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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [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: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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2
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Tabata S, Matsuda K, Soeda S, Nagai K, Izumi Y, Takahashi M, Motomura Y, Ichikawa Nagasato A, Moro K, Bamba T, Okada M. NFκB dynamics-dependent epigenetic changes modulate inflammatory gene expression and induce cellular senescence. FEBS J 2024. [PMID: 39011799 DOI: 10.1111/febs.17227] [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: 12/19/2023] [Revised: 04/14/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
Upregulation of nuclear factor κB (NFκB) signaling is a hallmark of aging and a major cause of age-related chronic inflammation. However, its effect on cellular senescence remains unclear. Here, we show that alteration of NFκB nuclear dynamics from oscillatory to sustained by depleting a negative feedback regulator of NFκB pathway, NFκB inhibitor alpha (IκBα), in the presence of tumor necrosis factor α (TNFα) promotes cellular senescence. Sustained NFκB activity enhanced inflammatory gene expression through increased NFκB-DNA binding and slowed the cell cycle. IκBα protein was decreased under replicative or oxidative stress in vitro. Furthermore, a decrease in IκBα protein and an increase in DNA-NFκB binding at the transcription start sites of age-associated genes in aged mouse hearts suggested that nuclear NFκB dynamics may play a critical role in the progression of aging. Our study suggests that nuclear NFκB dynamics-dependent epigenetic changes regulated over time in a living system, possibly through a decrease in IκBα, enhance the expression of inflammatory genes to advance the cells to a senescent state.
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Affiliation(s)
- Sho Tabata
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Japan
| | - Keita Matsuda
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Japan
| | - Shou Soeda
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Japan
| | - Kenshiro Nagai
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masatomo Takahashi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasutaka Motomura
- Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory for Innate Immune Systems, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Japan
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | | | - Kazuyo Moro
- Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory for Innate Immune Systems, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Japan
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Laboratory for Innate Immune Systems, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mariko Okada
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Japan
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3
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Zhou Z, Wang J, Wang J, Yang S, Wang R, Zhang G, Li Z, Shi R, Wang Z, Lu Q. Deciphering the tumor immune microenvironment from a multidimensional omics perspective: insight into next-generation CAR-T cell immunotherapy and beyond. Mol Cancer 2024; 23:131. [PMID: 38918817 PMCID: PMC11201788 DOI: 10.1186/s12943-024-02047-2] [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: 03/25/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Tumor immune microenvironment (TIME) consists of intra-tumor immunological components and plays a significant role in tumor initiation, progression, metastasis, and response to therapy. Chimeric antigen receptor (CAR)-T cell immunotherapy has revolutionized the cancer treatment paradigm. Although CAR-T cell immunotherapy has emerged as a successful treatment for hematologic malignancies, it remains a conundrum for solid tumors. The heterogeneity of TIME is responsible for poor outcomes in CAR-T cell immunotherapy against solid tumors. The advancement of highly sophisticated technology enhances our exploration in TIME from a multi-omics perspective. In the era of machine learning, multi-omics studies could reveal the characteristics of TIME and its immune resistance mechanism. Therefore, the clinical efficacy of CAR-T cell immunotherapy in solid tumors could be further improved with strategies that target unfavorable conditions in TIME. Herein, this review seeks to investigate the factors influencing TIME formation and propose strategies for improving the effectiveness of CAR-T cell immunotherapy through a multi-omics perspective, with the ultimate goal of developing personalized therapeutic approaches.
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Affiliation(s)
- Zhaokai Zhou
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jiahui Wang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Nephrology, Union Medical College Hospital, Chinese Academy of Medical Sciences, PekingBeijing, 100730, China
| | - Jiaojiao Wang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Shuai Yang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ruizhi Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Run Shi
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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Wu C, Zhang S, Hou C, Byers S, Ma J. In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment. Anal Chem 2024; 96:8254-8262. [PMID: 38728223 PMCID: PMC11140682 DOI: 10.1021/acs.analchem.3c02150] [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: 05/17/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.
