proteins. As expected, the heat treatment led to extensive changes in protein conformations, with 17% of the detected proteome displaying differential labeling. Compared to the normal controls, AD brain showed different Lys accessibility of tau and RNA splicing complexes, which are the hallmarks of AD pathology, as well as proteins involved in transcription, mitochondrial, and synaptic functions. To eliminate the possibility that the observed differential Lys labeling was caused by protein level change, the whole proteome was quantified with standard TMT-LC/LC-MS/MS for normalization. Thus, this native protein TMT method enables the proteome-wide measurement of Lys accessibility, representing a straightforward strategy to explore protein structure in any biological system.
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Affiliation(s)
- Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mingming Niu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multi-scale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY 10468, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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47
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Hunt LC, Schadeberg B, Stover J, Haugen B, Pagala V, Wang YD, Puglise J, Barton ER, Peng J, Demontis F. Antagonistic control of myofiber size and muscle protein quality control by the ubiquitin ligase UBR4 during aging. Nat Commun 2021; 12:1418. [PMID: 33658508 PMCID: PMC7930053 DOI: 10.1038/s41467-021-21738-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
Sarcopenia is a degenerative condition that consists in age-induced atrophy and functional decline of skeletal muscle cells (myofibers). A common hypothesis is that inducing myofiber hypertrophy should also reinstate myofiber contractile function but such model has not been extensively tested. Here, we find that the levels of the ubiquitin ligase UBR4 increase in skeletal muscle with aging, and that UBR4 increases the proteolytic activity of the proteasome. Importantly, muscle-specific UBR4 loss rescues age-associated myofiber atrophy in mice. However, UBR4 loss reduces the muscle specific force and accelerates the decline in muscle protein quality that occurs with aging in mice. Similarly, hypertrophic signaling induced via muscle-specific loss of UBR4/poe and of ESCRT members (HGS/Hrs, STAM, USP8) that degrade ubiquitinated membrane proteins compromises muscle function and shortens lifespan in Drosophila by reducing protein quality control. Altogether, these findings indicate that these ubiquitin ligases antithetically regulate myofiber size and muscle protein quality control.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bronwen Schadeberg
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jared Stover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benard Haugen
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vishwajeeth Pagala
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason Puglise
- College of Health & Human Performance Applied Physiology & Kinesiology, University of Florida, Gainesville, FL, USA
| | - Elisabeth R Barton
- College of Health & Human Performance Applied Physiology & Kinesiology, University of Florida, Gainesville, FL, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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48
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Yu K, Wang Z, Wu Z, Tan H, Mishra A, Peng J. High-Throughput Profiling of Proteome and Posttranslational Modifications by 16-Plex TMT Labeling and Mass Spectrometry. Methods Mol Biol 2021; 2228:205-224. [PMID: 33950493 PMCID: PMC8458009 DOI: 10.1007/978-1-0716-1024-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mass spectrometry (MS)-based proteomic profiling of whole proteome and protein posttranslational modifications (PTMs) is a powerful technology to measure the dynamics of proteome with high throughput and deep coverage. The reproducibility of quantification benefits not only from the fascinating developments in high-performance liquid chromatography (LC) and high-resolution MS with enhanced scan rates but also from the invention of multiplexed isotopic labeling strategies, such as the tandem mass tags (TMT). In this chapter, we introduce a 16-plex TMT-LC/LC-MS/MS protocol for proteomic profiling of biological and clinical samples. The protocol includes protein extraction, enzymatic digestion, PTM peptide enrichment, TMT labeling, and two-dimensional reverse-phase liquid chromatography fractionation coupled with tandem mass spectrometry (MS/MS) analysis, followed by computational data processing. In general, more than 10,000 proteins and tens of thousands of PTM sites (e.g., phosphorylation and ubiquitination) can be confidently quantified. This protocol provides a general protein measurement tool, enabling the dissection of protein dysregulation in any biological samples and human diseases.
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Affiliation(s)
- Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Liu D, Yang S, Kavdia K, Sifford JM, Wu Z, Xie B, Wang Z, Pagala VR, Wang H, Yu K, Dey KK, High AA, Serrano GE, Beach TG, Peng J. Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry. J Proteome Res 2020; 20:337-345. [PMID: 33175545 DOI: 10.1021/acs.jproteome.0c00426] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tandem mass tag (TMT)-based mass spectrometry (MS) enables deep proteomic profiling of more than 10,000 proteins in complex biological samples but requires up to 100 μg protein in starting materials during a standard analysis. Here, we present a streamlined protocol to quantify more than 9000 proteins with 0.5 μg protein per sample by 16-plex TMT coupled with two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). In this protocol, we optimized multiple conditions to reduce sample loss, including processing each sample in a single tube to minimize surface adsorption, increasing digestion enzymes to shorten proteolysis and function as carriers, eliminating a desalting step between digestion and TMT labeling, and developing miniaturized basic pH LC for prefractionation. By profiling 16 identical human brain tissue samples of Alzheimer's disease (AD), vascular dementia (VaD), and non-dementia controls, we directly compared this new microgram-scale protocol to the standard-scale protocol, quantifying 9116 and 10,869 proteins, respectively. Importantly, bioinformatics analysis indicated that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. Thus, this newly developed protocol is of general application for deep proteomics analysis of biological and clinical samples at sub-microgram levels.
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Affiliation(s)
- Danting Liu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Shu Yang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jeffrey M Sifford
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Boer Xie
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Vishwajeeth R Pagala
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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50
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Rausch M, Weiss A, Zoetemelk M, Piersma SR, Jimenez CR, van Beijnum JR, Nowak-Sliwinska P. Optimized Combination of HDACI and TKI Efficiently Inhibits Metabolic Activity in Renal Cell Carcinoma and Overcomes Sunitinib Resistance. Cancers (Basel) 2020; 12:E3172. [PMID: 33126775 PMCID: PMC7693411 DOI: 10.3390/cancers12113172] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/11/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is characterized by high histone deacetylase (HDAC) activity triggering both cell motility and the development of metastasis. Therefore, there is an unmet need to establish innovative strategies to advance the use of HDAC inhibitors (HDACIs). We selected a set of tyrosine kinase inhibitors (TKIs) and HDACIs to test them in combination, using the validated therapeutically guided multidrug optimization (TGMO) technique based on experimental testing and in silico data modeling. We determined a synergistic low-dose three-drug combination decreasing the cell metabolic activity in metastatic ccRCC cells, Caki-1, by over 80%. This drug combination induced apoptosis and showed anti-angiogenic activity, both in original Caki-1 and in sunitinib-resistant Caki-1 cells. Through phosphoproteomic analysis, we revealed additional targets to improve the translation of this combination in 3-D (co-)culture systems. Cell-cell and cell-environment interactions increased, reverting the invasive and metastatic phenotype of Caki-1 cells. Our data suggest that our optimized low-dose drug combination is highly effective in complex in vitro settings and promotes the activity of HDACIs.
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Affiliation(s)
- Magdalena Rausch
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
| | - Andrea Weiss
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Marloes Zoetemelk
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
| | - Sander R. Piersma
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan, 1117 Amsterdam, The Netherlands; (S.R.P.); (C.R.J.)
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1117 Amsterdam, The Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan, 1117 Amsterdam, The Netherlands; (S.R.P.); (C.R.J.)
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1117 Amsterdam, The Netherlands
| | - Judy R. van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-Location VUmc, VU University Amsterdam, 1117 Amsterdam, The Netherlands;
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (A.W.); (M.Z.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
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