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Jiang L, Luo M, Wang J, Ma Z, Zhang C, Zhang M, Zhang Q, Yang H, Li L. Advances in antitumor application of ROS enzyme-mimetic catalysts. NANOSCALE 2024; 16:12287-12308. [PMID: 38869451 DOI: 10.1039/d4nr02026j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The rapid growth of research on enzyme-mimetic catalysts (Enz-Cats) is expected to promote further advances in nanomedicine for biological detection, diagnosis and treatment of disease, especially tumors. ROS-based nanomedicines present fascinating potential in antitumor therapy owing to the rapid development of nanotechnology. In this review, we focus on the applications of Enz-Cats based on ROS in antitumor therapy. Firstly, the definition and category of ROS are introduced, and the key factors enhancing ROS levels are carefully elucidated. Then, the rationally engineered Enz-Cats via different synthetic approaches with high ROS-producing efficiencies are comprehensively discussed. Subsequently, oncotherapy application of Enz-Cats is comprehensively discussed, which integrates diverse synergistic treatment modalities and exhibits high efficiency in ROS generation. Finally, the challenges and future research direction of this field are presented. This review is dedicated to unraveling the enigmas surrounding the interplay of nanomedicine and organisms.
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Affiliation(s)
- Lingfeng Jiang
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Menglin Luo
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Jiawei Wang
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Zijun Ma
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Chuan Zhang
- Department of Radiology, Institute of Radiation and Therapy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
- Institute of Nanomedicine Innovation Research and Transformation, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Maochun Zhang
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Qing Zhang
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
| | - Hanfeng Yang
- Department of Radiology, Institute of Radiation and Therapy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
- Institute of Nanomedicine Innovation Research and Transformation, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Ling Li
- Department of Ultrasound, Institute of Ultrasound Teaching and Research, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
- Institute of Nanomedicine Innovation Research and Transformation, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
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Chen E, Ling AL, Reardon DA, Chiocca EA. Lessons learned from phase 3 trials of immunotherapy for glioblastoma: Time for longitudinal sampling? Neuro Oncol 2024; 26:211-225. [PMID: 37995317 PMCID: PMC10836778 DOI: 10.1093/neuonc/noad211] [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: 11/25/2023] Open
Abstract
Glioblastoma (GBM)'s median overall survival is almost 21 months. Six phase 3 immunotherapy clinical trials have recently been published, yet 5/6 did not meet approval by regulatory bodies. For the sixth, approval is uncertain. Trial failures result from multiple factors, ranging from intrinsic tumor biology to clinical trial design. Understanding the clinical and basic science of these 6 trials is compelled by other immunotherapies reaching the point of advanced phase 3 clinical trial testing. We need to understand more of the science in human GBMs in early trials: the "window of opportunity" design may not be best to understand complex changes brought about by immunotherapeutic perturbations of the GBM microenvironment. The convergence of increased safety of image-guided biopsies with "multi-omics" of small cell numbers now permits longitudinal sampling of tumor and biofluids to dissect the complex temporal changes in the GBM microenvironment as a function of the immunotherapy.
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Affiliation(s)
- Ethan Chen
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alexander L Ling
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Res 2024; 52:D1062-D1071. [PMID: 38000392 PMCID: PMC10767952 DOI: 10.1093/nar/gkad1068] [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: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.
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Affiliation(s)
- Xiaoxiang Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziao Gan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haowei Cui
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tian Lan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Etienne Caron
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Wenguang Shao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim YSB, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CHG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Antonio Chiocca E, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR. Investigative needle core biopsies for multi-omics in Glioblastoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.29.23300541. [PMID: 38234840 PMCID: PMC10793534 DOI: 10.1101/2023.12.29.23300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.