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Affiliation(s)
- Ci Wu
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, China
| | - Shen Zhang
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha 410000, China
| | - Chunyan Hou
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Stephen Byers
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Junfeng Ma
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
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5
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Luo R, Su J, Zhang W, Huang W, Zhou Q, Sun P, Zhao Y. Targeted delivery of NO donor and ROS scavenger for synergistic treatment of rheumatoid arthritis. Biomed Pharmacother 2024; 174:116540. [PMID: 38579400 DOI: 10.1016/j.biopha.2024.116540] [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: 12/09/2023] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
Rheumatoid arthritis (RA) is characterized by high level of reactive oxygen species (ROS) and proinflammatory cytokines, which facilitate the activation of the inflammatory signaling such as NF-κB pathway and exacerbate the development of inflammation. Herein, we designed a nanodrug by encapsulating the NO donor S-nitrosoglutathione (GSNO) into an emulsion and coating the surface with a polydopamine (PDA) layer to yield GSNO@PDA, which simultaneously scavenged the extra ROS and suppressed NF-κB signaling for potent RA treatment. To enhance the cellular uptake and NO generation efficiency, dextran sulfate (DS) and Cu2+ were anchored on the surface of GSNO@PDA to obtain the final formulation GSNO@PDA@DS. Our results demonstrated that GSNO@PDA@DS were successfully prepared and the modification of DS effectively boosted the cellular uptake of GSNO@PDA@DS. Moreover, GSNO@PDA@DS lowered cellular ROS and elevated intracellular NO, resulting in a decrease of M1 phenotype, inhibition of NF-κB pathway and down-regulation of proinflammatory cytokine tumor necrosis factor-α (TNF-α). Further in vivo studies confirmed that GSNO@PDA@DS significantly relieved symptoms and bone erosion by regulating the microenvironment of RA, highlighting the potential of GSNO@PDA@DS for RA therapy through ROS scavenging and NO-mediated suppression of inflammatory signaling.
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Affiliation(s)
- Rongrong Luo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jingjing Su
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Wenying Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Wenguang Huang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Qianqian Zhou
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Pengchao Sun
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Henan Province, Zhengzhou University, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Yongxing Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; Henan Key Laboratory of Nanomedicine for Targeting Diagnosis and Treatment, Henan Province, Zhengzhou University, Zhengzhou 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, PR China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450052, PR China.
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6
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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Long Q, Zhang Z, Li Y, Zhong Y, Liu H, Chang L, Ying Y, Zuo T, Wang Y, Xu P. Phosphoproteome reveals long-term potentiation deficit following treatment of ultra-low dose soman exposure in mice. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132211. [PMID: 37572605 DOI: 10.1016/j.jhazmat.2023.132211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Soman, a warfare nerve agent, poses a significant threat by inducing severe brain damage that often results in death. Nonetheless, our understanding of the biological changes underlying persistent neurocognitive dysfunction caused by low dosage of soman remains limited. This study used mice to examine the effects of different doses of soman over time. Phosphoproteomic analysis of the mouse brain is the first time to be used to detect toxic effects of soman at such low or ultra-low doses, which were undetectable based on measuring the activity of acetylcholinesterase at the whole-animal level. We also found that phosphoproteome alterations could accurately track the soman dose, irrespective of the sampling time. Moreover, phosphoproteome revealed a rapid and adaptive cellular response to soman exposure, with the points of departure 8-38 times lower than that of acetylcholinesterase activity. Impaired long-term potentiation was identified in phosphoproteomic studies, which was further validated by targeted quantitative proteomics, immunohistochemistry, and immunofluorescence analyses, with significantly increased levels of phosphorylation of protein phosphatase 1 in the hippocampus following soman exposure. This increase in phosphorylation inhibits long-term potentiation, ultimately leading to long-term memory dysfunction in mice.
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Affiliation(s)
- Qi Long
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China
| | - Yuxu Zhong
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Hongyan Liu
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Ying Ying
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Yong'an Wang
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China.
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8
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Wei H, Wu C, Yuan Y, Lai L. Uncovering the Achilles heel of genetic heterogeneity: machine learning-based classification and immunological properties of necroptosis clusters in Alzheimer's disease. Front Aging Neurosci 2023; 15:1249682. [PMID: 37799623 PMCID: PMC10548137 DOI: 10.3389/fnagi.2023.1249682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Background Alzheimer's disease (AD) is an age-associated neurodegenerative disease, and the currently available diagnostic modalities and therapeutic agents are unsatisfactory due to its high clinical heterogeneity. Necroptosis is a common type of programmed cell death that has been shown to be activated in AD. Methods In this study, we first investigated the expression profiles of necroptosis-related genes (NRGs) and the immune landscape of AD based on GSE33000 dataset. Next, the AD samples in the GSE33000 dataset were extracted and subjected to consensus clustering based upon the differentially expressed NRGs. Key genes associated with necroptosis clusters were identified using Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm, and then intersected with the key gene related to AD. Finally, we developed a diagnostic model for AD by comparing four different machine learning approaches. The discrimination performance and clinical relevance of the diagnostic model were assessed using various evaluation metrics, including the nomogram, calibration plot, decision curve analysis (DCA), and independent validation datasets. Results Aberrant expression patterns of NRGs and specific immune landscape were identified in the AD samples. Consensus clustering revealed that patients in the GSE33000 dataset could be classified into two necroptosis clusters, each with distinct immune landscapes and enriched pathways. The Extreme Gradient Boosting (XGB) was found to be the most optimal diagnostic model for the AD based on the predictive ability and reliability of the models constructed by four machine learning approaches. The five most important variables, including ACAA2, BHLHB4, CACNA2D3, NRN1, and TAC1, were used to construct a five-gene diagnostic model. The constructed nomogram, calibration plot, DCA, and external independent validation datasets exhibited outstanding diagnostic performance for AD and were closely related with the pathologic hallmarks of AD. Conclusion This work presents a novel diagnostic model that may serve as a framework to study disease heterogeneity and provide a plausible mechanism underlying neuronal loss in AD.
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Affiliation(s)
- Huangwei Wei
- Department of Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chunle Wu
- Department of Blood Transfusion, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yulin Yuan
- Department of Laboratory, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lichuan Lai
- Department of Laboratory, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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9
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Wang Y, Ye R, Fan L, Zhao X, Li L, Zheng H, Qiu Y, He X, Lu Y. A TNF-α blocking peptide that reduces NF-κB and MAPK activity for attenuating inflammation. Bioorg Med Chem 2023; 92:117420. [PMID: 37573821 DOI: 10.1016/j.bmc.2023.117420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023]
Abstract
Overexpression of tumor necrosis factor-α (TNF-α) is implicated in many inflammatory diseases, including septic shock, hepatitis, asthma, insulin resistance and autoimmune diseases, such as rheumatoid arthritis and Crohn's disease. The TNF-α signaling pathway is a valuable target, and anti-TNF-α drugs are successfully used to treat autoimmune and inflammatory diseases. Here, we study anti-inflammatory activity of an anti-TNF-α peptide (SN1-13, DEFHLELHLYQSW). In the cellular level assessment, SN1-13 inhibited TNF-α-induced cytotoxicity and blocks TNF-α-triggered signaling activities (IC50 = 15.40 μM). Moreover, the potential binding model between SN1-13 and TNF-α/TNFRs conducted through molecular docking revealed that SN1-13 could stunt TNF-α mediated signaling thought blocking TNF-α and its receptor TNFR1 and TNFR2. These results suggest that SN1-13 would be a potential lead peptide to treat TNF-α-mediated inflammatory diseases.
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Affiliation(s)
- Yue Wang
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130013, China
| | - Ruiwei Ye
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Liming Fan
- Department of Pharmacy, Shanghai Pudong New Area People's Hospital, Shanghai 201299, China
| | - Xin Zhao
- Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072,China
| | - Linxue Li
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Hao Zheng
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yan Qiu
- Department of Pharmacy, Shanghai Pudong New Area People's Hospital, Shanghai 201299, China.
| | - Xiuxia He
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130013, China.
| | - Yiming Lu
- School of Medicine, Shanghai University, Shanghai 200444, China; Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072,China.