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Oyadomari WY, Anthero GL, Silva MRDA, Porta LC, Oliveira V, Reid PF, Sant'Anna OA, Alves WA, Nani JV, Hayashi MAF. Evaluation of tumor growth remission in a murine model for subcutaneous solid tumors - Benefits of associating the antitumor agent crotamine with mesoporous nanosilica particles to achieve improved dosing frequency and efficacy. Int J Pharm 2023; 646:123420. [PMID: 37778514 DOI: 10.1016/j.ijpharm.2023.123420] [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: 04/11/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Crotamine is a highly cationic polypeptide first isolated from South American rattlesnake venom, which exhibits affinity for acidic lysosomal vesicles and proliferating cells. This cationic nature is pivotal for its in vitro cytotoxicity and in vivo anticancer actions. This study aimed to enhance the antitumor efficacy of crotamine by associating it with the mesoporous SBA-15 silica, known for its controlled release of various chemical agents, including large proteins. This association aimed to mitigate the toxic effects while amplifying the pharmacological potency of several compounds. Comprehensive characterization, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and zeta potential analysis, confirmed the successful association of crotamine with the non-toxic SBA-15 nanoparticles. The TEM imaging revealed nanoparticles with a nearly spherical shape and variations in uniformity upon crotamine association. Furthermore, DLS showed a narrow unimodal size distribution, emphasizing the formation of small aggregates. Zeta potential measurements indicated a distinct shift from negative to positive values upon crotamine association, underscoring its effective adsorption onto SBA-15. Intraperitoneal or oral administration of crotamine:SBA-15 in a murine melanoma model suggested the potential to reduce the frequency of crotamine doses without compromising efficacy. Interestingly, while the oral route enhanced the antitumor efficacy of crotamine, pH-dependent release from SBA-15 was observed. Thus, associating crotamine with SBA-15 could reduce the overall required dose to inhibit solid tumor growth, bolstering the prospect of crotamine as a potent anticancer agent.
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Affiliation(s)
- William Yoshio Oyadomari
- Laboratory of Molecular Pharmacology, Departamento de Farmacologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil; Departamento de Biofísica, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
| | - Gabriel Lessa Anthero
- Laboratory of Molecular Pharmacology, Departamento de Farmacologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
| | - Marcos R de A Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Brazil.
| | - Lucas C Porta
- Laboratory of Molecular Pharmacology, Departamento de Farmacologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
| | - Vitor Oliveira
- Departamento de Biofísica, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
| | | | | | - Wendel A Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Brazil.
| | - João V Nani
- Laboratory of Molecular Pharmacology, Departamento de Farmacologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
| | - Mirian Akemi Furuie Hayashi
- Laboratory of Molecular Pharmacology, Departamento de Farmacologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Brazil.
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Meng W, Schreiber RD, Lichti CF. Recent advances in immunopeptidomic-based tumor neoantigen discovery. Adv Immunol 2023; 160:1-36. [PMID: 38042584 DOI: 10.1016/bs.ai.2023.10.001] [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: 12/04/2023]
Abstract
The role of aberrantly expressed proteins in tumors in driving immune-mediated control of cancer has been well documented for more than five decades. Today, we know that both aberrantly expressed normal proteins as well as mutant proteins (neoantigens) can function as tumor antigens in both humans and mice. Next-generation sequencing (NGS) and high-resolution mass spectrometry (MS) technologies have made significant advances since the early 2010s, enabling detection of rare but clinically relevant neoantigens recognized by T cells. MS profiling of tumor-specific immunopeptidomes remains the most direct method to identify mutant peptides bound to cellular MHC. However, the need for use of large numbers of cells or significant amounts of tumor tissue to achieve neoantigen detection has historically limited the application of MS. Newer, more sensitive MS technologies have recently demonstrated the capacities to detect neoantigens from fewer cells. Here, we highlight recent advancements in immunopeptidomics-based characterization of tumor-specific neoantigens. Various tumor antigen categories and neoantigen identification approaches are also discussed. Furthermore, we summarize recent reports that achieved successful tumor neoantigen detection by MS using a variety of starting materials, MS acquisition modes, and novel ion mobility devices.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [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] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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Caron É, Perreault C. Introduction to the Special Issue: The Immunopeptidome. Semin Immunol 2023; 69:101798. [PMID: 37348326 DOI: 10.1016/j.smim.2023.101798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Affiliation(s)
- Étienne Caron
- CHU Sainte-Justine Research Center, and Department of Pathology and Cellular Biology, Université de Montréal, Montréal, Québec, Canada.
| | - Claude Perreault
- Institute for Immunology and Cancer, and Department of Medicine, Université de Montréal, Montréal, Québec, Canada.
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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