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10
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Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun 2023; 14:3599. [PMID: 37328457 PMCID: PMC10276052 DOI: 10.1038/s41467-023-39347-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
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Affiliation(s)
- Ana Martínez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kyle Fort
- Thermo Fisher Scientific, Bremen, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Yue Xuan
- Thermo Fisher Scientific, Bremen, Germany.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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11
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Wen C, Wu X, Lin G, Yan W, Gan G, Xu X, Chen XY, Chen X, Liu X, Fu G, Zhong CQ. Evaluation of DDA Library-Free Strategies for Phosphoproteomics and Ubiquitinomics Data-Independent Acquisition Data. J Proteome Res 2023. [PMID: 37256709 DOI: 10.1021/acs.jproteome.2c00735] [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: 06/02/2023]
Abstract
Phosphoproteomics and ubiquitinomics data-independent acquisition (DIA) mass spectrometry (MS) data is typically analyzed by using a data-dependent acquisition (DDA) spectral library. The performance of various library-free strategies for analyzing phosphoproteomics and ubiquitinomics DIA MS data has not been evaluated. In this study, we systematically compare four commonly used DDA library-free approaches including Spectronaut's directDIA, DIA-Umpire, DIA-MSFragger, and in silico-predicted library for analysis of phosphoproteomics SWATH, DIA, and diaPASEF data as well as ubiquitinomics diaPASEF data. Spectronaut's directDIA shows the highest sensitivity for phosphopeptide detection not only in synthetic phosphopeptide samples but also in phosphoproteomics SWATH-MS and DIA data from real biological samples, when compared to the other three library-free strategies. For phosphoproteomics diaPASEF data, Spectronaut's directDIA and the in silico-predicted library based on DIA-NN identify almost the same number of phosphopeptides as a project-specific DDA spectral library. However, only about 30% of the total phosphopeptides are commonly identified, suggesting that the library-free strategies for phospho-diaPASEF data need further improvement in terms of sensitivity. For ubiquitinomics diaPASEF data, the in silico-predicted library performs the best among the four workflows and detects ∼50% more K-GG peptides than a project-specific DDA spectral library. Our results demonstrate that Spectronaut's directDIA is suitable for the analysis of phosphoproteomics SWATH-MS and DIA MS data, while the in silico-predicted library based on DIA-NN shows substantial advantages for ubiquitinomics diaPASEF MS data.
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Affiliation(s)
- Chengwen Wen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xiurong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Guanzhong Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Wei Yan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Guohong Gan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xiao Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xiang-Yu Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd., Wuhan 430074, Hubei, China
| | - Xianming Liu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200030, China
| | - Guo Fu
- School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Chuan-Qi Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
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12
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Park JW, Tyl MD, Cristea IM. Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection. Biomolecules 2023; 13:biom13050869. [PMID: 37238738 DOI: 10.3390/biom13050869] [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: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.
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Affiliation(s)
- Ji Woo Park
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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13
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Swietlik JJ, Bärthel S, Falcomatà C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F. Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun 2023; 14:2642. [PMID: 37156840 PMCID: PMC10167354 DOI: 10.1038/s41467-023-38171-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.
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Affiliation(s)
- Jonathan J Swietlik
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Diana Fink
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Peter Landgraf
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniela C Dieterich
- Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Henrik Daub
- NEOsphere Biotechnologies GmbH, Martinsried, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany.
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14
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Li YX, Jiao P, Wang XP, Wang JP, Feng F, Bao BW, Dong YW, Luoreng ZM, Wei DW. RNA-seq reveals the role of miR-223 in alleviating inflammation of bovine mammary epithelial cells. Res Vet Sci 2023; 159:257-266. [PMID: 37192556 DOI: 10.1016/j.rvsc.2023.04.012] [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: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
Bovine mammary epithelial cells (bMECs) are involved in the early defense against the invasion of intramammary pathogens and are essential for the health of bovine mammary gland. MicroRNA (MiRNA) is a key factor that regulates cell state and physiological function. In the present study, the transcriptome profiles of miR-223 inhibitor transfection group (miR-223_Inhibitor) and negative control inhibitor transfection group (NC_Inhibitor) within bMECs were detected via the RNA sequencing (RNA-seq) platform. Based on these experiments, the differentially expressed mRNAs (DE-mRNAs) of the miR-223_Inhibitor transfection group were screened, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional analyses of DE-mRNAs were performed. The results revealed that compared with the NC_Inhibitor, 224 differentially expressed genes (DEGs) were identified in the miR-223_Inhibitor, including 184 upregulated and 40 downregulated genes. The functional annotation of the above DEGs indicated that some of these genes are involved in the immune response generated by extracellular substance stimulation, regulation of the activity of cytokines and chemokines, and the immune signaling pathways of NF-κB and TNF. Meanwhile, miR-223_inhibitor upregulated the immune key genes IRF1 and NFκBIA, cytokines IL-6 and IL-24, as well as chemokines CXCL3, CXCL5, and CCR6, triggering a signaling cascade response that exacerbated inflammation in bMECs. These results suggested that miR-223 plays an important role in inhibiting the inflammatory response and maintaining the stability of bMECs, and is a potential target for treating mastitis in dairy cows.
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Affiliation(s)
- Yan-Xia Li
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Peng Jiao
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Xing-Ping Wang
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Jin-Peng Wang
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Fen Feng
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Bin-Wu Bao
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Yi-Wen Dong
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
| | - Zhuo-Ma Luoreng
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China.
| | - Da-Wei Wei
- School of Agriculture, Ningxia University, Yinchuan, China; Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan, China
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15
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Yuan C, Liu L, Tayier B, Ma T, Guan L, Mu Y, Li Y. Experimental study on the optimization of ANM33 release in foam cells. Open Life Sci 2023; 18:20220564. [PMID: 36852402 PMCID: PMC9961968 DOI: 10.1515/biol-2022-0564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023] Open
Abstract
Given the miR-33's mechanistic relationships with multiple etiological factors in the pathogenesis of atherosclerosis (AS), we investigated the therapeutic potentials of dual-targeted microbubbles (HA-PANBs) in foam cell-specific release of anti-miR-33 (ANM33) oligonucleotides, resulting in the early prevention of AS progression and severity. The intracellular localization, loading optimization, and therapeutic effects of HA-PANBs were examined in detail in a co-cultured cell model of phagocytosis. Compared with non-targeting nanobubbles (NBs) and single-targeted microbubbles as controls, HA-PANBs efficiently delivered the ANM33 specifically to foam cells via sustained release, exhibiting its clinical value in mediating RNA silencing. Moreover, when used at a dose of 12 µg/mL HA-PANBs per 107 cells for 48 h, a higher release rate and drug efficacy were observed. Therefore, HA-PANBs, effectively targeting early AS foam cells, may represent a novel and optimal gene therapy approach for AS management.
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Affiliation(s)
- Chen Yuan
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Liyun Liu
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Baihetiya Tayier
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Ting Ma
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Lina Guan
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Yuming Mu
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
| | - Yanhong Li
- Department of Echocardiography, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China,Xinjiang Key Laboratory of Ultrasound Medicine, Urumqi, Xinjiang 830011, China
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16
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Tanzer MC. You are what you eat and how you digest it! A discussion on inflammatory efferocytosis. Front Cell Dev Biol 2023; 11:1132696. [PMID: 36846584 PMCID: PMC9947526 DOI: 10.3389/fcell.2023.1132696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Efferocytosis is a process by which phagocytes remove dead or dying cells. It is considered anti-inflammatory, as the removal process reduces potential inflammatory molecules originating from dead cells and results in the reprogramming of macrophages to an anti-inflammatory state. However, engulfment of infected dead cells, deregulated phagocytosis and perturbed digestion of apoptotic bodies induce inflammatory signalling pathways during efferocytosis. The affected inflammatory signalling molecules and the mechanism of activation are largely unknown. I discuss how the choice of dead cell cargo, the type of ingestion, and the digestion efficiency can influence phagocyte programming in the context of disease. I also present the latest findings, highlight knowledge gaps, and propose selected experimental approaches to fill them.
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17
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Horne CR, Samson AL, Murphy JM. The web of death: the expanding complexity of necroptotic signaling. Trends Cell Biol 2023; 33:162-174. [PMID: 35750616 DOI: 10.1016/j.tcb.2022.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 01/25/2023]
Abstract
The past decade has seen the emergence of the necroptosis programmed cell death pathway as an important contributor to the pathophysiology of myriad diseases. The receptor interacting protein kinase (RIPK)1 and RIPK3, and the pseudokinase executioner protein, mixed lineage kinase domain-like (MLKL), have grown to prominence as the core pathway components. Depending on cellular context, these proteins also serve as integrators of signals, such as post-translational modifications and protein or metabolite interactions, adding layers of complexity to pathway regulation. Here, we describe the emerging picture of the web of proteins that tune necroptotic signal transduction and how these events have diverged across species, presumably owing to selective pressures of pathogens upon the RIPK3-MLKL protein pair.
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Affiliation(s)
- Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - André L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
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18
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Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. Nat Commun 2023; 14:94. [PMID: 36609502 PMCID: PMC9822986 DOI: 10.1038/s41467-022-35740-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
A plethora of software suites and multiple classes of spectral libraries have been developed to enhance the depth and robustness of data-independent acquisition (DIA) data processing. However, how the combination of a DIA software tool and a spectral library impacts the outcome of DIA proteomics and phosphoproteomics data analysis has been rarely investigated using benchmark data that mimics biological complexity. In this study, we create DIA benchmark data sets simulating the regulation of thousands of proteins in a complex background, which are collected on both an Orbitrap and a timsTOF instruments. We evaluate four commonly used software suites (DIA-NN, Spectronaut, MaxDIA and Skyline) combined with seven different spectral libraries in global proteome analysis. Moreover, we assess their performances in analyzing phosphopeptide standards and TNF-α-induced phosphoproteome regulation. Our study provides a practical guidance on how to construct a robust data analysis pipeline for different proteomics studies implementing the DIA technique.
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19
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Franciosa G, Kverneland AH, Jensen AWP, Donia M, Olsen JV. Proteomics to study cancer immunity and improve treatment. Semin Immunopathol 2023; 45:241-251. [PMID: 36598558 PMCID: PMC10121539 DOI: 10.1007/s00281-022-00980-2] [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: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]
Abstract
Cancer survival and progression depend on the ability of tumor cells to avoid immune recognition. Advances in the understanding of cancer immunity and tumor immune escape mechanisms enabled the development of immunotherapeutic approaches. In patients with otherwise incurable metastatic cancers, immunotherapy resulted in unprecedented response rates with the potential for durable complete responses. However, primary and acquired resistance mechanisms limit the efficacy of immunotherapy. Further therapeutic advances require a deeper understanding of the interplay between immune cells and tumors. Most high-throughput studies within the past decade focused on an omics characterization at DNA and RNA level. However, proteins are the molecular effectors of genomic information; therefore, the study of proteins provides deeper understanding of cellular functions. Recent advances in mass spectrometry (MS)-based proteomics at a system-wide scale may allow translational and clinical discoveries by enabling the analysis of understudied post-translational modifications, subcellular protein localization, cell signaling, and protein-protein interactions. In this review, we discuss the potential contribution of MS-based proteomics to preclinical and clinical research findings in the context of tumor immunity and cancer immunotherapies.
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Affiliation(s)
- Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Anders H Kverneland
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Agnete W P Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marco Donia
- National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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20
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Abstract
Cell death, particularly that of tubule epithelial cells, contributes critically to the pathophysiology of kidney disease. A body of evidence accumulated over the past 15 years has ascribed a central pathophysiological role to a particular form of regulated necrosis, termed necroptosis, to acute tubular necrosis, nephron loss and maladaptive renal fibrogenesis. Unlike apoptosis, which is a non-immunogenic process, necroptosis results in the release of cellular contents and cytokines, which triggers an inflammatory response in neighbouring tissue. This necroinflammatory environment can lead to severe organ dysfunction and cause lasting tissue injury in the kidney. Despite evidence of a link between necroptosis and various kidney diseases, there are no available therapeutic options to target this process. Greater understanding of the molecular mechanisms, triggers and regulators of necroptosis in acute and chronic kidney diseases may identify shortcomings in current approaches to therapeutically target necroptosis regulators and lead to the development of innovative therapeutic approaches.
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21
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Zhao L, Hou C, Yan N. Neuroinflammation in retinitis pigmentosa: Therapies targeting the innate immune system. Front Immunol 2022; 13:1059947. [PMID: 36389729 PMCID: PMC9647059 DOI: 10.3389/fimmu.2022.1059947] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is an important cause of irreversible blindness worldwide and lacks effective treatment strategies. Although mutations are the primary cause of RP, research over the past decades has shown that neuroinflammation is an important cause of RP progression. Due to the abnormal activation of immunity, continuous sterile inflammation results in neuron loss and structural destruction. Therapies targeting inflammation have shown their potential to attenuate photoreceptor degeneration in preclinical models. Regardless of variations in genetic background, inflammatory modulation is emerging as an important role in the treatment of RP. We summarize the evidence for the role of inflammation in RP and mention therapeutic strategies where available, focusing on the modulation of innate immune signals, including TNFα signaling, TLR signaling, NLRP3 inflammasome activation, chemokine signaling and JAK/STAT signaling. In addition, we describe epigenetic regulation, the gut microbiome and herbal agents as prospective treatment strategies for RP in recent advances.
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Affiliation(s)
- Ling Zhao
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Hou
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Naihong Yan
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Naihong Yan,
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22
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Ciuffa R, Uliana F, Mannion J, Mehnert M, Tenev T, Marulli C, Satanowski A, Keller LML, Rodilla Ramírez PN, Ori A, Gstaiger M, Meier P, Aebersold R. Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics. Proc Natl Acad Sci U S A 2022; 119:e2117175119. [PMID: 36179048 PMCID: PMC9546619 DOI: 10.1073/pnas.2117175119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 07/28/2022] [Indexed: 12/03/2022] Open
Abstract
Protein-protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes-a goal that remains an unsolved challenge. Here we describe an experimental/computational strategy to achieve a modeling of PPIs that considers contextual information. This strategy defines the composition, stoichiometry, temporal organization, and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF-receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function.
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Affiliation(s)
- Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Federico Uliana
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonathan Mannion
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Cathy Marulli
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | | | | | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
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23
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [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: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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24
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Dräger NM, Sattler SM, Huang CTL, Teter OM, Leng K, Hashemi SH, Hong J, Aviles G, Clelland CD, Zhan L, Udeochu JC, Kodama L, Singleton AB, Nalls MA, Ichida J, Ward ME, Faghri F, Gan L, Kampmann M. A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states. Nat Neurosci 2022; 25:1149-1162. [PMID: 35953545 PMCID: PMC9448678 DOI: 10.1038/s41593-022-01131-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/24/2022] [Indexed: 12/12/2022]
Abstract
Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform to systematically elucidate functional consequences of genetic perturbations in human induced pluripotent stem cell-derived microglia. We developed an efficient 8-day protocol for the generation of microglia-like cells based on the inducible expression of six transcription factors. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the ‘druggable genome’. These screens uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing as the readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identified regulators of these states. A disease-associated state characterized by osteopontin (SPP1) expression was selectively depleted by colony-stimulating factor-1 (CSF1R) inhibition. Thus, our platform can systematically uncover regulators of microglial states, enabling their functional characterization and therapeutic targeting. Dräger et al. establish a rapid, scalable platform for iPSC-derived microglia. CRISPRi/a screens uncover roles of disease-associated genes in phagocytosis, and regulators of disease-relevant microglial states that can be targeted pharmacologically.
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Affiliation(s)
- Nina M Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Sydney M Sattler
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | - Olivia M Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Sayed Hadi Hashemi
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason Hong
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Giovanni Aviles
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Claire D Clelland
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Lihong Zhan
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Joe C Udeochu
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Lay Kodama
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew B Singleton
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Justin Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA.,Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,Data Tecnica International, LLC, Glen Echo, MD, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA. .,Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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25
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Skowronek P, Thielert M, Voytik E, Tanzer MC, Hansen FM, Willems S, Karayel Ö, Brunner AD, Meier F, Mann M. Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF. Mol Cell Proteomics 2022; 21:100279. [PMID: 35944843 PMCID: PMC9465115 DOI: 10.1016/j.mcpro.2022.100279] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022] Open
Abstract
Data-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry–based proteomics because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation–serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility (IM) separated quadrupole time-of-flight mass spectrometer. This requires alignment of the IM separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared with DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in the m/z and IM plane. This is implemented in the freely available py_diAID (Python package for DIA with an automated isolation design) package. In combination with in-depth project-specific proteomics libraries and the Evosep liquid chromatography system, we reproducibly identified over 7700 proteins in a human cancer cell line in 44 min with quadruplicate single-shot injections at high sensitivity. Even at a throughput of 100 samples per day (11 min liquid chromatography gradients), we consistently quantified more than 6000 proteins in mammalian cell lysates by injecting four replicates. We found that optimal dia-PASEF window placement facilitates in-depth phosphoproteomics with very high sensitivity, quantifying more than 35,000 phosphosites in a human cancer cell line stimulated with an epidermal growth factor in triplicate 21 min runs. This covers a substantial part of the regulated phosphoproteome with high sensitivity, opening up for extensive systems-biological studies. Optimal dia-PASEF window design with py_diAID combined with deep libraries. Quantification of the HeLa cell proteome to a depth of >7700 in only 44 min. Ion mobility–resolved phosphoproteomics determines >35,000 class I phosphosites. py_diAID is freely available as GUI, CLI, and Python modules.
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26
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A proteomic perspective on TNF-mediated signalling and cell death. Biochem Soc Trans 2022; 50:13-20. [PMID: 35166321 PMCID: PMC9022982 DOI: 10.1042/bst20211114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 01/19/2023]
Abstract
The tumour necrosis factor (TNF) is the most potent inducer of cell death amongst cytokines. It is crucial for processes including homeostasis, the development of the immune system and fighting infections. However, high levels of TNF due to genetic disorders or persistent infections can contribute to autoinflammatory and autoimmune diseases or life-threatening conditions like sepsis. These diseases generally display increased levels of cell death, which, downstream of the TNF receptor, can either be caspase-dependent (apoptosis) or caspase-independent (necroptosis). Significant efforts have been invested in unravelling and manipulating signalling mechanisms regulating these two different types of cell death. Here I discuss how modern proteomic approaches like phosphoproteomics and secretomics provide a novel perspective on this central cytokine and its effect on inflammation and cell survival.
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27
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Dichtl S, Sanin DE, Koss CK, Willenborg S, Petzold A, Tanzer MC, Dahl A, Kabat AM, Lindenthal L, Zeitler L, Satzinger S, Strasser A, Mann M, Roers A, Eming SA, El Kasmi KC, Pearce EJ, Murray PJ. Gene-selective transcription promotes the inhibition of tissue reparative macrophages by TNF. Life Sci Alliance 2022; 5:5/4/e202101315. [PMID: 35027468 PMCID: PMC8761491 DOI: 10.26508/lsa.202101315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/24/2022] Open
Abstract
Pro-inflammatory TNF is a highly gene-selective inhibitor of the gene expression program of tissue repair and wound healing macrophages. Anti-TNF therapies are a core anti-inflammatory approach for chronic diseases such as rheumatoid arthritis and Crohn’s Disease. Previously, we and others found that TNF blocks the emergence and function of alternative-activated or M2 macrophages involved in wound healing and tissue-reparative functions. Conceivably, anti-TNF drugs could mediate their protective effects in part by an altered balance of macrophage activity. To understand the mechanistic basis of how TNF regulates tissue-reparative macrophages, we used RNAseq, scRNAseq, ATACseq, time-resolved phospho-proteomics, gene-specific approaches, metabolic analysis, and signaling pathway deconvolution. We found that TNF controls tissue-reparative macrophage gene expression in a highly gene-specific way, dependent on JNK signaling via the type 1 TNF receptor on specific populations of alternative-activated macrophages. We further determined that JNK signaling has a profound and broad effect on activated macrophage gene expression. Our findings suggest that TNF’s anti-M2 effects evolved to specifically modulate components of tissue and reparative M2 macrophages and TNF is therefore a context-specific modulator of M2 macrophages rather than a pan-M2 inhibitor.
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Affiliation(s)
| | - David E Sanin
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Carolin K Koss
- Boehringer Ingelheim Pharma GmbH and Co KG, Biberach, Germany
| | | | - Andreas Petzold
- Deep Sequencing Group, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maria C Tanzer
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Dahl
- Deep Sequencing Group, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Agnieszka M Kabat
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | | | - Leonie Zeitler
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Matthias Mann
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sabine A Eming
- Department of Dermatology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | | | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Martinsried, Germany
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